1
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Zhang Z, Zhang J, Kang L, Qiu X, Xu S, Xu J, Guo Y, Niu Z, Niu B, Bi A, Zhao X, Xu D, Wang J, Yin C, Lu F. Structural variation discovery in wheat using PacBio high-fidelity sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39239888 DOI: 10.1111/tpj.17011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 08/09/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024]
Abstract
Structural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high-fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long-read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, revealing that low-coverage HiFi sequencing is sufficiently robust for high-quality SV discovery. This study thoroughly evaluated SV discovery approaches and established optimal workflows for investigating structural variations using low-coverage HiFi sequencing in the wheat genome, which will advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.
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Affiliation(s)
- Zhiliang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jijin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuebing Qiu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zelin Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beirui Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aoyue Bi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daxing Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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2
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Blommaert J, Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 2024; 116:110929. [PMID: 39216708 DOI: 10.1016/j.ygeno.2024.110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.
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Affiliation(s)
- Julie Blommaert
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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3
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Wang X, Liu Z, Zhang F, Xiao H, Cao S, Xue H, Liu W, Su Y, Liu Z, Zhong H, Zhang F, Ahmad B, Long Q, Zhang Y, Liu Y, Gan Y, Hou T, Jin Z, Wu X, Liu G, Wang Y, Peng Y, Zhou Y. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Curr Biol 2024; 34:3763-3777.e5. [PMID: 39094571 DOI: 10.1016/j.cub.2024.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/04/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated the haplotype-resolved genomes for two seedless grape cultivars, "Thompson Seedless" (TS, syn. "Sultania") and "Black Monukka" (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, and the identity-by-descent (IBD) results indicated that the origin of the seedlessness trait could be traced back to "Sultania." Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including previously unidentified candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 functional categories related to seed development. Machine learning-based genomic selection achieved a remarkable prediction accuracy of 97% for seedlessness in grapevines. Our findings highlight the polygenic nature of seedlessness and provide candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.
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Affiliation(s)
- Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Xue
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenwen Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenya Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Haixia Zhong
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Fuchun Zhang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Bilal Ahmad
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiming Long
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingchun Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuting Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Gan
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Hou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinyu Wu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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4
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Chen G, Shi G, Dai Y, Zhao R, Wu Q. Graph-Based Pan-Genome Reveals the Pattern of Deleterious Mutations during the Domestication of Saccharomyces cerevisiae. J Fungi (Basel) 2024; 10:575. [PMID: 39194902 DOI: 10.3390/jof10080575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
The "cost of domestication" hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used Saccharomyces cerevisiae, the world's oldest domesticated fungus, as a model to investigate the genomic characteristics of deleterious variants arising from fungal domestication. Employing a graph-based pan-genome approach, we identified 1,297,761 single nucleotide polymorphisms (SNPs), 278,147 insertion/deletion events (indels; <30 bp), and 19,967 non-redundant structural variants (SVs; ≥30 bp) across 687 S. cerevisiae isolates. Comparing these variants with synonymous SNPs (sSNPs) as neutral controls, we found that the majority of the derived nonsynonymous SNPs (nSNPs), indels, and SVs were deleterious. Heterozygosity was positively correlated with the impact of deleterious SNPs, suggesting a role of genetic diversity in mitigating their effects. The domesticated isolates exhibited a higher additive burden of deleterious SNPs (dSNPs) than the wild isolates, but a lower burden of indels and SVs. Moreover, the domesticated S. cerevisiae showed reduced rates of adaptive evolution relative to the wild S. cerevisiae. In summary, deleterious variants tend to be heterozygous, which may mitigate their harmful effects, but they also constrain breeding potential. Addressing deleterious alleles and minimizing the genetic load are crucial considerations for future S. cerevisiae breeding efforts.
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Affiliation(s)
- Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruilin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Cantu D, Massonnet M, Cochetel N. The wild side of grape genomics. Trends Genet 2024; 40:601-612. [PMID: 38777691 DOI: 10.1016/j.tig.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.
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Affiliation(s)
- Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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6
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Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
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Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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7
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Wang Y, Ding K, Li H, Kuang Y, Liang Z. Biography of Vitis genomics: recent advances and prospective. HORTICULTURE RESEARCH 2024; 11:uhae128. [PMID: 38966864 PMCID: PMC11220177 DOI: 10.1093/hr/uhae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/25/2024] [Indexed: 07/06/2024]
Abstract
The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kangyi Ding
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayang Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangfu Kuang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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8
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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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9
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Li X, Chen Y, Zhang Z, He Q, Tian T, Jiao Y, Cao L. Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress. Sci Rep 2024; 14:13917. [PMID: 38886497 PMCID: PMC11183051 DOI: 10.1038/s41598-024-64937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Chinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.
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Affiliation(s)
- Xu Li
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Yang Chen
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Zaiqi Zhang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
| | - Qin He
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Tingting Tian
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Yangmiao Jiao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
| | - Liang Cao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
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10
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Patel-Tupper D, Kelikian A, Leipertz A, Maryn N, Tjahjadi M, Karavolias NG, Cho MJ, Niyogi KK. Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression. SCIENCE ADVANCES 2024; 10:eadm7452. [PMID: 38848363 PMCID: PMC11160471 DOI: 10.1126/sciadv.adm7452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Understanding CRISPR-Cas9's capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo-from knockout to overexpression-using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.
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Affiliation(s)
- Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Armen Kelikian
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Anna Leipertz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Nina Maryn
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Michelle Tjahjadi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Nicholas G. Karavolias
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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11
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Wang P, Meng F, Yang Y, Ding T, Liu H, Wang F, Li A, Zhang Q, Li K, Fan S, Li B, Ma Z, Zhang T, Zhou Y, Zhao H, Wang X. De novo assembling a high-quality genome sequence of Amur grape ( Vitis amurensis Rupr .) gives insight into Vitis divergence and sex determination. HORTICULTURE RESEARCH 2024; 11:uhae117. [PMID: 38919553 PMCID: PMC11197301 DOI: 10.1093/hr/uhae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/09/2024] [Indexed: 06/27/2024]
Abstract
To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ~522 Mb of the Vitis amurensis (Va) genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that Vitis riparia (Vr) may have first split from the other two species, Va and Vitis vinifera (Vv). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with Vv and Vr. In contrast, Va has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to those of female Vv. However, the putative SDR of female Va has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.
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Affiliation(s)
| | - Fanbo Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yiming Yang
- Institute of Special Animal and Plant Sciences of CAAS, Changchun 130000, China
| | | | - Huiping Liu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Ao Li
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Ke Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences of CAAS, Changchun 130000, China
| | - Bo Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Zhiyao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Tianhao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | | | - Xiyin Wang
- North China University of Science and Technology, Tangshan 063000, China
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12
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Long Q, Cao S, Huang G, Wang X, Liu Z, Liu W, Wang Y, Xiao H, Peng Y, Zhou Y. Population comparative genomics discovers gene gain and loss during grapevine domestication. PLANT PHYSIOLOGY 2024; 195:1401-1413. [PMID: 38285049 PMCID: PMC11142336 DOI: 10.1093/plphys/kiae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/06/2023] [Accepted: 01/01/2024] [Indexed: 01/30/2024]
Abstract
Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.
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Affiliation(s)
- Qiming Long
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guizhou Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 C1P1, Ireland
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Wenwen Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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13
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Wang Y, Duchen P, Chávez A, Sree KS, Appenroth KJ, Zhao H, Höfer M, Huber M, Xu S. Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality. Commun Biol 2024; 7:581. [PMID: 38755313 PMCID: PMC11099151 DOI: 10.1038/s42003-024-06266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that genes associated with stress adaptations, flowering and embryogenesis were under positive selection. These data are consistent with the hypothesize that natural selection can shape the evolution of asexuality during habitat expansions, which alters genomic and epigenomic diversity levels.
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Affiliation(s)
- Yangzi Wang
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Pablo Duchen
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Alexandra Chávez
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, 48161, Münster, Germany
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periya, 671320, India
| | - Klaus J Appenroth
- Matthias Schleiden Institute - Plant Physiology, Friedrich Schiller University of Jena, 07743, Jena, Germany
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, 6100641, Chengdu, China
| | - Martin Höfer
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Meret Huber
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, 48161, Münster, Germany
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany.
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany.
- Institute for Quantitative and Computational Biosciences, University of Mainz, 55218, Mainz, Germany.
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14
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Shi T, Zhang X, Hou Y, Jia C, Dan X, Zhang Y, Jiang Y, Lai Q, Feng J, Feng J, Ma T, Wu J, Liu S, Zhang L, Long Z, Chen L, Street NR, Ingvarsson PK, Liu J, Yin T, Wang J. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. MOLECULAR PLANT 2024; 17:725-746. [PMID: 38486452 DOI: 10.1016/j.molp.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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Affiliation(s)
- Tingting Shi
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xinxin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yukang Hou
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Lai
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jianju Feng
- College of Horticulture and Forestry, Tarim University, Alar 843300, China
| | - Tao Ma
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiali Wu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Shuyu Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Lei Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zhiqin Long
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Liyang Chen
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Västerbotten, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, Jiangsu, China.
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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15
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Calderón L, Carbonell-Bejerano P, Muñoz C, Bree L, Sola C, Bergamin D, Tulle W, Gomez-Talquenca S, Lanz C, Royo C, Ibáñez J, Martinez-Zapater JM, Weigel D, Lijavetzky D. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation. HORTICULTURE RESEARCH 2024; 11:uhae080. [PMID: 38766532 PMCID: PMC11101320 DOI: 10.1093/hr/uhae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/08/2024] [Indexed: 05/22/2024]
Abstract
To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.
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Affiliation(s)
- Luciano Calderón
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Claudio Muñoz
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
- Facultad de Ciencias Agrarias (UNCuyo), Cátedra Fitopatología, Chacras de Coria 5505, Mendoza, Argentina
| | - Laura Bree
- Vivero Mercier Argentina, Perdriel 5500, Mendoza, Argentina
| | - Cristobal Sola
- Vivero Mercier Argentina, Perdriel 5500, Mendoza, Argentina
| | | | - Walter Tulle
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
| | - Sebastian Gomez-Talquenca
- Plant Virology Laboratory, Instituto Nacional de Tecnología Agropecuaria, Luján de Cuyo 5534, Mendoza, Argentina
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - José Miguel Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logroño 26007, La Rioja, Spain
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza (CONICET-UNCuyo), Genetica y Genomica de Vid, Chacras de Coria 5505, Mendoza, Argentina
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16
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David G, Bertolotti A, Layer R, Scofield D, Hayward A, Baril T, Burnett HA, Gudmunds E, Jensen H, Husby A. Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations. Genome Biol Evol 2024; 16:evae049. [PMID: 38489588 PMCID: PMC11018544 DOI: 10.1093/gbe/evae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.
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Affiliation(s)
- Gabriel David
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Ryan Layer
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Douglas Scofield
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Hamish A Burnett
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Erik Gudmunds
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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17
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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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18
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Aversano R, Iovene M, Esposito S, L'Abbate A, Villano C, Di Serio E, Cardone MF, Bergamini C, Cigliano RA, D'Amelia V, Frusciante L, Carputo D. Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina. BMC PLANT BIOLOGY 2024; 24:88. [PMID: 38317087 PMCID: PMC10845522 DOI: 10.1186/s12870-024-04778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
| | - Marina Iovene
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy.
| | - Salvatore Esposito
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
- Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics (CREA-CI), Foggia, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maria Francesca Cardone
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | - Carlo Bergamini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | | | - Vincenzo D'Amelia
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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19
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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20
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Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. HORTICULTURE RESEARCH 2024; 11:uhad252. [PMID: 38269295 PMCID: PMC10807706 DOI: 10.1093/hr/uhad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/18/2023] [Indexed: 01/26/2024]
Abstract
The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.
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Affiliation(s)
- Yanhong Song
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lifeng Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Gang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xia Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Aline Muyle
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier 34000, France
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570000, China
| | - Houcheng Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
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21
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Cochetel N, Minio A, Guarracino A, Garcia JF, Figueroa-Balderas R, Massonnet M, Kasuga T, Londo JP, Garrison E, Gaut BS, Cantu D. A super-pangenome of the North American wild grape species. Genome Biol 2023; 24:290. [PMID: 38111050 PMCID: PMC10729490 DOI: 10.1186/s13059-023-03133-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. RESULTS Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. CONCLUSIONS This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
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Affiliation(s)
- Noé Cochetel
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Jadran F Garcia
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | | | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA, USA
| | - Jason P Londo
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA.
- Genome Center, University of California Davis, Davis, CA, USA.
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22
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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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23
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Xiao H, Liu Z, Wang N, Gaut BS, Zhou Y. Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication. Proc Natl Acad Sci U S A 2023; 120:e2314162120. [PMID: 38011557 DOI: 10.1073/pnas.2314162120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Nan Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 95616
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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24
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Srivastava R, Bazakos C, Tsachaki M, Žanko D, Kalantidis K, Tsiantis M, Laurent S. Genealogical Analyses of 3 Cultivated and 1 Wild Specimen of Vitis vinifera from Greece. Genome Biol Evol 2023; 15:evad226. [PMID: 38128270 PMCID: PMC10735296 DOI: 10.1093/gbe/evad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Grapevine (Vitis vinifera) has been an important crop with considerable cultural and economic significance for over 2,500 years, and Greece has been an important entry point into Europe for lineages that were domesticated in Western Asia and the Caucasus. However, whole-genome-based investigation of the demographic history of Greek cultivars relative to other European lineages has only started recently. To understand how Greek cultivars relate to Eurasian domesticated and wild populations, we sequenced 3 iconic domesticated strains ('Xinomavro,' 'Agiorgitiko,' 'Mavrotragano') along with 1 wild accession (the vinetree of Pausanias-a historically important wild specimen) and analyzed their genomic diversity together with a large sample of publicly available domesticated and wild strains. We also reconstructed genealogies by leveraging the powerful tsinfer methodology which has not previously been used in this system. We show that cultivated strains from Greece differ genetically from other strains in Europe. Interestingly, all the 3 cultivated Greek strains clustered with cultivated and wild accessions from Transcaucasia, South Asia, and the Levant and are amongst the very few cultivated European strains belonging to this cluster. Furthermore, our results indicate that 'Xinomavro' shares close genealogical proximity with European elite cultivars such as 'Chardonnay,' 'Riesling,' and 'Gamay' but not 'Pinot.' Therefore, the proximity of 'Xinomavro' to Gouais/Heunisch Weiss is confirmed and the utility of ancestral recombination graph reconstruction approaches to study genealogical relationships in crops is highlighted.
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Affiliation(s)
- Rachita Srivastava
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki 57001, Greece
| | | | - Danijela Žanko
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion 71500, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion 70013, Greece
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- BioNTech, Mainz, Germany
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25
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Zou C, Sapkota S, Figueroa-Balderas R, Glaubitz J, Cantu D, Kingham BF, Sun Q, Cadle-Davidson L. A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus. PLANT PHYSIOLOGY 2023; 193:2321-2336. [PMID: 37706526 DOI: 10.1093/plphys/kiad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Surya Sapkota
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Jeff Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
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26
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Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat Commun 2023; 14:7377. [PMID: 37968318 PMCID: PMC10651928 DOI: 10.1038/s41467-023-43270-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.
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Affiliation(s)
- Ting Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shiyao Duan
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Chen Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China.
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China.
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27
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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28
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Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:989-1002. [PMID: 37639371 DOI: 10.1111/tpj.16433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.
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Affiliation(s)
- Ben N Mansfeld
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Shujun Ou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Erik Burchard
- USDA ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | | | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
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29
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Zhang X, Chen Y, Wang L, Yuan Y, Fang M, Shi L, Lu R, Comes HP, Ma Y, Chen Y, Huang G, Zhou Y, Zheng Z, Qiu Y. Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization. HORTICULTURE RESEARCH 2023; 10:uhad203. [PMID: 38046854 PMCID: PMC10689057 DOI: 10.1093/hr/uhad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.
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Affiliation(s)
- Xinyi Zhang
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yang Chen
- Systematic and Evolutionary Botany and Biodiversity Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Lingyun Wang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ye Yuan
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016, Zhejiang, China
| | - Mingya Fang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Lin Shi
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, 5020, Austria
| | - Yazhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yuanyuan Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Guizhou Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture; Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, Guangdong, China
| | - Zhaisheng Zheng
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, 321000, Zhejiang, China
| | - Yingxiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
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30
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Zhang K, Du M, Zhang H, Zhang X, Cao S, Wang X, Wang W, Guan X, Zhou P, Li J, Jiang W, Tang M, Zheng Q, Cao M, Zhou Y, Chen K, Liu Z, Fang Y. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. HORTICULTURE RESEARCH 2023; 10:uhad205. [PMID: 38046853 PMCID: PMC10689054 DOI: 10.1093/hr/uhad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar 'Yan73' was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi), Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in 'Cabernet Sauvignon' and 'Yan73' were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of 'Yan73' were higher than those of 'Cabernet Sauvignon'. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of 'Yan73' haplotype 2 genome. The 'Yan73' T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.
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Affiliation(s)
- Kekun Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mengrui Du
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Hongyan Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xiaoqian Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wenrui Wang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xueqiang Guan
- Shandong Grape Research Institute, Shanda South Road, Jinan 250199, China
| | - Penghui Zhou
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | - Jin Li
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | | | - Meiling Tang
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Qiuling Zheng
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Muming Cao
- Viticulture and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Keqin Chen
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yulin Fang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
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31
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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32
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. HORTICULTURE RESEARCH 2023; 10:uhad153. [PMID: 37701454 PMCID: PMC10493638 DOI: 10.1093/hr/uhad153] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/14/2023]
Abstract
Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of 'Baxijiao' (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4, and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families related to anther and pollen development was observed, which could be associated with parthenocarpy and sterility of the Cavendish cultivar. Finally, much fewer resistance genes were identified in 'Baxijiao' than in M. acuminata, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to explore for molecular analysis of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding, and genetic improvement of banana.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rida Arshad
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xu Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei-Ming Li
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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Urra C, Sanhueza D, Pavez C, Tapia P, Núñez-Lillo G, Minio A, Miossec M, Blanco-Herrera F, Gainza F, Castro A, Cantu D, Meneses C. Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study. G3 (BETHESDA, MD.) 2023; 13:jkad145. [PMID: 37395733 PMCID: PMC10468313 DOI: 10.1093/g3journal/jkad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains unexplored, and tools to discriminate unequivocally clones have been lacking. This study aimed to uncover genetic variations among a group of clonal selections of 4 important Vitis vinifera cultivars: Cabernet sauvignon, Sauvignon blanc, Chardonnay, and Merlot, and use this information to develop genetic markers to discriminate the clones of these cultivars. We sequenced with short-read sequencing technology the genomes of 18 clones, including biological replicates for a total of 46 genomes. Sequences were aligned to their respective cultivar's reference genome for variant calling. We used reference genomes of Cabernet sauvignon, Chardonnay, and Merlot and developed a de novo genome assembly of Sauvignon blanc using long-read sequencing. On average, 4 million variants were detected for each clone, with 74.2% being single nucleotide variants and 25.8% being small insertions or deletions (InDel). The frequency of these variants was consistent across all clones. From these variants, we validated 46 clonal markers using high-throughput amplicon sequencing for 77.7% of the evaluated clones, most of them small InDel. These results represent an advance in grapevine genotyping strategies and will benefit the viticulture industry for the characterization and identification of the plant material.
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Affiliation(s)
- Claudio Urra
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Dayan Sanhueza
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Catalina Pavez
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Patricio Tapia
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Gerardo Núñez-Lillo
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2263782, Chile
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616-5270, USA
| | - Matthieu Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Francisca Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
| | - Felipe Gainza
- Center for Research and Innovation, Viña Concha y Toro S.A, Pencahue, Talca 3460000, Chile
| | - Alvaro Castro
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616-5270, USA
| | - Claudio Meneses
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program Millenium Institute Center for Genome Regulation, CRG, Santiago 8331150, Chile
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Xiao H, Liu Z, Wang N, Long Q, Cao S, Huang G, Liu W, Peng Y, Riaz S, Walker AM, Gaut BS, Zhou Y. Adaptive and maladaptive introgression in grapevine domestication. Proc Natl Acad Sci U S A 2023; 120:e2222041120. [PMID: 37276420 PMCID: PMC10268302 DOI: 10.1073/pnas.2222041120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning-based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.
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Affiliation(s)
- Hua Xiao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi830091, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Nan Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Qiming Long
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Shuo Cao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Guizhou Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Wenwen Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Yanling Peng
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA95616
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, CA95616
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
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Morales-Cruz A, Aguirre-Liguori J, Massonnet M, Minio A, Zaccheo M, Cochetel N, Walker A, Riaz S, Zhou Y, Cantu D, Gaut BS. Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Commun Biol 2023; 6:580. [PMID: 37253933 DOI: 10.1038/s42003-023-04938-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (Vitis vinifera) are not resistant to the bacterium. Here we study a wild grapevine species, V. arizonica, that segregates for resistance. Using genome-wide association, we identify candidate resistance genes. Resistance-associated kmers are shared with a sister species of V. arizonica but not with more distant species, suggesting that resistance evolved more than once. Finally, resistance is climate dependent, because individuals from low ( < 10 °C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in colder climates. In fact, climate is as effective a predictor of resistance phenotypes as some genetic markers. We extend our climate observations to additional crops, predicting that increased pathogen pressure is more likely for grapevines and almonds than some other susceptible crops.
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Affiliation(s)
- Abraham Morales-Cruz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Jonas Aguirre-Liguori
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Mélanie Massonnet
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Andrea Minio
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Mirella Zaccheo
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Noe Cochetel
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Andrew Walker
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Summaira Riaz
- San Joaquin Valley Agricultural Center, United States Dept of Agriculture, Parlier, CA, USA
| | - Yongfeng Zhou
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Agricultural Genomics Institute at Shenzhen, The Chinese Academy of Agricultural Sciences, No. 7 Pengfei Road, Shenzen, 518120, China.
| | - Dario Cantu
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA.
- Dept. of Viticulture and Enology, One Shields Avenue, University of California Davis, Davis, CA, 95616-5270, USA.
| | - Brandon S Gaut
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Dept. of Ecology and Evolutionary Biology, 321 Steinhaus Hall UC Irvine, Irvine, CA, 92617-2525, USA.
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Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 2023; 186:2313-2328.e15. [PMID: 37146612 DOI: 10.1016/j.cell.2023.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
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Affiliation(s)
- Yaoyao Wu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Dawei Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Hu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Hongbo Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, Denmark
| | - Shaoqun Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xinyan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhigui Bao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Yu Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; School of Agriculture, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yao Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100094, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Edeline Gagnon
- Technische Universität München, TUM School of Life Sciences, Emil-Ramann-Strasse 2, 85354 Freising, Germany
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chunzhi Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Thomas Städler
- Institute of Integrative Biology and Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Ithaca, NY 14853, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, Zhong H, Wang Y, Zhang K, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus JT, Ware D, Wu X, Wang H, Liu C, Fang Y, Rustenholz C, Cheng Z, Xiao H, Zhou Y. The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding. HORTICULTURE RESEARCH 2023; 10:uhad061. [PMID: 37213686 PMCID: PMC10199708 DOI: 10.1093/hr/uhad061] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/02/2023] [Indexed: 05/23/2023]
Abstract
Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
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Affiliation(s)
- Xiaoya Shi
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Siyang Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yue Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenwen Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanling Peng
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Nan Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yiwen Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Fan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hui Xue
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haixia Zhong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Amandine Velt
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Komlan Avia
- SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jérôme Grimplet
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Systems Biotech Program, Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Xinyu Wu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Haibo Wang
- Fruit Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng 125100, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450004, China
| | - Yuling Fang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | | | - Zongming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Xiao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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41
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Jiao Y, Li X, Huang X, Liu F, Zhang Z, Cao L. The Identification of SQS/ SQE/ OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina. Molecules 2023; 28:2782. [PMID: 36985754 PMCID: PMC10051230 DOI: 10.3390/molecules28062782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The tuberous roots of Potentilla anserina (Pan) are an edible and medicinal resource in Qinghai-Tibetan Plateau, China. The triterpenoids from tuberous roots have shown promising anti-cancer, hepatoprotective, and anti-inflammatory properties. In this study, we carried out phylogenetic analysis of squalene synthases (SQSs), squalene epoxidases (SQEs), and oxidosqualene cyclases (OSCs) in the pathway of triterpenes. In total, 6, 26, and 20 genes of SQSs, SQEs, and OSCs were retrieved from the genome of Pan, respectively. Moreover, 6 SQSs and 25 SQEs genes expressed in two sub-genomes (A and B) of Pan. SQSs were not expanded after whole-genome duplication (WGD), and the duplicated genes were detected in SQEs. Twenty OSCs were divided into two clades of cycloartenol synthases (CASs) and β-amyrin synthases (β-ASs) by a phylogenetic tree, characterized with gene duplication and evolutionary divergence. We speculated that β-ASs and CASs may participate in triterpenes synthesis. The data presented act as valuable references for future studies on the triterpene synthetic pathway of Pan.
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Affiliation(s)
- Yangmiao Jiao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmacy, Hunan University of Medicine, Huaihua 418000, China
| | - Xu Li
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmacy, Hunan University of Medicine, Huaihua 418000, China
| | - Fan Liu
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Zaiqi Zhang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Liang Cao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
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42
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Bosman RN, Vervalle JAM, November DL, Burger P, Lashbrooke JG. Grapevine genome analysis demonstrates the role of gene copy number variation in the formation of monoterpenes. FRONTIERS IN PLANT SCIENCE 2023; 14:1112214. [PMID: 37008487 PMCID: PMC10061021 DOI: 10.3389/fpls.2023.1112214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Volatile organic compounds such as terpenes influence the quality parameters of grapevine through their contribution to the flavour and aroma profile of berries. Biosynthesis of volatile organic compounds in grapevine is relatively complex and controlled by multiple genes, the majority of which are unknown or uncharacterised. To identify the genomic regions that associate with modulation of these compounds in grapevine berries, volatile metabolic data generated via GC-MS from a grapevine mapping population was used to identify quantitative trait loci (QTLs). Several significant QTLs were associated with terpenes, and candidate genes were proposed for sesquiterpene and monoterpene biosynthesis. For monoterpenes, loci on chromosomes 12 and 13 were shown to be associated with geraniol and cyclic monoterpene accumulation, respectively. The locus on chromosome 12 was shown to contain a geraniol synthase gene (VvGer), while the locus on chromosome 13 contained an α-terpineol synthase gene (VvTer). Molecular and genomic investigation of VvGer and VvTer revealed that these genes were found in tandemly duplicated clusters, displaying high levels of hemizygosity. Gene copy number analysis further showed that not only did VvTer and VvGer copy numbers vary within the mapping population, but also across recently sequenced Vitis cultivars. Significantly, VvTer copy number correlated with both VvTer gene expression and cyclic monoterpene accumulation in the mapping population. A hypothesis for a hyper-functional VvTer allele linked to increased gene copy number in the mapping population is presented and can potentially lead to selection of cultivars with modulated terpene profiles. The study highlights the impact of VvTPS gene duplication and copy number variation on terpene accumulation in grapevine.
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Affiliation(s)
- Robin Nicole Bosman
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, South Africa
| | | | - Danielle Lisa November
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, South Africa
| | - Phyllis Burger
- Department for Crop Development, Agricultural Research Council - Infruitec-Nietvoorbij, Stellenbosch, South Africa
| | - Justin Graham Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, South Africa
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43
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Zhao J, Li X, Qiao L, Zheng X, Wu B, Guo M, Feng M, Qi Z, Yang W, Zheng J. Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:37. [PMID: 36897407 DOI: 10.1007/s00122-023-04283-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Jiajia Zhao
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaohua Li
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Meijun Guo
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Jinzhong University, Jinzhong, China
| | - Meichen Feng
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wude Yang
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China.
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China.
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44
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Pei D, Song S, Kang J, Zhang C, Wang J, Dong T, Ge M, Pervaiz T, Zhang P, Fang J. Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes. Genes (Basel) 2023; 14:genes14030663. [PMID: 36980935 PMCID: PMC10048371 DOI: 10.3390/genes14030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars (‘PN40024’, ‘Cabernet Sauvignon’, ‘Carménère’, ‘Chardonnay’, ‘Merlot’, ‘Riesling’, ‘Zinfandel’, ‘Shine Muscat’, and ‘Muscat Hamburg’) with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.
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Affiliation(s)
- Dan Pei
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyan Song
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Zhenjiang 212400, China
| | - Jun Kang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Zhang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Wang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianyu Dong
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengqing Ge
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 22963, USA
| | - Peian Zhang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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45
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Dong Y, Duan S, Xia Q, Liang Z, Dong X, Margaryan K, Musayev M, Goryslavets S, Zdunić G, Bert PF, Lacombe T, Maul E, Nick P, Bitskinashvili K, Bisztray GD, Drori E, De Lorenzis G, Cunha J, Popescu CF, Arroyo-Garcia R, Arnold C, Ergül A, Zhu Y, Ma C, Wang S, Liu S, Tang L, Wang C, Li D, Pan Y, Li J, Yang L, Li X, Xiang G, Yang Z, Chen B, Dai Z, Wang Y, Arakelyan A, Kuliyev V, Spotar G, Girollet N, Delrot S, Ollat N, This P, Marchal C, Sarah G, Laucou V, Bacilieri R, Röckel F, Guan P, Jung A, Riemann M, Ujmajuridze L, Zakalashvili T, Maghradze D, Höhn M, Jahnke G, Kiss E, Deák T, Rahimi O, Hübner S, Grassi F, Mercati F, Sunseri F, Eiras-Dias J, Dumitru AM, Carrasco D, Rodriguez-Izquierdo A, Muñoz G, Uysal T, Özer C, Kazan K, Xu M, Wang Y, Zhu S, Lu J, Zhao M, Wang L, Jiu S, Zhang Y, Sun L, Yang H, Weiss E, Wang S, Zhu Y, Li S, Sheng J, Chen W. Dual domestications and origin of traits in grapevine evolution. Science 2023; 379:892-901. [PMID: 36862793 DOI: 10.1126/science.add8655] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.
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Affiliation(s)
- Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Qiuju Xia
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Kristine Margaryan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Yerevan State University, 0014 Yerevan, Armenia
| | - Mirza Musayev
- Genetic Resources Institute, Azerbaijan National Academy of Sciences, AZ1106 Baku, Azerbaijan
| | | | - Goran Zdunić
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia
| | - Pierre-François Bert
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Thierry Lacombe
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Erika Maul
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | | | - György Dénes Bisztray
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Elyashiv Drori
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel.,Eastern Regional R&D Center, 40700 Ariel, Israel
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences, University of Milano, 20133 Milano, Italy
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Carmen Florentina Popescu
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - Rosa Arroyo-Garcia
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | - Ali Ergül
- Biotechnology Institute, Ankara University, 06135 Ankara, Turkey
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Shufen Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Liu Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Chunping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Dawei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Yunbing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Jingxian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Xuzhen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Guisheng Xiang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zijiang Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Baozheng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Arsen Arakelyan
- Institute of Molecular Biology, NAS RA, 0014 Yerevan, Armenia.,Armenian Bioinformatics Institute, 0014 Yerevan, Armenia.,Biomedicine and Pharmacy, RAU, 0051 Yerevan, Armenia
| | - Varis Kuliyev
- Institute of Bioresources, Nakhchivan Branch of the Azerbaijan National Academy of Sciences, AZ7000 Nakhchivan, Azerbaijan
| | - Gennady Spotar
- National Institute of Viticulture and Winemaking Magarach, Yalta 298600, Crimea
| | - Nabil Girollet
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Serge Delrot
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Nathalie Ollat
- Bordeaux University, Bordeaux Sciences Agro, INRAE, UMR EGFV, ISVV, 33882 Villenave d'Ornon, France
| | - Patrice This
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Cécile Marchal
- Vassal-Montpellier Grapevine Biological Resources Center, INRAE, 34340 Marseillan-Plage, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Roberto Bacilieri
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro Montpellier, 34398 Montpellier, France
| | - Franco Röckel
- Julius Kühn Institute (JKI) - Federal Research Center for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
| | - Pingyin Guan
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andreas Jung
- Historische Rebsorten-Sammlung, Rebschule (K39), 67599 Gundheim, Germany
| | - Michael Riemann
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Levan Ujmajuridze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | | | - David Maghradze
- LEPL Scientific Research Center of Agriculture, 0159 Tbilisi, Georgia
| | - Maria Höhn
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Gizella Jahnke
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Erzsébet Kiss
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Tamás Deák
- Hungarian University of Agriculture and Life Sciences (MATE), 1118 Budapest, Hungary
| | - Oshrit Rahimi
- Department of Chemical Engineering, Ariel University, 40700 Ariel, Israel
| | - Sariel Hübner
- Galilee Research Institute (Migal), Tel-Hai Academic College, 12210 Upper Galilee, Israel
| | - Fabrizio Grassi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy.,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Francesco Mercati
- Institute of Biosciences and Bioresources, National Research Council, 90129 Palermo, Italy
| | - Francesco Sunseri
- Department AGRARIA, University Mediterranea of Reggio Calabria, Reggio 89122 Calabria, Italy
| | - José Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária, I.P./INIAV-Dois Portos, 2565-191 Torres Vedras, Portugal.,Green-it Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Anamaria Mirabela Dumitru
- National Research and Development Institute for Biotechnology in Horticulture, Stefanesti, 117715 Arges, Romania
| | - David Carrasco
- Center for Plant Biotechnology and Genomics, UPM-INIA/CSIC, Pozuelo de Alarcon, 28223 Madrid, Spain
| | | | | | - Tamer Uysal
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Cengiz Özer
- Viticulture Research Institute, Ministry of Agriculture and Forestry, 59200 Tekirdağ, Turkey
| | - Kemal Kazan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Meilong Xu
- Institute of Horticulture, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750002, China
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Jiang Lu
- Center for Viticulture and Oenology, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Maoxiang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | - Lei Sun
- Zhengzhou Fruit Research Institutes, CAAS, Zhengzhou 450009, China
| | | | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Oenology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
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46
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Abstract
Glacial cycles and wild adaptations shaped grape domestication and the rise of wine.
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Affiliation(s)
- Robin G Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Warwick, UK
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47
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Yan C, Song MH, Jiang D, Ren JL, Lv Y, Chang J, Huang S, Zaher H, Li JT. Genomic evidence reveals intraspecific divergence of the hot-spring snake (Thermophis baileyi), an endangered reptile endemic to the Qinghai-Tibet plateau. Mol Ecol 2023; 32:1335-1350. [PMID: 36073004 DOI: 10.1111/mec.16687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Understanding how and why species evolve requires knowledge on intraspecific divergence. In this study, we examined intraspecific divergence in the endangered hot-spring snake (Thermophis baileyi), an endemic species on the Qinghai-Tibet Plateau (QTP). Whole-genome resequencing of 58 sampled individuals from 15 populations was performed to identify the drivers of intraspecific divergence and explore the potential roles of genes under selection. Our analyses resolved three groups, with major intergroup admixture occurring in regions of group contact. Divergence probably occurred during the Pleistocene as a result of glacial climatic oscillations, Yadong-Gulu rift, and geothermal fields differentiation, while complex gene flow between group pairs reflected a unique intraspecific divergence pattern on the QTP. Intergroup fixed loci involved selected genes functionally related to divergence and local adaptation, especially adaptation to hot spring microenvironments in different geothermal fields. Analysis of structural variants, genetic diversity, inbreeding, and genetic load indicated that the hot-spring snake population has declined to a low level with decreased diversity, which is important for the conservation management of this endangered species. Our study demonstrated that the integration of demographic history, gene flow, genomic divergence genes, and other information is necessary to distinguish the evolutionary processes involved in speciation.
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Affiliation(s)
- Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Mangkang Biodiversity and Ecological Station, Tibet Ecological Safety Monitor Network, Changdu, China
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48
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Zhang L, Chaturvedi S, Nice CC, Lucas LK, Gompert Z. Population genomic evidence of selection on structural variants in a natural hybrid zone. Mol Ecol 2023; 32:1497-1514. [PMID: 35398939 DOI: 10.1111/mec.16469] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.
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Affiliation(s)
- Linyi Zhang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, Utah State University, Logan, Utah, USA
| | - Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Chris C Nice
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, Utah, USA
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49
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Solares E, Morales-Cruz A, Balderas RF, Focht E, Ashworth VETM, Wyant S, Minio A, Cantu D, Arpaia ML, Gaut BS. Insights into the domestication of avocado and potential genetic contributors to heterodichogamy. G3 (BETHESDA, MD.) 2023; 13:jkac323. [PMID: 36477810 PMCID: PMC9911064 DOI: 10.1093/g3journal/jkac323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
The domestication history of the avocado (Persea americana) remains unclear. We created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. Our genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91%, and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate population genomics, based on a sample of 34 resequenced accessions that represented the 3 botanical groups of P. americana. Our analyses were consistent with 3 separate domestication events; we estimated that the Mexican group diverged from the Lowland (formerly known as "West Indian") and Guatemalan groups >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan group, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types, providing preliminary evidence for potential candidate genes involved in pollination and floral development.
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Affiliation(s)
- Edwin Solares
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Abraham Morales-Cruz
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Rosa Figueroa Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Eric Focht
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Vanessa E T M Ashworth
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Skylar Wyant
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Mary Lu Arpaia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon S Gaut
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
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50
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Zheng X, Zhong L, Pang H, Wen S, Li F, Lou D, Ge J, Fan W, Wang T, Han Z, Qiao W, Pan X, Zhu Y, Wang J, Tang C, Wang X, Zhang J, Xu Z, Kim SR, Kohli A, Ye G, Olsen KM, Fang W, Yang Q. Lost genome segments associate with trait diversity during rice domestication. BMC Biol 2023; 21:20. [PMID: 36726089 PMCID: PMC9893545 DOI: 10.1186/s12915-023-01512-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.
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Affiliation(s)
- Xiaoming Zheng
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China ,grid.419387.00000 0001 0729 330XInternational Rice Research Institute, DAPO box 7777, Metro Manila, the Philippines ,grid.410727.70000 0001 0526 1937Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Zhong
- grid.260463.50000 0001 2182 8825College of life science, Nanchang University, Nanchang, China
| | - Hongbo Pang
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, Shenyang, China
| | - Siyu Wen
- grid.410727.70000 0001 0526 1937Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Li
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Danjing Lou
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinyue Ge
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weiya Fan
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin, China
| | - Zhenyun Han
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weihua Qiao
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaowu Pan
- grid.410598.10000 0004 4911 9766Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yebao Zhu
- grid.418033.d0000 0001 2229 4212Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jilin Wang
- grid.464380.d0000 0000 9885 0994Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Cuifeng Tang
- grid.410732.30000 0004 1799 1111Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xinhua Wang
- grid.464347.6Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Jing Zhang
- grid.135769.f0000 0001 0561 6611Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China ,grid.484195.5Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Zhijian Xu
- grid.452720.60000 0004 0415 7259Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Sung Ryul Kim
- grid.419387.00000 0001 0729 330XInternational Rice Research Institute, DAPO box 7777, Metro Manila, the Philippines
| | - Ajay Kohli
- grid.419387.00000 0001 0729 330XInternational Rice Research Institute, DAPO box 7777, Metro Manila, the Philippines
| | - Guoyou Ye
- grid.419387.00000 0001 0729 330XInternational Rice Research Institute, DAPO box 7777, Metro Manila, the Philippines ,grid.289247.20000 0001 2171 7818Crop Biotech Institute & Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Kenneth M. Olsen
- grid.4367.60000 0001 2355 7002Biology Department, Washington University, Campus Box 1137, St. Louis, MO 63130 USA
| | - Wei Fang
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qingwen Yang
- grid.410727.70000 0001 0526 1937National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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