Abstract
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach.
Highlights
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family
We find that the linkage disequilibrium (LD) values of peak genome-wide association study (GWAS) signals in peach exhibit different patterns from those reported for annual crops
Peak association signals for fruit hairiness, fruit shape, flesh adhesion, flesh texture and non-acidity were located close to the candidate genes identified by linkage analysis
Summary
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. 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 Consortium[6]. 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 technology[7] and perform higher resolution GWAS8. These findings may help inform peach breeding as well as future sequencing studies and GWAS of peach and other fruit crops
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