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

Genome Biology
Yong LiLirong Wang

Abstract

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. 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 r...Continue Reading

References

Oct 10, 1980·Nucleic Acids Research·M G Murray, W F Thompson
Feb 13, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·C. EtienneE. Dirlewanger
May 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·Elisabeth DirlewangerPere Arús
May 29, 2004·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·B QuilotK Moreau
Sep 25, 2004·The Journal of Heredity·D G BielenbergA G Abbott
Oct 3, 2007·PLoS Genetics·Ana L CaicedoMichael D Purugganan
Jan 21, 2009·Genetics·Jeffrey Ross-IbarraBrandon S Gaut
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 13, 2010·Science·Mark Tester, Peter Langridge
Oct 26, 2010·Nature Genetics·Xuehui HuangBin Han
Dec 21, 2010·American Journal of Human Genetics·Jian YangPeter M Visscher
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jun 5, 2012·Nature Genetics·Yinping JiaoJinsheng Lai
Jun 20, 2013·Molecular Biology and Evolution·Pavlos PavlidisNikolaos Alachiotis
Jul 17, 2013·The Plant Journal : for Cell and Molecular Biology·Rachele FalchiMichele Morgante
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Oct 13, 2014·Nature Genetics·Tao LinSanwen Huang
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 10, 2015·Nature Biotechnology·Alyssa C FrazeeJeffrey T Leek
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Aug 11, 2015·Nature Methods·Colby ChiangIra M Hall
Jan 11, 2016·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Jan 28, 2016·Horticulture Research·Marco CirilliAngelo Ciacciulli
Aug 26, 2016·Nature Protocols·Mihaela PerteaSteven L Salzberg
Oct 22, 2016·G3 : Genes - Genomes - Genetics·Dianne VelascoJeffrey Ross-Ibarra

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Citations

Jan 29, 2020·Ecology and Evolution·Ting ShiZhihong Gao
May 12, 2020·The Plant Journal : for Cell and Molecular Biology·Sara PinosioMichele Morgante
Nov 2, 2020·Journal of Experimental Botany·Long LiRuilian Jing
Mar 19, 2021·Frontiers in Plant Science·Cassia da Silva LingeKsenija Gasic
Jun 27, 2021·Nature Communications·Alexis GroppiVéronique Decroocq
Jul 28, 2021·Current Biology : CB·Xia WangQiang Xu
Sep 5, 2021·The New Phytologist·Vítor da Silveira FalavignaFernando Andrés
Dec 23, 2021·Nature Communications·Gabriele MagrisMichele Morgante

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Methods Mentioned

BETA
genotyping
PCA
PCR
RNA-Seq

Software Mentioned

BOTTLENECK
Beagle
SpeedSeq
GCTA
py
BEDtools
SAMtools
genomencov
EMMAX emmax - kin
SURIVER

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