Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

Abstract

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.

Genome-wide association study of 12 agronomic traits in peach

“…In this study, a clear association signal was located at 13,740,117 bp on scaffold_8 (Table 1), with a −log 10 P value of 121.47. This is in agreement with the recent results using SNP arrays (scaffold_8: 13,756,987 bp)6. Unfortunately, we were unable to further analyse these candidate genes, as few characterization studies have been performed on kernel taste and on these two flower shape traits.…”

“…For the non-acidity fruit trait, we determined that the SNP of scaffold_5: 541,075 bp was a leading SNP, as previously reported in a QTL study (scaffold_5: 467,067.. 2,270,122 bp)6. The association signal found in the present study was located between two genes, ppa006413m and ppa006339m (Fig.…”

“…Both association and expression analyses supported PpCAD1 as a candidate gene for fruit shape. First, the association signal location correlated with a fruit shape-related quantitative trait locus (QTL)617 (Fig. 1b).…”

“…7), which significantly associated with flesh colour, was ∼0.67 Mb away from the ccd4 gene. However, according to a recent study6 the SNP having the strongest association with fruit flesh colour is located behind the ccd4 gene (scaffold_1: 26,749,525 bp), and relatively distant from the gene. The gene ppa027093m , which is involved in the function of flavanone 3-hydroxylase and NAD(P)H-dependent 6'-deoxychalcone synthase, was found in that associated region in our study.…”

“…Recently, a genome-wide association study (GWAS) was performed using 1,580 peach accessions and genotype data for 5,378 polymorphic SNPs (single-nucleotide polymorphisms) derived from the 9K SNP array developed by the International Peach SNP Consortium6. 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.…”