Genome-Wide SNP Discovery and Identification of Age-Related Resistance Loci in Cucumber By QTL-Seq

Fruit rot due to infection by Phytophthora capsici is a major problem affecting cucumber (Cucumber sativus L.) production. In our prior study, age-related resistance (ARR) of cucumber fruit to P. capsici was observed in select cultivars. Young fruits are highly susceptible to the pathogen, but as they reach the end of exponential growth (~10-12dpp), they become resistant, exhibiting no disease symptom development or minimal necrosis limited to the site of inoculation. Genetic factors underlying the expression of ARR in cucumber are not yet known. In this study, two F₂ populations, composed of 194 and 161 individuals, derived from crosses between ARR-expressing (ARR+, “Poinsett” or “Vlaspik”) and non-ARR expressing (ARR-, “Gy14”) cultivars were evaluated for ARR. Progeny exhibiting extreme phenotypes (resistant or susceptible) were selected and pooled separately for bulked segregant analysis (BSA) using whole genome sequencing (16-20X coverage) and genome-wide SNP profiling. Prior to variant calling, the sequence data were pre-processed and aligned to the cucumber reference genome Chinese long v.2 using BWA. SNP discovery performed using GATK variant calling tools and hard filters revealed 604,667 SNPs between “Gy14” and “Poinsett” (a pickling and slicing cultivar, respectively) and 472,429 SNPs between “Gy14” and “Vlaspik,” (two pickling cultivars) with an average frequency of 1-2 SNP(s) per kb. SNP indices and Δ SNP indices will be calculated from the susceptible and resistant F₂ bulked progeny to identify loci associated with ARR.