Comparative population genomics reveals the domestication history of the peach,

Abstract

Background: Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. Results: We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.

Genome-wide association study of 12 agronomic traits in peach

“…These results reveal that GWAS can be employed to find candidate genes for specific qualitative traits in peach, even using relatively few accessions. However, this may have only been possible in peach due to its low rate of polymorphism, resulting from self-pollination and grafting7. On the other hand, results for fruit hairiness and fruit flesh colour were not consistent with the results of gene identification obtained through reverse genetics45.…”

“…Among the 129 accessions, 84 were resequenced as part of our previous study focusing on the evolution and identification of gene regions where domestication had the greatest influence in P. persica 7; 45 accessions were newly added to balance the biased trait segregation (Methods and Supplementary Fig. 1).…”

“…Considering that LD decay was about 20–50 kb for the different subgroups of cultivated peach7, we subsequently performed candidate gene searches in the space defined by ±25 kb on either side of the significant association peaks for each agronomic trait. This allowed several candidate genes to be identified that may be responsible for the qualitative traits examined here (Table 1).…”

“…For example, considering the LD decay of edible peach (14 kb)7, about 16,042 SNPs will cover the total peach genome (224.6 Mb)46. However, domestication regions exhibited faster decay than total genome and more SNPs need to be identified in the domestication regions containing key genes to carry out association analysis.…”

“…This analysis provided valuable genetic information, but could not precisely determine the candidate genes controlling major agronomic traits in peach due to low coverage of SNPs. An alternative approach, to identify candidate genes is to discover whole-genome-wide SNPs using resequencing technology7 and then perform higher resolution GWAS8. This approach has been successfully applied to species with short life cycles91011.…”