Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F-1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172-182cM), LG4 (48-54cM), and LG7 (62-70cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40-46cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

Automated summary

This study validated major QTLs for three key phenological traits through a multiple pedigree-linked families approach. Haplotype characterization of genomic regions differentiated this study from previous QTL studies. The results provide peach breeders with haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests for selecting desired QTL alleles in early seedling stages.