Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach

Abstract

Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F₁ and F₂ families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identified in two seasons (2011 and 2012) and the average datasets (average of two seasons). A target region spanning 10,981,971-11,298,736 bp on chromosome 4 of peach reference genome used for haplotype analysis revealed four haplotypes with significant differences in trait values among different diplotype combinations. Favorable alleles at the target region for both RPT and SSC were determined and a DNA test for predicting RPT and SSC was developed. Two Kompetitive Allele Specific PCR (KASP) assays were validated on 84 peach cultivars and 163 seedlings from the CUPBP, with only one assay (Ppe.RPT/SSC-1) needed to predict between early and late-season ripening cultivars and low and high SSC. These results advance our understanding of the genetic basis of RPT and SSC and facilitate selection of new peach cultivars with the desired RPT and SSC.

Figure 1

Ripening time (RPT; in Julian days, JD) (a), soluble solids concentration (SSC; in °Brix) (b) and haplotype effects in the Clemson University peach breeding material. Effects were based on diplotypes observed for qRPT_SC_4.1 and qSSC_SC_4.1 QTLs. Only diplotypes represented by eight or more individuals were included. N represents the number of individuals containing the phenotypic data for RPT and SSC observed in each dyplotype. Significantly different (Steele–Dwass, p < 0.05) phenotypic means are identified by different letters.

Figure 2

Comparison of observed ripening time (a) and soluble solid concentration (b) for the three different genotypes (AA, AB, and BB) of SNP_IGA_411637 (Ppe.RPT/SSC_1.1) in Arkansas (AR), South Carolina (SC) and Texas (TX) peach breeding populations. Phenotypic means that were significantly different (Tukey and Student T tests, p < 0.05 for three and two classes, respectively) are represented by different letters. White triangles and black horizontal lines represent mean and median phenotypic values, respectively, in each peach breeding population. R² represents the proportion of variance in the dependent variable explained by the independent variable.

Figure 3

Ppe.RPT/SSC KASP assays validation in 84 peach samples using real-time (a) and endpoint (b) PCRs. Yellow triangles, diamonds, squares, and circles indicate genotypes AA, AB, BB, and non-template controls, respectively.

Figure 4

Comparison of the predicted and observed phenotypes for ripening time (RPT) (a) and soluble solid concentration (SSC) (b) in 84 peach cultivars used for assay development and validation. Phenotypic means that were significantly different (Tukey, p < 0.05) are represented by different letters. White triangles represent mean phenotypic values. Black horizontal lines represent median phenotypic values.

Figure 5

Comparison of the predicted and observed phenotypes for ripening time (a) and soluble solid concentration (b) in the Clemson University peach breeding program’s breeding materials across five different seasons and BLUP values. Phenotypic means that were significantly different (Tukey test, p < 0.05) are represented by different letters. Black triangles represent mean observed trait values, and horizontal lines represent median observed trait values.