Genome-wide association study of 12 agronomic traits in peach

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.

Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

“…To assess the genetic variations in peach, we previously sampled a core collection of 129 peach accessions distributed throughout the world (Cao et al ., ). For the present study, a total of 418 peach accessions, including 45 varieties belonging to wild related species and 373 belonging to P. persica , were resequenced.…”

“…The region associated with malic acid content at the top of Chr. 5 identified in our GWAS analysis is consistent with the results of previous studies using map‐based cloning (Boudehri et al ., ) and the evaluation of malic acid as a qualitative trait in non‐acidic fruit (Cao et al ., ). In addition, a total of 16 genes were found at the QTLs controlling malic acid content from 5 357 897 bp to 5 571 577 bp in Chr.…”

“…Peach ( Prunus persica ) is an important deciduous fruit crop thought to have been domesticated more than 5000 years ago in the middle and lower Changjiang or Pearl River region of China (Cao et al ., ). The subsequent westward movement of peach could have brought it to Persia between the 2nd and 1st century BC.…”

“…In peach, signals associated with significant traits were identified using GWAS on data from a 9K SNP array (Micheletti et al ., ). Furthermore, GWAS have been applied to selected domestication traits in peach including fruit weight and soluble solid content (SSC, mainly including acid and sugar) (Cao et al ., ). The exhibition of these traits has been referred to as the ‘domestication syndrome’ in tomato, pepper and melon (Guo and Simmons, ).…”

“…The exhibition of these traits has been referred to as the ‘domestication syndrome’ in tomato, pepper and melon (Guo and Simmons, ). However, the association signals for those traits were not strong due to the small population size utilized in a study on peach (Cao et al ., ). For other important domestication traits, such as the polyphenol content in fruit, using association analysis for gene discovery is also an exciting process, because phenols are a major class of bioactive compounds responsible for health benefits (Sun et al ., ) by reducing damage from oxidative stress (Byrne et al ., ; Cantin et al ., ) and suppressing the growth and differentiation of human cancer cells (Lea et al ., ).…”