Identification of loci for single/double flower trait by combining genome-wide association analysis and bulked segregant analysis in peach (Prunus persica)

Background Peach is a typical perennial fruit crop that can be categorized both as an ornamental and edible crop. Double flower is an important appearance trait, in which breeders are pursuing in high-quality ornamental peach breeding. The single/double flower character in peach is controlled by one gene, Dl, and the underlying genetic mechanism is unknown. Objective In this study, we explored the genetic basis of single/double flower trait in peach in a genome-wide association study using 1 042 687 SNPs characterized in 201 accessions. Methodology Four loci were identified to be significantly associated with the trait on chromosomes (Chr.) 1, 2 and 6. Besides, the bulked segregant analysis (BSA) was performed with two DNA bulks (single and double flower pool) from the F-1 population plants of a cross 'Juhuatao' x 'Honggengansutao'. Results We found a genomic region on Chr. 2 by the BSA, which overlapped the association peak on Chr. 2 in the GWAS-denoted as a region harbouring Dl. Finally, a candidate gene was identified by expression analysis of different plant tissues. Conclusion Our results provide insights into the genetic basis of flower shape and might facilitate marker-assisted selection breeding for ornamental peach.