Fruit cracking and firmness DNA test development and evaluation in sweet cherry

Abstract

One application of DNA-informed breeding, which has potential to increase the effectiveness of traditional breeding methods, is the use of DNA-based diagnostic tests to estimate genetic potential of breeding individuals. In sweet cherry (<italic>Prunus avium</italic> L.), cracked or soft fruit are major industry challenges. Recent research detected two quantitative trait loci (QTLs) for fruit cracking and firmness differing in trait levels associated with QTL haplotypic variation. Also, a DNA test for cracking (Pav-G5Crack-SSR), using a single simple sequence repeat (SSR) marker, was previously developed but not yet validated on breeding germplasm. In addition to SSR markers, single nucleotide polymorphism (SNP) markers can be used for developing locus-specific DNA tests and run as simple assays such as high-resolution melting (HRM). The objective of this research was to develop and evaluate the predictiveness of DNA tests for fruit cracking and firmness in sweet cherry. Unselected seedlings from pedigree-connected families were screened with the Pav-G5Crack-SSR DNA test. DNA tests were also created from four SNP markers with HRM assays, using two years of cracking and firmness data for evaluation. Pav-G5Crack-SSR explained 12–15% of the cracking phenotypic variance, while Pav-G1Crack-SNP and Pav-G5Crack-SNP (which targeted the same QTL as Pav-G5Crack-SSR) together explained 16–30% of the cracking phenotypic variance. Pav-G1Firm-SNP and Pav-G3Firm-SNP together explained 22–28% of the firmness phenotypic variance. All three DNA tests can be implemented in breeding programs to enhance effectiveness in breeding for decreased cracking incidence and increased fruit firmness in sweet cherry.