QTL Mapping for Phytochemical Compounds in Peach [Prunus persica (L.) Batsch]

Genetic control and location of QTLs associated with phytochemical compounds in peach were evaluated using bi-parental mapping and genome wide association study (GWAS). The bi-parental mapping was conducted in an F₂ population (ZC²) derived from cross between two peach cultivars ‘Zin Dai’ x ‘Crimson Lady’. GWAS was performed on an association panel of 105 peach and nectarine accessions from Clemson University’s peach germplasm, representing modern peach cultivars available and/or produced for the U.S. market. Antioxidant capacity and phenolic compound accumulation (total phenolics, flavonoids and anthocyanin) were evaluated for two years on all material. The ZC² progeny were genotyped using IPSC 9K peach SNP array v1., and the association panel was genotyped using genotyping-by-sequencing (GBS).  The genetic linkage map was constructed with 908 SNP markers distributed among eight linkage groups, with 347 SNPs uniquely mapped. The map covers a genetic distance of ~ 336 cM, with an average marker density of 1.07 cM/ marker. Total of 10 QTLs associated with phytochemical (PC) traits were identified on 5 linkage groups (LGs). Two major QTLs were observed on two linkage groups, LG 6 and 8. Major QTL on LG6, qPC.ZC-6.1 was associated with all phytochemical compounds measured, while qPC.ZC-8.1 exhibited association only with total phenolics and anthocyanin content. GWAS was performed on a dataset of 35,198 SNPs and all phytochemical compounds using the General Linear Model (GLM), and accounted for the population structure within the analyzed germplasm. Significant association (P < 0.05) was observed for 94 SNPs covering the entire genome. Majority of SNPs (90) were associated with anthocyanin accumulation and spread across all LGs, while 4 SNPs were associated with both antioxidant capacity and flavonoid content. Although none of the SNPs associated with phytochemical content detected via GWAS overlapped with the single QTL identified using the bi-parental population, many were found in flanking regions. Furthermore, a single SNP associated with anthocyanin on LG3 flanked the major blush QTL PprMYB10 detected previously in the same progeny. Feasibility of enabling marker-assisted breeding for phytochemical composition will be discussed.