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Horiuchi A, Masuda K, Shirasawa K, Onoue N, Matsuzaki R, Tao R, Kubo Y, Ushijima K, Akagi T. Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon. DNA Res 2023; 30:dsad015. [PMID: 37326063 PMCID: PMC10468310 DOI: 10.1093/dnares/dsad015] [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: 03/08/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023] Open
Abstract
Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties in applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characteristics, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.
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Affiliation(s)
- Ayano Horiuchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | | | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Ryusuke Matsuzaki
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Koichiro Ushijima
- 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
- Japan Science and Technology Agency (JST), PRESTO, Saitama 332-0012, Japan
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2
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Cirilli M, Rossini L, Chiozzotto R, Baccichet I, Florio FE, Mazzaglia A, Turco S, Bassi D, Gattolin S. Less is more: natural variation disrupting a miR172 gene at the di locus underlies the recessive double-flower trait in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2022; 22:318. [PMID: 35786350 PMCID: PMC9252053 DOI: 10.1186/s12870-022-03691-w] [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: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND With the domestication of ornamental plants, artificial selective pressure favored the propagation of mutations affecting flower shape, and double-flower varieties are now readily available for many species. In peach two distinct loci control the double-flower phenotype: the dominant Di2 locus, regulated by the deletion of the binding site for miR172 in the euAP2 PETALOSA gene Prupe.6G242400, and the recessive di locus, of which the underlying factor is still unknown. RESULTS Based on its genomic location a candidate gene approach was used to identify genetic variants in a diverse panel of ornamental peach accessions and uncovered three independent mutations in Prupe.2G237700, the gene encoding the transcript for microRNA miR172d: a ~5.0 Kb LTR transposable element and a ~1.2 Kb insertion both positioned upstream of the sequence encoding the pre-miR172d within the transcribed region of Prupe.2G237700, and a ~9.5 Kb deletion encompassing the whole gene sequence. qRT-PCR analysis confirmed that expression of pre-miR172d was abolished in di/di genotypes homozygous for the three variants. CONCLUSIONS Collectively, PETALOSA and the mutations in micro-RNA miR172d identified in this work provide a comprehensive collection of the genetic determinants at the base of the double-flower trait in the peach germplasms.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy.
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Remo Chiozzotto
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Irina Baccichet
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Francesco Elia Florio
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | | | - Silvia Turco
- DAFNE Department - University of Tuscia, 01100, Viterbo, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133, Milan, Italy
| | - Stefano Gattolin
- CNR - National Research Council of Italy, Institute of Agricultural Biology and Biotechnology (IBBA), 20133, Milan, Italy.
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3
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Han L, Lan T, Lu Y, Zhou M, Li H, Lu H, Wang Q, Li X, Du S, Guan C, Zhang Y, Sahu SK, Qian P, Zhang S, Zhou H, Guo W, Chai H, Wang S, Liu Q, Liu H, Hou Z. Equus roundworms (Parascaris univalens) are undergoing rapid divergence while genes involved in metabolic as well as anthelminic resistance are under positive selection. BMC Genomics 2022; 23:489. [PMID: 35787772 PMCID: PMC9252044 DOI: 10.1186/s12864-022-08702-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/10/2022] [Indexed: 12/30/2022] Open
Abstract
Background The evolution of parasites is often directly affected by the host's environment. Studies on the evolution of the same parasites in different hosts are of great interest and are highly relevant to our understanding of divergence. Methods Here we performed whole-genome sequencing of Parascaris univalens from different Equus hosts (horses, zebras and donkeys). Phylogenetic and selection analyses were performed to study the divergence and adaptability of P. univalens. Results At the genetic level, multiple lines of evidence indicate that P. univalens is mainly separated into two clades (horse-derived and zebra & donkey-derived). This divergence began 300–1000 years ago, and we found that most of the key enzymes related to glycolysis were under strong positive selection in zebra & donkey-derived roundworms, whereas the lipid-related metabolic system was under positive selection in horse-derived roundworms, indicating that the adaptive evolution of metabolism has occurred over the past few centuries. In addition, we found that some drug-related genes showed a significantly higher degree of selection in diverse populations. Conclusions This work reports the adaptive evolution and divergence trend of P. univalens in different hosts for the first time. Its results indicate that the divergence of P. univalens is a continuous, dynamic process. Furthermore, the continuous monitoring of the effects of differences in nutritional and drug histories on the rapid evolution of roundworms is conducive to further understanding host-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08702-6.
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Affiliation(s)
- Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China. .,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haorong Lu
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuyun Li
- Harbin Northern Forest Zoo, Harbin, 150040, China
| | - Shan Du
- Inner Mongolia Agriculture University, Hohhot, 010000, China
| | - Chunyu Guan
- Harbin Northern Forest Zoo, Harbin, 150040, China
| | - Yong Zhang
- Center for Animal Disease Control and Prevention of Ordos, Inner Mongolia Ordos, 017000, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Puyi Qian
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shaofang Zhang
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongcheng Zhou
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150040, China
| | - Hongliang Chai
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.,Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin, 150040, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Quan Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China. .,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China. .,Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin, 150040, China.
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4
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Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biol 2022; 20:139. [PMID: 35698132 PMCID: PMC9195245 DOI: 10.1186/s12915-022-01342-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/30/2022] [Indexed: 12/25/2022] Open
Abstract
Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear. Results To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. Conclusions In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01342-y.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| | - Zhen Peng
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Xing Zhao
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Kuozhan Liu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Pere Arus
- IRTA, Centre de Recerca en Agrigenòmica, CSIC-IRTA-UAB-UB, Campus UAB - Edifici CRAG, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Jinlong Wu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China. .,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
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5
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Drincovich MF. Identifying sources of metabolomic diversity and reconfiguration in peach fruit: taking notes for quality fruit improvement. FEBS Open Bio 2021; 11:3211-3217. [PMID: 34176215 PMCID: PMC8634865 DOI: 10.1002/2211-5463.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 11/11/2022] Open
Abstract
The metabolomic content determines many of the important features of a fruit, such as its taste, flavor, color, nutritional value, and abiotic or biotic resistance. Peach (Prunus persica (L.) Batsch) is one of the best genetically characterized species used as a model for Rosaceae, the drupes of which are a source of minerals, vitamins, fiber, and antioxidant compounds for healthy diets around the world. During the last few years, a great advance in the analysis of the metabolic diversity and reconfiguration in different peach varieties in response to developmental and environmental factors has occurred. These studies have shown that the great phenotypic diversity among different peach varieties is correlated with differential metabolomic content. Besides, the fruit metabolome of each peach variety is not static; on the contrary, it is drastically configured in response to both developmental and environmental signals, and moreover, it was found that these metabolic reconfigurations are also variety dependent. In the present review, the main sources of metabolic diversity and conditions that induce modifications in the peach fruit metabolome are summarized. It is postulated that comparison of the metabolic reconfigurations that take place among the fruits from different varieties may help us better understand peach fruit metabolism and their key drivers, which in turn may aid in the future design of high‐quality peach fruits.
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Affiliation(s)
- María F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
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6
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Differentiation of peach cultivars by image analysis based on the skin, flesh, stone and seed textures. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03797-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe peaches belonging to different cultivars can be characterized by differentiation in properties. The aim of this study was to evaluate the usefulness of individual parts of fruit (skin, flesh, stone and seed) for cultivar discrimination of peaches based on textures determined using image analysis. Discriminant analysis was performed using the classifiers of Bayes net, logistic, SMO, multi-class classifier and random forest based on a set of combined textures selected from all color channels R, G, B, L, a, b, X, Y, Z and for textures selected separately for RGB, Lab and XYZ color spaces. In the case of sets of textures selected from all color channels (R, G, B, L, a, b, X, Y, Z), the accuracy of 100% was observed for flesh, stones and seeds for selected classifiers. The sets of textures selected from RGB color space produced the correctness equal to 100% in the case of flesh and seeds of peaches. In the case of Lab and XYZ color spaces, slightly lower accuracies than for RGB color space were obtained and the accuracy reaching 100% was noted only for the discrimination of seeds of peaches. The research proved the usefulness of selected texture parameters of fruit flesh, stones and seeds for successful discrimination of peach cultivars with an accuracy of 100%. The distinguishing between cultivars may be important for breeders, consumers and the peach industry for ensuring adequate processing conditions and equipment parameters. The cultivar identification of fruit by human may be characterized by large errors. The molecular or chemical methods may require special equipment or be time-consuming. The image analysis may ensure objective, rapid and relatively inexpensive procedure and high accuracy for peach cultivar discrimination.
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7
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Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. Nat Commun 2021; 12:3604. [PMID: 34127667 PMCID: PMC8203738 DOI: 10.1038/s41467-021-23879-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.
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8
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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9
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Numaguchi K, Akagi T, Kitamura Y, Ishikawa R, Ishii T. Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1551-1567. [PMID: 33048374 DOI: 10.1111/tpj.15020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.
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Affiliation(s)
- Koji Numaguchi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, Minabe, Higashi-honjo 1416-7, Wakayama, 645-0021, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Tsushima-naka 1-1-1, Okayama, 700-8530, Japan
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, Minabe, Higashi-honjo 1416-7, Wakayama, 645-0021, Japan
| | - Ryo Ishikawa
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
| | - Takashige Ishii
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan
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10
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Aramburu O, Ceballos F, Casanova A, Le Moan A, Hemmer-Hansen J, Bekkevold D, Bouza C, Martínez P. Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot ( Scophthalmus maximus). Front Genet 2020; 11:296. [PMID: 32346384 PMCID: PMC7169425 DOI: 10.3389/fgene.2020.00296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (FROH) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populations.
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Affiliation(s)
- Oscar Aramburu
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Johannesburg, South Africa
| | - Adrián Casanova
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alan Le Moan
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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11
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Shi T, Luo W, Li H, Huang X, Ni Z, Gao H, Iqbal S, Gao Z. Association between blooming time and climatic adaptation in Prunus mume. Ecol Evol 2020; 10:292-306. [PMID: 31988729 PMCID: PMC6972806 DOI: 10.1002/ece3.5894] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X-76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA-LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.
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Affiliation(s)
- Ting Shi
- Nanjing Agricultural UniversityNanjingChina
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Wenjie Luo
- Nanjing Agricultural UniversityNanjingChina
| | - Hantao Li
- Nanjing Agricultural UniversityNanjingChina
| | - Xiao Huang
- Nanjing Agricultural UniversityNanjingChina
| | - Zhaojun Ni
- Nanjing Agricultural UniversityNanjingChina
| | - Haidong Gao
- Genepioneer Biotechnologies Co. LtdNanjingChina
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12
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Noorai RE, Shankar V, Freese NH, Gregorski CM, Chapman SC. Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PLoS One 2019; 14:e0225834. [PMID: 31821332 PMCID: PMC6903725 DOI: 10.1371/journal.pone.0225834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Gallus gallus (chicken) is phenotypically diverse, with over 60 recognized breeds, among the myriad species within the Aves lineage. Domestic chickens have been under artificial selection by humans for thousands of years for agricultural purposes. The North American Araucana (NAA) breed arose as a cross between the Chilean “Collonocas” that laid blue eggs and was rumpless and the “Quetros” that had unusual tufts but with tail. NAAs were introduced from South America in the 1940s and have been kept as show birds by enthusiasts since then due to several distinctive traits: laying eggs with blue eggshells, characteristic ear-tufts, a pea comb, and rumplessness. The population has maintained variants for clean-faced and tufted, as well as tailed and rumplessness traits making it advantageous for genetic studies. Genome resequencing of six NAA chickens with a mixture of these traits was done to 71-fold coverage using Illumina HiSeq 2000 paired-end reads. Trimmed and concordant reads were mapped to the Gallus_gallus-5.0 reference genome (galGal5), generated from a female Red Junglefowl (UCD001). To identify candidate genes that are associated with traits of the NAA, their genome was compared with the Korean Araucana, Korean Domestic and White Leghorn breeds. Genomic regions with significantly reduced levels of heterogeneity were detected on five different chromosomes in NAA. The sequence data generated confirm the identity of variants responsible for the blue eggshells, pea comb, and rumplessness traits of NAA and propose one for ear-tufts.
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Affiliation(s)
- Rooksana E. Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, United States of America
- * E-mail:
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Nowlan H. Freese
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Christopher M. Gregorski
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Susan C. Chapman
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
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13
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Cao K, Li Y, Deng CH, Gardiner SE, Zhu G, Fang W, Chen C, Wang X, Wang L. Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1954-1970. [PMID: 30950186 PMCID: PMC6737019 DOI: 10.1111/pbi.13112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 05/21/2023]
Abstract
Crop evolution is a long-term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome-wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue-specific expression patterns indicated that the up-regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up-regulated selection genes were identified in leaves and seeds than in the other organs. Genome-wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large-scale characterization of key agronomic traits in this crop species.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR)Palmerston North Research CentrePalmerston NorthNew Zealand
| | - Gengrui Zhu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology)Ministry of AgricultureZhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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14
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Liu J, Rasheed A, He Z, Imtiaz M, Arif A, Mahmood T, Ghafoor A, Siddiqui SU, Ilyas MK, Wen W, Gao F, Xie C, Xia X. Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2509-2523. [PMID: 31139853 DOI: 10.1007/s00122-019-03367-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.
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Affiliation(s)
- Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
- Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Abdul Ghafoor
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Sadar Uddin Siddiqui
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Weie Wen
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Chaojie Xie
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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15
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Nadachowska-Brzyska K, Burri R, Ellegren H. Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers. Mol Ecol 2019; 28:2290-2304. [PMID: 30653779 PMCID: PMC6852393 DOI: 10.1111/mec.15021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/19/2023]
Abstract
Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.
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Affiliation(s)
| | - Reto Burri
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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16
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Fuller DQ, Stevens CJ. Between domestication and civilization: the role of agriculture and arboriculture in the emergence of the first urban societies. VEGETATION HISTORY AND ARCHAEOBOTANY 2019; 28:263-282. [PMID: 31118541 PMCID: PMC6499764 DOI: 10.1007/s00334-019-00727-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/26/2019] [Indexed: 05/25/2023]
Abstract
The transition to urbanism has long focused on annual staple crops (cereals and legumes), perhaps at the expense of understanding other changes within agricultural practices that occurred between the end of the initial domestication period and urbanisation. This paper examines the domestication and role of fruit tree crops within urbanisation in both Western Asia and China, using a combination of evidence for morphological change and a database that documents both the earliest occurrence of tree fruit crops and their spread beyond their wild range. In Western Asia the domestication of perennial fruit crops likely occurs between 6500 bc and 3500 bc, although it accompanies a shift in location from that of the earliest domestications within the Fertile Crescent to Mesopotamia, where the earliest urban societies arose. For China, fruit-tree domestication dates between ca 4000 and 2500 bc, commencing after millet domestication and rice domestication in Northern and Southern China, respectively, but within the period that led up to the urban societies that characterised the Longshan period in the Yellow River basin and the Liangzhu Culture in the Lower Yangtze. These results place the domestication of major fruit trees between the end of the domestication of staple annual crops and the rise of urbanism. On this basis it is argued that arboriculture played a fundamental role within the re-organisation of existing land use, shifting the emphasis from short-term returns of cereal crops into longer term investment in the developing agricultural landscape in both Western and East Asia. In this respect perennial tree crops can be placed alongside craft specialisation, such as metallurgy and textiles, in the formation of urban centres and the shaping the organisational administration that accompanied the rise of urbanism.
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Affiliation(s)
- Dorian Q. Fuller
- Institute of Archaeology, University of London, 31-34 Gordon Square, London, WC1H 0PY UK
- School of Archaeology and Museology, Northwest University, Xi’an, Shaanxi 710069 China
| | - Chris J. Stevens
- Institute of Archaeology, University of London, 31-34 Gordon Square, London, WC1H 0PY UK
- School of Archaeology and Museology, Peking University, Beijing, 100871 China
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17
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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18
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Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Nat Commun 2018; 9:5404. [PMID: 30573726 PMCID: PMC6302090 DOI: 10.1038/s41467-018-07744-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 11/20/2018] [Indexed: 11/24/2022] Open
Abstract
Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops. Peach is an economically important fruit crop. Here, the authors carry out a large-scale population genomics analysis of peach, describing its demographic history as well as genes associated with domestication and edibility traits.
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19
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Hiraoka Y, Fukatsu E, Mishima K, Hirao T, Teshima KM, Tamura M, Tsubomura M, Iki T, Kurita M, Takahashi M, Watanabe A. Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar). FRONTIERS IN PLANT SCIENCE 2018; 9:1322. [PMID: 30254658 PMCID: PMC6141754 DOI: 10.3389/fpls.2018.01322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement.
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Affiliation(s)
- Yuichiro Hiraoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Eitaro Fukatsu
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Tomonori Hirao
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | | | - Miho Tamura
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Taiichi Iki
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Takizawa, Japan
| | - Manabu Kurita
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
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20
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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21
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Huang L, Yang M, Li L, Li H, Yang D, Shi T, Yang P. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:2-15. [PMID: 29052958 DOI: 10.1111/jipb.12606] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/28/2017] [Indexed: 05/11/2023]
Abstract
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.
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Affiliation(s)
- Longyu Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Ling Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
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22
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LaBonte NR, Zhao P, Woeste K. Signatures of Selection in the Genomes of Chinese Chestnut ( Castanea mollissima Blume): The Roots of Nut Tree Domestication. FRONTIERS IN PLANT SCIENCE 2018; 9:810. [PMID: 29988533 PMCID: PMC6026767 DOI: 10.3389/fpls.2018.00810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 05/18/2023]
Abstract
Chestnuts (Castanea) are major nut crops in East Asia and southern Europe, and are unique among temperate nut crops in that the harvested seeds are starchy rather than oily. Chestnut species have been cultivated for three millennia or more in China, so it is likely that artificial selection has affected the genome of orchard-grown chestnuts. The genetics of Chinese chestnut (Castanea mollissima Blume) domestication are also of interest to breeders of hybrid American chestnut, especially if the low-growing, branching habit of Chinese chestnut, an impediment to American chestnut restoration, is partly the result of artificial selection. We resequenced genomes of wild and orchard-derived Chinese chestnuts and identified selective sweeps based on pooled whole-genome SNP datasets. We present candidate gene loci for chestnut domestication and discuss the potential phenotypic effects of candidate loci, some of which may be useful genes for chestnut improvement in Asia and North America. Selective sweeps included predicted genes potentially related to flower phenology and development, fruit maturation, and secondary metabolism, and included some genes homologous to domestication candidates in other woody plants.
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Affiliation(s)
- Nicholas R. LaBonte
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Nicholas R. LaBonte
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Keith Woeste
- Hardwood Tree Improvement and Regeneration Center, Northern Research Station, USDA Forest Service, West Lafayette, IN, United States
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23
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Cirilli M, Flati T, Gioiosa S, Tagliaferri I, Ciacciulli A, Gao Z, Gattolin S, Geuna F, Maggi F, Bottoni P, Rossini L, Bassi D, Castrignanò T, Chillemi G. PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data. PLANT & CELL PHYSIOLOGY 2018; 59:e2. [PMID: 29216377 DOI: 10.1093/pcp/pcx183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/16/2017] [Indexed: 05/06/2023]
Abstract
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Tiziano Flati
- Cineca, HPC High Performance Computing Department, Rome, Italy
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Silvia Gioiosa
- Cineca, HPC High Performance Computing Department, Rome, Italy
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | | | - Angelo Ciacciulli
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Zhongshan Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Stefano Gattolin
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Francesco Maggi
- Department of Computer Science, 'Sapienza' University of Rome, Via Salaria 113, 00198 Rome, Italy
| | - Paolo Bottoni
- Department of Computer Science, 'Sapienza' University of Rome, Via Salaria 113, 00198 Rome, Italy
| | - Laura Rossini
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Daniele Bassi
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
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Cirilli M, Rossini L, Geuna F, Palmisano F, Minafra A, Castrignanò T, Gattolin S, Ciacciulli A, Babini AR, Liverani A, Bassi D. Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2017; 17:192. [PMID: 29100531 PMCID: PMC5670703 DOI: 10.1186/s12870-017-1117-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties. For this purpose, a genome-wide association (GWA) approach was applied in a panel of accessions phenotyped for virus susceptibility and genotyped with the IPSC peach 9 K SNP Array, and coupled with an high-coverage resequencing of the tolerant accession 'Kamarat'. RESULTS Genome-wide association identified three highly significant associated loci on chromosome 2 and 3, accounting for most of the reduction in PPV-M susceptibility within the analysed peach population. The exploration of associated intervals through whole-genome comparison of the tolerant accession 'Kamarat' and other susceptible accessions, including the PPV-resistant wild-related species P. davidiana, allow the identification of allelic variants in promising candidate genes, including an RTM2-like gene already characterized in A. thaliana. CONCLUSIONS The present study is the first effort to identify genetic factors involved in Sharka disease in peach germplasm through a GWA approach. We provide evidence of the presence of quantitative resistant loci in a collection of peach accessions, identifying major loci and highly informative SNPs that could be useful for marker assisted selection. These results could serve as reference bases for future research aimed at the comprehension of genetic mechanism regulating the complex peach-PPV interaction.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura Basile-Caramia (CRSFA), via Cisternino, 281 Locorotondo, Bari, Italy
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), via Amendola 122/D, Bari, Italy
| | - Tiziana Castrignanò
- CINECA, SCAI Super Computing Applications and Innovation, via dei Tizii 6, Rome, Italy
| | - Stefano Gattolin
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | | | - Alessandro Liverani
- CREA, Research Centre for Olive, Citrus and Tree Fruit, via La Canapona 1 bis, Forlì, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
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25
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Biscarini F, Nazzicari N, Bink M, Arús P, Aranzana MJ, Verde I, Micali S, Pascal T, Quilot-Turion B, Lambert P, da Silva Linge C, Pacheco I, Bassi D, Stella A, Rossini L. Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies. BMC Genomics 2017; 18:432. [PMID: 28583089 PMCID: PMC5460546 DOI: 10.1186/s12864-017-3781-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. Results A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). Conclusions This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3781-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filippo Biscarini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | - Marco Bink
- Wageningen UR Biometris, Wageningen, The Netherlands.,Present Address: Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, Boxmeer NL, 5830AC, The Netherlands
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Centro di Ricerca per la Frutticoltura (CREA-FRU), Via di Fioranello 52, Roma, Italy
| | | | | | - Patrick Lambert
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | | | - Igor Pacheco
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.,Institute of Nutrition and Food Technology - INTA, Universidad de Chile, Av El Líbano 5524, Santiago, Chile
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy
| | - Alessandra Stella
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.,IBBA-CNR, Via Edoardo Bassini, 15, Milan, 20133, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy. .,Università degli Studi di Milano - DiSAA, Via Celoria 2, Milano, Italy.
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26
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Abstract
The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
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