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Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. THE NEW PHYTOLOGIST 2024. [PMID: 38798271 DOI: 10.1111/nph.19862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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2
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He X, Qi Z, Liu Z, Chang X, Zhang X, Li J, Wang M. Pangenome analysis reveals transposon-driven genome evolution in cotton. BMC Biol 2024; 22:92. [PMID: 38654264 DOI: 10.1186/s12915-024-01893-2] [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: 10/22/2023] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. RESULTS Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. CONCLUSIONS Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.
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Affiliation(s)
- Xin He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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3
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Liu Y, Zhou Y, Cheng F, Zhou R, Yang Y, Wang Y, Zhang X, Soltis DE, Xiao N, Quan Z, Li J. Chromosome-level genome of putative autohexaploid Actinidia deliciosa provides insights into polyploidisation and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:73-89. [PMID: 38112590 DOI: 10.1111/tpj.16592] [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: 07/27/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Actinidia ('Mihoutao' in Chinese) includes species with complex ploidy, among which diploid Actinidia chinensis and hexaploid Actinidia deliciosa are economically and nutritionally important fruit crops. Actinidia deliciosa has been proposed to be an autohexaploid (2n = 174) with diploid A. chinensis (2n = 58) as the putative parent. A CCS-based assembly anchored to a high-resolution linkage map provided a chromosome-resolved genome for hexaploid A. deliciosa yielded a 3.91-Gb assembly of 174 pseudochromosomes comprising 29 homologous groups with 6 members each, which contain 39 854 genes with an average of 4.57 alleles per gene. Here we provide evidence that much of the hexaploid genome matches diploid A. chinensis; 95.5% of homologous gene pairs exhibited >90% similarity. However, intragenome and intergenome comparisons of synteny indicate chromosomal changes. Our data, therefore, indicate that if A. deliciosa is an autoploid, chromosomal rearrangement occurred following autohexaploidy. A highly diversified pattern of gene expression and a history of rapid population expansion after polyploidisation likely facilitated the adaptation and niche differentiation of A. deliciosa in nature. The allele-defined hexaploid genome of A. deliciosa provides new genomic resources to accelerate crop improvement and to understand polyploid genome evolution.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Yi Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, 10008, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, 10008, China
| | - Yanchang Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Zhanjun Quan
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
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4
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Miao L, Xu W, Liu Y, Huang X, Chen Z, Wang H, Wang Z, Chen Y, Song Q, Zhang J, Han F, Peng H, Yao Y, Xin M, Hu Z, Ni Z, Sun Q, Xing J, Guo W. Reshaped DNA methylation cooperating with homoeolog-divergent expression promotes improved root traits in synthesized tetraploid wheat. THE NEW PHYTOLOGIST 2024; 242:507-523. [PMID: 38362849 DOI: 10.1111/nph.19593] [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: 11/01/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive. Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (SlSl and AA) and their synthetic allotetraploid wheat line (SlSlAA), which displayed elongated root hair and improved root capability for nitrate uptake and assimilation after tetraploidization. Globally decreased DNA methylation levels with a reduced difference between subgenomes were observed in the roots of SlSlAA. DNA methylation changes in first exon showed strong connections with altered transcription during tetraploidization. Homoeolog-specific transcription was associated with biased DNA methylation as shaped by homoeologous sequence variation. The hypomethylated promoters showed significantly enriched binding sites for MYB, which may affect gene transcription in response to root hair growth. Two master regulators in root hair elongation pathway, AlCPC and TuRSL4, exhibited upregulated transcription levels accompanied by hypomethylation in promoter, which may contribute to the elongated root hair. The upregulated nitrate transporter genes, including NPFs and NRTs, also are significantly associated with hypomethylation, indicating an epigenetic-incorporated regulation manner in improving nitrogen use efficiency. Collectively, these results provided new insights into epigenetic changes in response to crop polyploidization and underscored the importance of epigenetic regulation in improving crop traits.
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Affiliation(s)
- Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weiya Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiangyi Huang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhe Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huifang Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, 266000, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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5
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Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. Nat Commun 2024; 15:2491. [PMID: 38509076 PMCID: PMC10954716 DOI: 10.1038/s41467-024-46861-0] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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6
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Zhu F, Lu J, Sun K, Deng C, Xu Y. Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing. BMC Genom Data 2024; 25:23. [PMID: 38408920 PMCID: PMC10895795 DOI: 10.1186/s12863-024-01208-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: 03/03/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates. METHODS In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species. RESULTS A total of 51,849 nonredundant full-length transcript assemblies (with an N50 length of 2980 bp) from I. braminus were generated and fully annotated using various gene function databases. Our analysis provides preliminary evidence supporting a recent genome duplication event in I. braminus. Phylogenetic analysis indicated that the divergence of I. braminus subgenomes occurred approximately 11.5 ~ 15 million years ago (Mya). The full-length transcript resource generated as part of this research will facilitate transcriptome analysis and genomic evolution studies in the future.
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Affiliation(s)
- Fei Zhu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China.
| | - Jing Lu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Ke Sun
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, 610000, Chengdu, China
| | - Yu Xu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
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7
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Zhang F, Wang Y, Lin Y, Wang H, Wu Y, Ren W, Wang L, Yang Y, Zheng P, Wang S, Yue J, Liu Y. Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid. MOLECULAR HORTICULTURE 2024; 4:4. [PMID: 38317251 PMCID: PMC10845759 DOI: 10.1186/s43897-024-00083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/23/2024] [Indexed: 02/07/2024]
Abstract
Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops.
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Affiliation(s)
- Feng Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- School of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, 323000, China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Hongtao Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Wangmei Ren
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lihuan Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Pengpeng Zheng
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Songhu Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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8
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Song H, Zhang Q, Hu H. polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species. Brief Bioinform 2024; 25:bbae106. [PMID: 38517695 PMCID: PMC10959164 DOI: 10.1093/bib/bbae106] [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: 10/30/2023] [Revised: 12/22/2023] [Accepted: 02/26/2024] [Indexed: 03/24/2024] Open
Abstract
Given the universality of autopolyploid species in nature, it is crucial to develop genomic selection methods that consider different allele dosages for autopolyploid breeding. However, no method has been developed to deal with autopolyploid data regardless of the ploidy level. In this study, we developed a modified genomic best linear unbiased prediction (GBLUP) model (polyGBLUP) through constructing additive and dominant genomic relationship matrices based on different allele dosages. polyGBLUP could carry out genomic prediction for autopolyploid species regardless of the ploidy level. Through comprehensive simulations and analysis of real data of autotetraploid blueberry and guinea grass and autohexaploid sweet potato, the results showed that polyGBLUP achieved higher prediction accuracy than GBLUP and its superiority was more obvious when the ploidy level of autopolyploids is high. Furthermore, when the dominant effect was added to polyGBLUP (polyGDBLUP), the greater the dominance degree, the more obvious the advantages of polyGDBLUP over the diploid models in terms of prediction accuracy, bias, mean squared error and mean absolute error. For real data, the superiority of polyGBLUP over GBLUP appeared in blueberry and sweet potato populations and a part of the traits in guinea grass population due to the high correlation coefficients between diploid and polyploidy genomic relationship matrices. In addition, polyGDBLUP did not produce higher prediction accuracy than polyGBLUP for most traits of real data as dominant genetic variance was not captured for these traits. Our study will be a significant promising method for genomic prediction of autopolyploid species.
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Affiliation(s)
- Hailiang Song
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou, 311799, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271001, China
| | - Hongxia Hu
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou, 311799, China
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9
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-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: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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10
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Chai J, Xue L, Lei J, Yao W, Zhang M, Deng Z, Yu F. All nonhomologous chromosomes and rearrangements in Saccharum officinarum × Saccharum spontaneum allopolyploids identified by oligo-based painting. FRONTIERS IN PLANT SCIENCE 2023; 14:1176914. [PMID: 37868320 PMCID: PMC10588481 DOI: 10.3389/fpls.2023.1176914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023]
Abstract
Modern sugarcane cultivars (Saccharum spp., 2n = 100~120) are complex polyploids primarily derived from interspecific hybridization between S. officinarum and S. spontaneum. Nobilization is the theory of utilizing wild germplasm in sugarcane breeding, and is the foundation for utilizing S. spontaneum for stress resistance. However, the exact chromosomal transmission remains elusive due to a lack of chromosome-specific markers. Here, we applied chromosome-specific oligonucleotide (oligo)-based probes for identifying chromosomes 1-10 of the F1 hybrids between S. officinarum and S. spontaneum. Then, S. spontaneum-specific repetitive DNA probes were used to distinguish S. spontaneum in these hybrids. This oligo- fluorescence in situ hybridization (FISH) system proved to be an efficient tool for revealing individual chromosomal inheritance during nobilization. We discovered the complete doubling of S. officinarum-derived chromosomes in most F1 hybrids. Notably, we also found defective S. officinarum-derived chromosome doubling in the F1 hybrid Yacheng75-4191, which exhibited 1.5n transmission for all nonhomologous chromosomes. Altogether, these results highlight the presence of variable chromosome transmission in nobilization between S. officinarum and S. spontaneum, including 1.5n + n and 2n + n. These findings provide robust chromosome markers for in-depth studies into the molecular mechanism underlying chromosome doubling during the nobilization, as well as tracing chromosomal inheritance for sugarcane breeding.
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Affiliation(s)
- Jin Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Li Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Jiawei Lei
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
| | - Zuhu Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fan Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
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11
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Walczyk AM, Hersch-Green EI. Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series. AMERICAN JOURNAL OF BOTANY 2023; 110:e16218. [PMID: 37551707 DOI: 10.1002/ajb2.16218] [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: 03/23/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited. METHODS We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use. RESULTS Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions. CONCLUSIONS N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.
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Affiliation(s)
- Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Biology Department, Gustavus Adolphus College, 800 West College Avenue, St. Peter, MN, 56082, USA
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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12
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Yu RM, Zhang N, Zhang BW, Liang Y, Pang XX, Cao L, Chen YD, Zhang WP, Yang Y, Zhang DY, Pang EL, Bai WN. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol 2023; 21:168. [PMID: 37553642 PMCID: PMC10408227 DOI: 10.1186/s12915-023-01668-1] [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: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. RESULTS Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. CONCLUSIONS Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
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Affiliation(s)
- Rui-Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ning Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Dan Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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13
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Jin X, Du H, Zhu C, Wan H, Liu F, Ruan J, Mower JP, Zhu A. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. NATURE PLANTS 2023; 9:1252-1266. [PMID: 37537397 DOI: 10.1038/s41477-023-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.
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Affiliation(s)
- Xin Jin
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chumeng Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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14
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Xu T, Liu Z, Zhan D, Pang Z, Zhang S, Li C, Kang X, Yang J. Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:117. [PMID: 37480079 PMCID: PMC10360242 DOI: 10.1186/s13068-023-02366-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Lignin is a major restriction factor for the industrial production of biomass resources, such as pulp and bioenergy. Eucalyptus is one of the most important sources of pulp and bioenergy. After polyploidization, the lignin content of forest trees is generally reduced, which is considered a beneficial genetic improvement. However, the differences in the lignin content between triploid and diploid Eucalyptus and the underlying regulatory mechanism are still unclear. RESULTS We conducted a comprehensive analysis at the phenotypic, transcriptional and metabolite levels between Eucalyptus urophylla triploids and diploids to reveal the effects of polyploidization on the lignin content and lignin metabolic pathway. The results showed that the lignin content of Eucalyptus urophylla triploid stems was significantly lower than that of diploids. Lignin-related metabolites were differentially accumulated between triploids and diploids, among which coniferaldehyde, p-coumaryl alcohol, sinapaldehyde and coniferyl alcohol had significant positive correlations with lignin content, indicating that they might be primarily contributing metabolites. Most lignin biosynthetic genes were significantly downregulated, among which 11 genes were significantly positively correlated with the lignin content and above metabolites. Furthermore, we constructed a co-expression network between lignin biosynthetic genes and transcription factors based on weighted gene co-expression network analysis. The network identified some putative orthologues of secondary cell wall (SCW)-related transcription factors, among which MYB52, MYB42, NAC076, and LBD15 were significantly downregulated in Eucalyptus urophylla triploids. In addition, potential important transcription factors, including HSL1, BEE3, HHO3, and NAC046, also had high degrees of connectivity and high edge weights with lignin biosynthetic genes, indicating that they might also be involved in the variation of lignin accumulation between triploid and diploid Eucalyptus urophylla. CONCLUSIONS The results demonstrated that some lignin-related metabolites, lignin biosynthetic genes and transcription factors in Eucalyptus urophylla triploids may be relatively sensitive in response to the polyploidization effect, significantly changing their expression levels, which ultimately correlated with the varied lignin content. The analysis of the underlying formation mechanism could provide beneficial information for the development and utilization of polyploid biomass resources, which will be also valuable for genetic improvement in other bioenergy plants.
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Affiliation(s)
- Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dingju Zhan
- Guangxi Bagui R&D Institute for Forest Tree and Flower Breeding, Nanning, 530025, China
| | - Zhenwu Pang
- Guangxi Bagui R&D Institute for Forest Tree and Flower Breeding, Nanning, 530025, China
| | - Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhe Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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15
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. THE NEW PHYTOLOGIST 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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16
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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17
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Liu X, Yan R, Liu H, Zhang S, Wang R, Zhang B, Sun L. Genome-Wide Expression Analysis of Long Noncoding RNAs and Their Target Genes in Metafemale Drosophila. Int J Mol Sci 2023; 24:ijms24098381. [PMID: 37176087 PMCID: PMC10179461 DOI: 10.3390/ijms24098381] [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: 03/07/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Aneuploidy is usually more detrimental than altered ploidy of the entire set of chromosomes. To explore the regulatory mechanism of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of metafemale Drosophila. The results showed that most genes on the X chromosome undergo dosage compensation, while the genes on the autosomal chromosomes mainly present inverse dosage effects. Furthermore, long noncoding RNAs (lncRNAs) have been identified as key regulators of gene expression, and they are more sensitive to dosage changes than mRNAs. We analyzed differentially expressed mRNAs (DEGs) and differentially expressed lncRNAs (DELs) in metafemale Drosophila and performed functional enrichment analyses of DEGs and the target genes of DELs, and we found that they are involved in several important biological processes. By constructing lncRNA-mRNA interaction networks and calculating the maximal clique centrality (MCC) value of each node in the network, we also identified two key candidate lncRNAs (CR43940 and CR42765), and two of their target genes, Sin3A and MED1, were identified as inverse dosage modulators. These results suggest that lncRNAs play an important role in the regulation of genomic imbalances. This study may deepen the understanding of the gene expression regulatory mechanisms in aneuploidy from the perspective of lncRNAs.
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Affiliation(s)
- Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ran Yan
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Haosheng Liu
- State Key Laboratory of Earth Surface Process and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bowen Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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18
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Anneberg TJ, O'Neill EM, Ashman TL, Turcotte MM. Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs. THE NEW PHYTOLOGIST 2023; 238:1294-1304. [PMID: 36740596 DOI: 10.1111/nph.18794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Elizabeth M O'Neill
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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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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20
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Li G, Wu Y, Bai Y, Zhao N, Jiang Y, Li N, Lin X, Liu B, Xu C. Patterns of Chromosomal Variation, Homoeologous Exchange, and Their Relationship with Genomic Features in Early Generations of a Synthetic Rice Segmental Allotetraploid. Int J Mol Sci 2023; 24:ijms24076065. [PMID: 37047036 PMCID: PMC10094486 DOI: 10.3390/ijms24076065] [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: 02/02/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Polyploidization is a driving force in plant evolution. Chromosomal variation often occurs at early generations following polyploid formation due to meiotic pairing irregularity that may compromise segregation fidelity and cause homoeologous exchange (HE). The trends of chromosomal variation and especially factors affecting HE remain to be fully deciphered. Here, by whole-genome resequencing, we performed nuanced analyses of patterns of chromosomal number variation and explored genomic features that affect HE in two early generations of a synthetic rice segmental allotetraploid. We found a wide occurrence of whole-chromosome aneuploidy and, to a lesser extent, also large segment gains/losses in both generations (S2 and S4) of the tetraploids. However, while the number of chromosome gains was similar between S2 and S4, that of losses in S4 was lower than in S2. HEs were abundant across all chromosomes in both generations and showed variable correlations with different genomic features at chromosomal and/or local scales. Contents of genes and transposable elements (TEs) were positively and negatively correlated with HE frequencies, respectively. By dissecting TEs into different classes, retrotransposons were found to be negatively correlated with HE frequency to a stronger extent than DNA transposons, whereas miniature terminal inverted elements (MITEs) showed a strong positive correlation. Local HE frequencies in the tetraploids and homologous recombination (HR) rates in diploids within 1 Mb sliding windows were significantly correlated with each other and showed similar overall distribution profiles. Nonetheless, non-concordant trends between HE and HR rates were found at distal regions in some chromosomes. At local scale, both shared and polymorphic retrotransposons between parents were negatively correlated with HE frequency; in contrast, both shared and polymorphic MITEs showed positive correlations with HE frequency. Our results shed new light on the patterns of chromosomal number variation and reveal genomic features influencing HE frequency in early generations following plant polyploidization.
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Affiliation(s)
- Guo Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yuhui Jiang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agriculture, Changchun 130033, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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21
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Wang H, Dang J, Guo Q, Liang G. qPCR Genotyping of Polyploid Species. Methods Mol Biol 2023; 2638:115-122. [PMID: 36781638 DOI: 10.1007/978-1-0716-3024-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
A simple and cost-effective method for genotyping polyploid plants using quantitative PCR (qPCR) is described in this chapter. There is no additional operation, only simultaneous amplification of alleles and reference sequences with constant copy number in the genome. The qPCR genotyping can detect the genotypes of important traits in polyploid plants without whole genome sequencing data.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China.
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22
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Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads. Gene 2023; 852:147065. [PMID: 36435508 DOI: 10.1016/j.gene.2022.147065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.
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23
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Wang Y, Yu J, Jiang M, Lei W, Zhang X, Tang H. Sequencing and Assembly of Polyploid Genomes. Methods Mol Biol 2023; 2545:429-458. [PMID: 36720827 DOI: 10.1007/978-1-0716-2561-3_23] [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] [Indexed: 06/18/2023]
Abstract
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in highly complex genome structures, posing challenges to genome assembly and phasing. Recent advances in sequencing technologies and genome assembly algorithms have enabled high-quality, near-complete chromosome-level assemblies of polyploid genomes. Advances in novel sequencing technologies include highly accurate single-molecule sequencing with HiFi reads, chromosome conformation capture with Hi-C technique, and linked reads sequencing. Additionally, new computational approaches have also significantly improved the precision and reliability of polyploid genome assembly and phasing, such as HiCanu, hifiasm, ALLHiC, and PolyGembler. Herein, we review recently published polyploid genomes and compare the various sequencing, assembly, and phasing approaches that are utilized in these genome studies. Finally, we anticipate that accurate and telomere-to-telomere chromosome-level assembly of polyploid genomes could ultimately become a routine procedure in the near future.
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Affiliation(s)
- Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaxin Yu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengwei Jiang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenlong Lei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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24
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Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, Yang B, Pires JC. Prospects of Feral Crop De Novo Redomestication. PLANT & CELL PHYSIOLOGY 2022; 63:1641-1653. [PMID: 35639623 DOI: 10.1093/pcp/pcac072] [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: 02/14/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.
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Affiliation(s)
- Michael T Pisias
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Harmeet Singh Bakala
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO 63132, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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25
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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26
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Chai Z, Fang J, Huang C, Huang R, Tan X, Chen B, Yao W, Zhang M. A novel transcription factor, ScAIL1, modulates plant defense responses by targeting DELLA and regulating gibberellin and jasmonic acid signaling in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6727-6743. [PMID: 35986920 DOI: 10.1093/jxb/erac339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
DELLA proteins are important repressors of gibberellin signaling, regulating plant development and defense responses through crosstalk with various phytohormones. Sugarcane ScGAI encodes a DELLA protein that regulates culm development. However, it is unclear which transcription factors mediate the transcription of ScGAI. Here, we identified two different ScGAI promoter sequences that cooperatively regulate ScGAI transcription. We also identified a nuclear-localized AP2 family transcription factor, ScAIL1, which inhibits the transcription of ScGAI by directly binding to two ScGAI promoters. ScAIL1 was expressed in all sugarcane tissues tested and was induced by gibberellin and various stressors, including NaCl, polyethylene glycol, and pathogenic fungi and bacteria. Overexpression of ScAIL1 in rice significantly improved resistance to bacterial blight and rice blast, while reducing growth and development. In addition, several genes associated with stress responses were significantly up-regulated in transgenic rice overexpressing ScAIL1. Endogenous phytohormone content and expression analysis further revealed that ScAIL1-overexpressing lines improved resistance to bacterial blight and rice blast instead of promoting growth, and that this response was associated with increased jasmonic acid synthesis and gibberellin inactivation. These results provide molecular evidence that the role of ScAIL1 in the plant defense response is related to jasmonic acid and gibberellin signaling.
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Affiliation(s)
- Zhe Chai
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Jinlan Fang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Cuilin Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Run Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Xuan Tan
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
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27
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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28
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of “foreign” recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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29
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Correr FH, Furtado A, Franco Garcia AA, Henry RJ, Rodrigues Alves Margarido G. Allele expression biases in mixed-ploid sugarcane accessions. Sci Rep 2022; 12:8778. [PMID: 35610293 PMCID: PMC9130122 DOI: 10.1038/s41598-022-12725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Antonio Augusto Franco Garcia
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
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30
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Zhang W, Shi H, Zhou Y, Liang X, Luo X, Xiao C, Li Y, Xu P, Wang J, Gong W, Zou Q, Tao L, Kang Z, Tang R, Li Z, Yang J, Fu S. Rapid and Synchronous Breeding of Cytoplasmic Male Sterile and Maintainer Line Through Mitochondrial DNA Rearrangement Using Doubled Haploid Inducer in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:871006. [PMID: 35557722 PMCID: PMC9087798 DOI: 10.3389/fpls.2022.871006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
When homozygously fertile plants were induced using doubled haploid (DH) induction lines Y3380 and Y3560, the morphology of the induced F1 generation was basically consistent with the female parent, but the fertility was separated, showing characteristics similar to cytoplasmic male sterile (CMS) and maintainer lines. In this study, the morphology, fertility, ploidy, and cytoplasm genotype of the induced progeny were identified, and the results showed that the sterile progeny was polima cytoplasm sterile (pol CMS) and the fertile progeny was nap cytoplasm. The molecular marker and test-cross experimental results showed that the fertile progeny did not carry the restorer gene of pol CMS and the genetic distance between the female parent and the offspring was 0.002. This suggested that those inductions which produced sterile and fertile progeny were coordinated to CMS and maintainer lines. Through the co-linearity analysis of the mitochondrial DNA (mtDNA), it was found that the rearrangement of mtDNA by DH induction was the key factor that caused the transformation of fertility (nap) into sterility (pol). Also, when heterozygous females were induced with DH induction lines, the induction F2 generation also showed the segregation of fertile and sterile lines, and the genetic distance between sterile and fertile lines was approximately 0.075. Therefore, the induction line can induce different types of female parents, and the breeding of the sterile line and the maintainer line can be achieved through the rapid synchronization of sister crosses and self-crosses. The induction of DH inducer in B. napus can provide a new model for the innovation of germplasm resources and open up a new way for its application.
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Affiliation(s)
- Wei Zhang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Ying Zhou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Xingyu Liang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuan Luo
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaowen Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yun Li
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jisheng Wang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Wanzhuo Gong
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Qiong Zou
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Lanrong Tao
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zeming Kang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Rong Tang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Zhuang Li
- Agricultural College, Sichuan Agricultural University, Chengdu, China
| | - Jin Yang
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
| | - Shaohong Fu
- Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, China
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Wang Z, Yang J, Cheng F, Li P, Xin X, Wang W, Yu Y, Zhang D, Zhao X, Yu S, Zhang F, Dong Y, Su T. Subgenome dominance and its evolutionary implications in crop domestication and breeding. HORTICULTURE RESEARCH 2022; 9:uhac090. [PMID: 35873727 PMCID: PMC9297153 DOI: 10.1093/hr/uhac090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 05/29/2023]
Abstract
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.
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Affiliation(s)
| | | | | | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
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Javadian N, Karimzadeh G, Sharifi M, Moieni A. Effect of ploidy level on podophyllotoxin content and expression of genes related to its biosynthesis in callus cultures of Linum album. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01082-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Masuda K, Ikeda Y, Matsuura T, Kawakatsu T, Tao R, Kubo Y, Ushijima K, Henry IM, Akagi T. Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. NATURE PLANTS 2022; 8:217-224. [PMID: 35301445 DOI: 10.1038/s41477-022-01107-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 05/29/2023]
Abstract
In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- JST-PRESTO, Saitama, Japan.
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Rodríguez-Parra A, Picazo-Aragonés J, Balao F. Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040518. [PMID: 35214851 PMCID: PMC8878694 DOI: 10.3390/plants11040518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 05/14/2023]
Abstract
Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.
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Li M, Hou L, Zhang C, Yang W, Liu X, Zhao H, Pang X, Li Y. Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:829765. [PMID: 35185994 PMCID: PMC8854171 DOI: 10.3389/fpls.2022.829765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/12/2022] [Indexed: 06/02/2023]
Abstract
The effects of whole-genome duplication span multiple levels. Previous study reported that the autotetraploid sour jujube exhibited superior drought tolerance than diploid. However, the difference in water transport system between diploids and autotetraploids and its mechanism remain unclear. Here, we found the number of xylem vessels and parenchyma cells in autotetraploid sour jujube increased to nearly twice that of diploid sour jujube, which may be closely related to the differences in xylem vessel differentiation-related ZjVND7 targets between the two ploidy types. Although the five enriched binding motifs are different, the most reliable motif in both diploid and autotetraploid sour jujube was CTTNAAG. Additionally, ZjVND7 targeted 236 and 321 genes in diploids and autotetraploids, respectively. More identified targeted genes of ZjVND7 were annotated to xylem development, secondary wall synthesis, cell death, cell division, and DNA endoreplication in autotetraploids than in diploids. SMR1 plays distinct roles in both proliferating and differentiated cells. Under drought stress, the binding signal of ZjVND7 to ZjSMR1 was stronger in autotetraploids than in diploids, and the fold-changes in the expression of ZjVND7 and ZjSMR1 were larger in the autotetraploids than in the diploids. These results suggested that the targeted regulation of ZjVND7 on ZjSMR1 may play valuable roles in autotetraploids in the response to drought stress. We hypothesized that the binding of ZjVND7 to ZjSMR1 might play a role in cell division and transdifferentiation from parenchyma cells to vessels in the xylem. This regulation could prolong the cell cycle and regulate endoreplication in response to drought stress and abscisic acid, which may be stronger in polyploids.
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Affiliation(s)
- Meng Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chenxing Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Weicong Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xinru Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Li M, Hu M, Xiao Y, Wu X, Wang J. The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus. HORTICULTURE RESEARCH 2022; 9:uhab075. [PMID: 35043208 PMCID: PMC8923814 DOI: 10.1093/hr/uhab075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Bozinovic G, Feng Z, Shea D, Oleksiak MF. Cardiac physiology and metabolic gene expression during late organogenesis among F. heteroclitus embryo families from crosses between pollution-sensitive and -resistant parents. BMC Ecol Evol 2022; 22:3. [PMID: 34996355 PMCID: PMC8739662 DOI: 10.1186/s12862-022-01959-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 01/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The teleost fish Fundulus heteroclitus inhabit estuaries heavily polluted with persistent and bioaccumulative chemicals. While embryos of parents from polluted sites are remarkably resistant to toxic sediment and develop normally, embryos of parents from relatively clean estuaries, when treated with polluted sediment extracts, are developmentally delayed, displaying deformities characteristic of pollution-induced embryotoxicity. To gain insight into parental effects on sensitive and resistant phenotypes during late organogenesis, we established sensitive, resistant, and crossed embryo families using five female and five male parents from relatively clean and predominantly PAH-polluted estuaries each, measured heart rates, and quantified individual embryo expression of 179 metabolic genes. RESULTS Pollution-induced embryotoxicity manifested as morphological deformities, significant developmental delays, and altered cardiac physiology was evident among sensitive embryos resulting from crosses between females and males from relatively clean estuaries. Significantly different heart rates among several geographically unrelated populations of sensitive, resistant, and crossed embryo families during late organogenesis and pre-hatching suggest site-specific adaptive cardiac physiology phenotypes relative to pollution exposure. Metabolic gene expression patterns (32 genes, 17.9%, at p < 0.05; 11 genes, 6.1%, at p < 0.01) among the embryo families indicate maternal pollutant deposition in the eggs and parental effects on gene expression and metabolic alterations. CONCLUSION Heart rate differences among sensitive, resistant, and crossed embryos is a reliable phenotype for further explorations of adaptive mechanisms. While metabolic gene expression patterns among embryo families are suggestive of parental effects on several differentially expressed genes, a definitive adaptive signature and metabolic cost of resistant phenotypes is unclear and shows unexpected sensitive-resistant crossed embryo expression profiles. Our study highlights physiological and metabolic gene expression differences during a critical embryonic stage among pollution sensitive, resistant, and crossed embryo families, which may contribute to underlying resistance mechanisms observed in natural F. heteroclitus populations living in heavily contaminated estuaries.
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Affiliation(s)
- Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA.
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Damian Shea
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Marjorie F Oleksiak
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA
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Tossi VE, Martínez Tosar LJ, Laino LE, Iannicelli J, Regalado JJ, Escandón AS, Baroli I, Causin HF, Pitta-Álvarez SI. Impact of polyploidy on plant tolerance to abiotic and biotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:869423. [PMID: 36072313 PMCID: PMC9441891 DOI: 10.3389/fpls.2022.869423] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.
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Affiliation(s)
- Vanesa E. Tossi
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Leandro J. Martínez Tosar
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biotecnología, Alimentos, Agro y Ambiental (DEBAL), Facultad de Ingeniería y Ciencias Exactas, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Leandro E. Laino
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Jesica Iannicelli
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - José Javier Regalado
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Alejandro Salvio Escandón
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
| | - Irene Baroli
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Irene Baroli,
| | - Humberto Fabio Causin
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Humberto Fabio Causin,
| | - Sandra Irene Pitta-Álvarez
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- *Correspondence: Sandra Irene Pitta-Álvarez, ;
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Syngelaki E, Paetzold C, Hörandl E. Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae). Genes (Basel) 2021; 12:genes12111818. [PMID: 34828424 PMCID: PMC8625111 DOI: 10.3390/genes12111818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps.
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Affiliation(s)
- Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
- Correspondence:
| | - Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany;
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
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Luo X, Yang J, Zhu Z, Huang L, Ali A, Javed HH, Zhang W, Zhou Y, Yin L, Xu P, Liang X, Li Y, Wang J, Zou Q, Gong W, Shi H, Tao L, Kang Z, Tang R, Liu H, Fu S. Genetic characteristics and ploidy trigger the high inducibility of double haploid (DH) inducer in Brassica napus. BMC PLANT BIOLOGY 2021; 21:538. [PMID: 34784885 PMCID: PMC8594162 DOI: 10.1186/s12870-021-03311-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/27/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Our recently reported doubled haploid (DH) induction lines e.g., Y3380 and Y3560 are allo-octoploid (AAAACCCC, 2n = 8× ≈ 76), which can induce the maternal parent to produce DH individuals. Whether this induction process is related to the production of aneuploid gametes form male parent and genetic characteristics of the male parent has not been reported yet. RESULTS Somatic chromosome counts of DH inducer parents, female wax-less parent (W1A) and their F1 hybrid individuals revealed the reliability of flow cytometry analysis. Y3560 has normal chromosome behavior in metaphase I and anaphase I, but chromosome division was not synchronized in the tetrad period. Individual phenotypic identification and flow cytometric fluorescence measurement of F1 individual and parents revealed that DH individuals can be distinguished on the basis of waxiness trait. The results of phenotypic identification and flow cytometry can identify the homozygotes or heterozygotes of F1 generation individuals. The data of SNP genotyping coupled with phenotypic waxiness trait revealed that the genetic distance between W1A and F1 homozygotes were smaller as compared to their heterozygotes. It was found that compared with allo-octoploids, aneuploidy from allo-octoploid segregation did not significantly increase the DH induction rate, but reduced male infiltration rate and heterozygous site rate of induced F1 generation. The ploidy, SNP genotyping and flow cytometry results cumulatively shows that DH induction is attributed to the key genes regulation from the parents of Y3560 and Y3380, which significantly increase the induction efficiency as compared to ploidy. CONCLUSION Based on our findings, we hypothesize that genetic characteristics and aneuploidy play an important role in the induction of DH individuals in Brassca napus, and the induction process has been explored. It provides an important insight for us to locate and clone the genes that regulate the inducibility in the later stage.
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Affiliation(s)
- Xuan Luo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Asif Ali
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hafiz Hassan Javed
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ying Zhou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xingyu Liang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Wanzhuo Gong
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Haoran Shi
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China
| | - Hailan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China.
- Chengdu Research Branch, National Rapeseed Genetic Improvement Center, Chengdu, 611130, China.
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Martín AC, Alabdullah AK, Moore G. A separation-of-function ZIP4 wheat mutant allows crossover between related chromosomes and is meiotically stable. Sci Rep 2021; 11:21811. [PMID: 34750469 PMCID: PMC8575954 DOI: 10.1038/s41598-021-01379-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Many species, including most flowering plants, are polyploid, possessing multiple genomes. During polyploidisation, fertility is preserved via the evolution of mechanisms to control the behaviour of these multiple genomes during meiosis. On the polyploidisation of wheat, the major meiotic gene ZIP4 duplicated and diverged, with the resulting new gene TaZIP4-B2 being inserted into chromosome 5B. Previous studies showed that this TaZIP4-B2 promotes pairing and synapsis between wheat homologous chromosomes, whilst suppressing crossover between related (homoeologous) chromosomes. Moreover, in wheat, the presence of TaZIP4-B2 preserves up to 50% of grain number. The present study exploits a 'separation-of-function' wheat Tazip4-B2 mutant named zip4-ph1d, in which the Tazip4-B2 copy still promotes correct pairing and synapsis between homologues (resulting in the same pollen profile and fertility normally found in wild type wheat), but which also allows crossover between the related chromosomes in wheat haploids of this mutant. This suggests an improved utility for the new zip4-ph1d mutant line during wheat breeding, compared to the previously described CRISPR Tazip4-B2 and ph1 mutant lines. The results also reveal that loss of suppression of homoeologous crossover between wheat chromosomes does not in itself reduce wheat fertility when promotion of homologous pairing and synapsis by TaZIP4-B2 is preserved.
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Affiliation(s)
- Azahara C Martín
- Crop Genetics Department, John Innes Centre, Colney, Norwich, NR4 7UH, UK.
| | | | - Graham Moore
- Crop Genetics Department, John Innes Centre, Colney, Norwich, NR4 7UH, UK
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Chen T, Sheng Y, Hao Z, Long X, Fu F, Liu Y, Tang Z, Ali A, Peng Y, Liu Y, Lu L, Hu X, Shi J, Chen J. Transcriptome and proteome analysis suggest enhanced photosynthesis in tetraploid Liriodendron sino-americanum. TREE PHYSIOLOGY 2021; 41:1953-1971. [PMID: 33791793 PMCID: PMC8498940 DOI: 10.1093/treephys/tpab039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/17/2021] [Indexed: 06/01/2023]
Abstract
Polyploidy generally provides an advantage in phenotypic variation and growth vigor. However, the underlying mechanisms remain poorly understood. The tetraploid Liriodendron sino-americanum (Liriodendron × sinoamericanum P.C Yieh ex C.B. Shang & Zhang R.Wang) exhibits altered morphology compared with its diploid counterpart, including larger, thicker and deeper green leaves, bigger stomata, thicker stems and increased tree height. Such characteristics can be useful in ornamental and industrial applications. To elucidate the molecular mechanisms behind this variation, we performed a comparative transcriptome and proteome analysis. Our transcriptome data indicated that some photosynthesis genes and pathways were differentially altered and enriched in tetraploid L. sino-americanum, mainly related to F-type ATPase, the cytochrome b6/f complex, photosynthetic electron transport, the light harvesting chlorophyll protein complexes, and photosystem I and II. Most of the differentially expressed proteins we could identify are also involved in photosynthesis. Our physiological results showed that tetraploids have an enhanced photosynthetic capacity, concomitant with great levels of sugar and starch in leaves. This suggests that tetraploid L. sino-americanum might experience comprehensive transcriptome reprogramming of genes related to photosynthesis. This study has especially emphasized molecular changes involved in photosynthesis that accompany polyploidy, and provides a possible explanation for the altered phenotype of polyploidy plants in comparison with their diploid form.
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Affiliation(s)
- Tingting Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yu Sheng
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Xiaofei Long
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Fangfang Fu
- College of Forestry, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yang Liu
- School of Forestry, Northeast Forestry University, 26 Hexing Rd, Xiangfang District, Harbin 150040, China
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineer and Resource Utilization, Northeast Forestry University, 26 Hexing Rd, Xiangfang District, Harbin 150040, China
| | - Asif Ali
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Lu Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 266 Jufeng Rd, Baoshan, Shanghai 201900, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
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Wang H, Dang J, Wu D, Xie Z, Yan S, Luo J, Guo Q, Liang G. Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica). PLANT METHODS 2021; 17:93. [PMID: 34479588 PMCID: PMC8418031 DOI: 10.1186/s13007-021-00792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/24/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. RESULTS We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. CONCLUSIONS qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Shuang Yan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jingnan Luo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China.
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Tavan M, Sarikhani H, Mirjalili MH, Rigano MM, Azizi A. Triterpenic and phenolic acids production changed in Salvia officinalis via in vitro and in vivo polyploidization: A consequence of altered genes expression. PHYTOCHEMISTRY 2021; 189:112803. [PMID: 34144408 DOI: 10.1016/j.phytochem.2021.112803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 05/02/2023]
Abstract
The induction of polyploidy is an efficient technique for creating a diversity of genetic, phenotypic, and phytochemical novelties in plant taxa. Sage (Salvia officinalis L.) is a well-known medicinal plant rich of valuable bioactive molecules such as triterpenic and phenolic acids. In the present study, the effect of in vitro and in vivo polyploidization on morphological characteristics, anatomical structures, phytochemical traits, and expression level of the genes involved in the biosynthesis of major triterpenic acids (ursolic, betulinic, and oleanolic acids) of the plant was studied. The sterile seeds treated with different concentrations (0, 0.05, 0.1, and 0.2%) of colchicine for 24 and 48 h were considered for polyploidy induction. Flow cytometry and chromosome counting were used to confirm the ploidy level of diploid (2n = 2x = 14, 2C DNA = 1.10 pg) and tetraploid (2n = 4x = 28, 2C DNA = 2.12 pg) plants after seven months. The highest polyploidy induction was obtained by applying 0.1% (w/v) colchicine for 48 h with an efficiency of 19.05% in vitro tetraploidy. Polyploids showed differences in leaf shape and color, leaf and stem thickness, trichrome density, root length, plant height, and number of leaves compared to diploid plants. There was also a significant decrease in rosmarinic acid content in polyploid (plants) as compared to diploid plants. Although a significant decrease in ursolic acid content was observed in polyploids, betulinic acid content associated with the expression levels of genes encoding enzymes being active in triterpene biosynthesis such as squalene epoxidase (SQE) and lupeol synthase (LUS). The expression of SQE and LUS was significantly increased in in vitro tertaploids (2.9-fold) and in vivo mixoploids (2.4-fold). The results confirm the idea that induced polyploidy can randomly alter breeding traits of plants as well as the content of bioactive compounds.
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Affiliation(s)
- Mansoureh Tavan
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
| | - Hassan Sarikhani
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
| | - Mohammad Hossein Mirjalili
- Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 1983969411, Tehran, Iran.
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Naples, Italy.
| | - Ali Azizi
- Department of Horticultural Science, Faculty of Agriculture, Bu Ali Sina University, 65174, Hamedan, Iran.
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Yadav S, Wei X, Joyce P, Atkin F, Deomano E, Sun Y, Nguyen LT, Ross EM, Cavallaro T, Aitken KS, Hayes BJ, Voss-Fels KP. Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2235-2252. [PMID: 33903985 PMCID: PMC8263546 DOI: 10.1007/s00122-021-03822-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/21/2021] [Indexed: 05/29/2023]
Abstract
Non-additive genetic effects seem to play a substantial role in the expression of complex traits in sugarcane. Including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. In the recent decade, genetic progress has been slow in sugarcane. One reason might be that non-additive genetic effects contribute substantially to complex traits. Dense marker information provides the opportunity to exploit non-additive effects in genomic prediction. In this study, a series of genomic best linear unbiased prediction (GBLUP) models that account for additive and non-additive effects were assessed to improve the accuracy of clonal prediction. The reproducible kernel Hilbert space model, which captures non-additive genetic effects, was also tested. The models were compared using 3,006 genotyped elite clones measured for cane per hectare (TCH), commercial cane sugar (CCS), and Fibre content. Three forward prediction scenarios were considered to investigate the robustness of genomic prediction. By using a pseudo-diploid parameterization, we found significant non-additive effects that accounted for almost two-thirds of the total genetic variance for TCH. Average heterozygosity also had a major impact on TCH, indicating that directional dominance may be an important source of phenotypic variation for this trait. The extended-GBLUP model improved the prediction accuracies by at least 17% for TCH, but no improvement was observed for CCS and Fibre. Our results imply that non-additive genetic variance is important for complex traits in sugarcane, although further work is required to better understand the variance component partitioning in a highly polyploid context. Genomics-based breeding will likely benefit from exploiting non-additive genetic effects, especially in designing crossing schemes. These findings can help to improve clonal prediction, enabling a more accurate identification of variety candidates for the sugarcane industry.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Priya Joyce
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Felicity Atkin
- Sugar Research Australia, Meringa, Gordonvale, QLD, 4865, Australia
| | - Emily Deomano
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Yue Sun
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Loan T Nguyen
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Tony Cavallaro
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Karen S Aitken
- Agriculture and Food, CSIRO, QBP, St. Lucia, QLD, 4067, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia.
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Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae. Genomics 2021; 113:3185-3197. [PMID: 34182082 DOI: 10.1016/j.ygeno.2021.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/26/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022]
Abstract
Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.
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Konstantinov DK, Zubairova US, Ermakov AA, Doroshkov AV. Comparative transcriptome profiling of a resistant vs susceptible bread wheat ( Triticum aestivum L.) cultivar in response to water deficit and cold stress. PeerJ 2021; 9:e11428. [PMID: 34026365 PMCID: PMC8123233 DOI: 10.7717/peerj.11428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/19/2021] [Indexed: 11/28/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.
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Affiliation(s)
- Dmitrii K Konstantinov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Ulyana S Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Anton A Ermakov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexey V Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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Oh Y, Barbey CR, Chandra S, Bai J, Fan Z, Plotto A, Pillet J, Folta KM, Whitaker VM, Lee S. Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:639345. [PMID: 34017348 PMCID: PMC8129584 DOI: 10.3389/fpls.2021.639345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/16/2021] [Indexed: 06/01/2023]
Abstract
Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, FaFAD1. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing FaFAD1, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of FaFAD1 and determined the allele dosage of FaFAD1 that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus FaFAD1 that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence-absence variation of FaFAD1 was discovered among γ-D producers and non-producers. To explore the genomic structure of FaFAD1 in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the FaFAD1 region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of FaFAD1 presence and absence polymorphism in producing γ-D and proposes that both alleles of FaFAD1 are required to produce the highest content of fruity aroma in strawberry fruit.
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Affiliation(s)
- Youngjae Oh
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Christopher R. Barbey
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Saket Chandra
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Jinhe Bai
- Horticultural Research Laboratory, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Fort Pierce, FL, United States
| | - Zhen Fan
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Anne Plotto
- Horticultural Research Laboratory, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Fort Pierce, FL, United States
| | - Jeremy Pillet
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Kevin M. Folta
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Vance M. Whitaker
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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50
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Voss-Fels KP, Wei X, Ross EM, Frisch M, Aitken KS, Cooper M, Hayes BJ. Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1493-1511. [PMID: 33587151 DOI: 10.1007/s00122-021-03785-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 01/27/2021] [Indexed: 05/14/2023]
Abstract
Simulations highlight the potential of genomic selection to substantially increase genetic gain for complex traits in sugarcane. The success rate depends on the trait genetic architecture and the implementation strategy. Genomic selection (GS) has the potential to increase the rate of genetic gain in sugarcane beyond the levels achieved by conventional phenotypic selection (PS). To assess different implementation strategies, we simulated two different GS-based breeding strategies and compared genetic gain and genetic variance over five breeding cycles to standard PS. GS scheme 1 followed similar routines like conventional PS but included three rapid recurrent genomic selection (RRGS) steps. GS scheme 2 also included three RRGS steps but did not include a progeny assessment stage and therefore differed more fundamentally from PS. Under an additive trait model, both simulated GS schemes achieved annual genetic gains of 2.6-2.7% which were 1.9 times higher compared to standard phenotypic selection (1.4%). For a complex non-additive trait model, the expected annual rates of genetic gain were lower for all breeding schemes; however, the rates for the GS schemes (1.5-1.6%) were still greater than PS (1.1%). Investigating cost-benefit ratios with regard to numbers of genotyped clones showed that substantial benefits could be achieved when only 1500 clones were genotyped per 10-year breeding cycle for the additive genetic model. Our results show that under a complex non-additive genetic model, the success rate of GS depends on the implementation strategy, the number of genotyped clones and the stage of the breeding program, likely reflecting how changes in QTL allele frequencies change additive genetic variance and therefore the efficiency of selection. These results are encouraging and motivate further work to facilitate the adoption of GS in sugarcane breeding.
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Affiliation(s)
- Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Giessen, Germany
| | - Karen S Aitken
- Agriculture and Food, CSIRO, QBP, St. Lucia, QLD, 4067, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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