Pedigree Based QTL Analysis (PBA) for Fruit Traits in the University of Arkansas Peach Breeding Program

A genome-wide quantitative trait loci (QTL) analysis was conducted for peach ripening date and acidity using a pedigree-based analysis (PBA) approach with the University of Arkansas RosBREED peach and nectarine breeding program germplasm. A total of 1947 polymorphic single nucleotide polymorphism (SNP) markers and four years of ripening date and acidity data from six pedigree-connected F₁ families were analyzed using FlexQTL™ software. Repeatable QTLs were detected at the G4mat locus on LG4 and the D locus on LG5 over four years. Approximately 60% of acidity variation was explained by genome-wide QTLs and 59% of that was solely explained by the D locus. In addition, nearly, 75% of ripening date variation was explained by genome-wide QTLs, and approximately 74% was explained by the G4mat locus. No minor QTLs were detected for either trait. Haplotyping was conducted for both loci, and based on average effect the alleles were grouped into meaningful categories. Haplotypes associated with the G4mat locus were grouped into five categories [VE, E, M, L, VL], and haplotypes associated with the D locus were grouped into two categories [high and low] based on unselected material. An SSR marker, CPPCT040, was also used to screen RosBREED University of Arkansas germplasm at the D locus and alleles of this SSR marker were associated with high and low acidity. Genetic information of QTL alleles associated with ripening date and acidity will inform University of Arkansas peach and nectarine breeding program through development and implementation of DNA-based markers for genetic selection of desirable alleles and efficient development of improved cultivars.