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Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

BACKGROUND: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artifici...

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Autores principales: Li, Yong, Cao, Ke, Zhu, Gengrui, Fang, Weichao, Chen, Changwen, Wang, Xinwei, Zhao, Pei, Guo, Jian, Ding, Tiyu, Guan, Liping, Zhang, Qian, Guo, Wenwu, Fei, Zhangjun, Wang, Lirong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383288/
https://www.ncbi.nlm.nih.gov/pubmed/30791928
http://dx.doi.org/10.1186/s13059-019-1648-9
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author Li, Yong
Cao, Ke
Zhu, Gengrui
Fang, Weichao
Chen, Changwen
Wang, Xinwei
Zhao, Pei
Guo, Jian
Ding, Tiyu
Guan, Liping
Zhang, Qian
Guo, Wenwu
Fei, Zhangjun
Wang, Lirong
author_facet Li, Yong
Cao, Ke
Zhu, Gengrui
Fang, Weichao
Chen, Changwen
Wang, Xinwei
Zhao, Pei
Guo, Jian
Ding, Tiyu
Guan, Liping
Zhang, Qian
Guo, Wenwu
Fei, Zhangjun
Wang, Lirong
author_sort Li, Yong
collection PubMed
description BACKGROUND: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood. RESULTS: Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions. By focusing on a set of quantitative trait loci (QTLs), we provide evidence supporting that distinct phases of domestication and improvement have led to an increase in fruit size and taste and extended its geographic distribution. Fruit size was predominantly selected during domestication, and selection for large fruits has led to the loss of genetic diversity in several fruit weight QTLs. In contrast, fruit taste-related QTLs were successively selected for by domestication and improvement, with more QTLs selected for during improvement. Genome-wide association studies of 11 agronomic traits suggest a set of candidate genes controlling these traits and potential markers for molecular breeding. Candidate loci for genes that contributed to the adaption to low-chill regions were identified. Furthermore, the genomic bases of divergent selection for fruit texture and local breeding for different flavors between Asian and European/North American cultivars were also determined. CONCLUSIONS: Our results elucidate the genetic basis of peach evolution and provide new resources for future genomics-guided peach breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1648-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-63832882019-03-01 Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history Li, Yong Cao, Ke Zhu, Gengrui Fang, Weichao Chen, Changwen Wang, Xinwei Zhao, Pei Guo, Jian Ding, Tiyu Guan, Liping Zhang, Qian Guo, Wenwu Fei, Zhangjun Wang, Lirong Genome Biol Research BACKGROUND: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood. RESULTS: Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions. By focusing on a set of quantitative trait loci (QTLs), we provide evidence supporting that distinct phases of domestication and improvement have led to an increase in fruit size and taste and extended its geographic distribution. Fruit size was predominantly selected during domestication, and selection for large fruits has led to the loss of genetic diversity in several fruit weight QTLs. In contrast, fruit taste-related QTLs were successively selected for by domestication and improvement, with more QTLs selected for during improvement. Genome-wide association studies of 11 agronomic traits suggest a set of candidate genes controlling these traits and potential markers for molecular breeding. Candidate loci for genes that contributed to the adaption to low-chill regions were identified. Furthermore, the genomic bases of divergent selection for fruit texture and local breeding for different flavors between Asian and European/North American cultivars were also determined. CONCLUSIONS: Our results elucidate the genetic basis of peach evolution and provide new resources for future genomics-guided peach breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1648-9) contains supplementary material, which is available to authorized users. BioMed Central 2019-02-21 /pmc/articles/PMC6383288/ /pubmed/30791928 http://dx.doi.org/10.1186/s13059-019-1648-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Li, Yong
Cao, Ke
Zhu, Gengrui
Fang, Weichao
Chen, Changwen
Wang, Xinwei
Zhao, Pei
Guo, Jian
Ding, Tiyu
Guan, Liping
Zhang, Qian
Guo, Wenwu
Fei, Zhangjun
Wang, Lirong
Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_full Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_fullStr Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_full_unstemmed Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_short Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_sort genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383288/
https://www.ncbi.nlm.nih.gov/pubmed/30791928
http://dx.doi.org/10.1186/s13059-019-1648-9
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