Journal Article

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

Cao, Ke, Chen, Changwen, Guo, Wenwu, Li, Yong, Zhang, Qian, Wang, Xinwei, Wang, Lirong, Fang, Weichao, Fei, Zhangjun, Zhao, Pei, Guo, Jian, Guan, Liping, Ding, Tiyu, Zhu, Gengrui

2019

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / artificial selection / Bioinformatics / Biomedical and Life Sciences / Breeding history / Cold Temperature / Crops / Cultivars / Domestication / Evolution / Evolutionary Biology / Flavors / Food quality / Fruit - genetics / fruit size / fruit texture / fruit weight / Fruits / Genetic diversity / genetic variation / genome / Genome, Plant / Genome-wide association studies / Genomes / Genomic analysis / Genomics / Geographical distribution / Human Genetics / Human selection / humans / Improvement / Life Sciences / Microbial Genetics and Genomics / peaches / Plant Breeding / Plant Genetics and Genomics / Population / Prunus persica / Prunus persica - genetics / Quantitative Trait Loci / quantitative traits / Selection, Genetic / Taste / Whole genome resequencing