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 artificia...
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Autor*in:	Li, Yong [verfasserIn] 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

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Genomics Whole genome resequencing Domestication Improvement Human selection Breeding history

Anmerkung:	© The Author(s). 2019

Übergeordnetes Werk:	Enthalten in: Genome biology - London : BioMed Central, 2000, 20(2019), 1 vom: 21. Feb.
Übergeordnetes Werk:	volume:20 ; year:2019 ; number:1 ; day:21 ; month:02

Links:	Volltext

DOI / URN:	10.1186/s13059-019-1648-9

Katalog-ID:	SPR030033853

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520			\|a 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.
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allfields	10.1186/s13059-019-1648-9 doi (DE-627)SPR030033853 (SPR)s13059-019-1648-9-e DE-627 ger DE-627 rakwb eng Li, Yong verfasserin aut Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 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. Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213 Cao, Ke aut Zhu, Gengrui aut Fang, Weichao aut Chen, Changwen aut Wang, Xinwei aut Zhao, Pei aut Guo, Jian aut Ding, Tiyu aut Guan, Liping aut Zhang, Qian aut Guo, Wenwu aut Fei, Zhangjun aut Wang, Lirong aut Enthalten in Genome biology London : BioMed Central, 2000 20(2019), 1 vom: 21. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:20 year:2019 number:1 day:21 month:02 https://dx.doi.org/10.1186/s13059-019-1648-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 21 02
spelling	10.1186/s13059-019-1648-9 doi (DE-627)SPR030033853 (SPR)s13059-019-1648-9-e DE-627 ger DE-627 rakwb eng Li, Yong verfasserin aut Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 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. Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213 Cao, Ke aut Zhu, Gengrui aut Fang, Weichao aut Chen, Changwen aut Wang, Xinwei aut Zhao, Pei aut Guo, Jian aut Ding, Tiyu aut Guan, Liping aut Zhang, Qian aut Guo, Wenwu aut Fei, Zhangjun aut Wang, Lirong aut Enthalten in Genome biology London : BioMed Central, 2000 20(2019), 1 vom: 21. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:20 year:2019 number:1 day:21 month:02 https://dx.doi.org/10.1186/s13059-019-1648-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 21 02
allfields_unstemmed	10.1186/s13059-019-1648-9 doi (DE-627)SPR030033853 (SPR)s13059-019-1648-9-e DE-627 ger DE-627 rakwb eng Li, Yong verfasserin aut Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 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. Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213 Cao, Ke aut Zhu, Gengrui aut Fang, Weichao aut Chen, Changwen aut Wang, Xinwei aut Zhao, Pei aut Guo, Jian aut Ding, Tiyu aut Guan, Liping aut Zhang, Qian aut Guo, Wenwu aut Fei, Zhangjun aut Wang, Lirong aut Enthalten in Genome biology London : BioMed Central, 2000 20(2019), 1 vom: 21. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:20 year:2019 number:1 day:21 month:02 https://dx.doi.org/10.1186/s13059-019-1648-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 21 02
allfieldsGer	10.1186/s13059-019-1648-9 doi (DE-627)SPR030033853 (SPR)s13059-019-1648-9-e DE-627 ger DE-627 rakwb eng Li, Yong verfasserin aut Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 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. Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213 Cao, Ke aut Zhu, Gengrui aut Fang, Weichao aut Chen, Changwen aut Wang, Xinwei aut Zhao, Pei aut Guo, Jian aut Ding, Tiyu aut Guan, Liping aut Zhang, Qian aut Guo, Wenwu aut Fei, Zhangjun aut Wang, Lirong aut Enthalten in Genome biology London : BioMed Central, 2000 20(2019), 1 vom: 21. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:20 year:2019 number:1 day:21 month:02 https://dx.doi.org/10.1186/s13059-019-1648-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 21 02
allfieldsSound	10.1186/s13059-019-1648-9 doi (DE-627)SPR030033853 (SPR)s13059-019-1648-9-e DE-627 ger DE-627 rakwb eng Li, Yong verfasserin aut Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 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. Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213 Cao, Ke aut Zhu, Gengrui aut Fang, Weichao aut Chen, Changwen aut Wang, Xinwei aut Zhao, Pei aut Guo, Jian aut Ding, Tiyu aut Guan, Liping aut Zhang, Qian aut Guo, Wenwu aut Fei, Zhangjun aut Wang, Lirong aut Enthalten in Genome biology London : BioMed Central, 2000 20(2019), 1 vom: 21. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:20 year:2019 number:1 day:21 month:02 https://dx.doi.org/10.1186/s13059-019-1648-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 21 02
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source	Enthalten in Genome biology 20(2019), 1 vom: 21. Feb. volume:20 year:2019 number:1 day:21 month:02
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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. 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author	Li, Yong
spellingShingle	Li, Yong misc Genomics misc Whole genome resequencing misc Domestication misc Improvement misc Human selection misc Breeding history Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
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topic_title	Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history Genomics (dpeaa)DE-He213 Whole genome resequencing (dpeaa)DE-He213 Domestication (dpeaa)DE-He213 Improvement (dpeaa)DE-He213 Human selection (dpeaa)DE-He213 Breeding history (dpeaa)DE-He213
topic	misc Genomics misc Whole genome resequencing misc Domestication misc Improvement misc Human selection misc Breeding history
topic_unstemmed	misc Genomics misc Whole genome resequencing misc Domestication misc Improvement misc Human selection misc Breeding history
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title	Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
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title_full	Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
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author_browse	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
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title_sort	genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
title_auth	Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
abstract	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. © The Author(s). 2019
abstractGer	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. © The Author(s). 2019
abstract_unstemmed	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. © The Author(s). 2019
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title_short	Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history
url	https://dx.doi.org/10.1186/s13059-019-1648-9
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author2	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
author2Str	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
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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. 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Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

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