2018 ASHS Annual Conference

Germplasm collections are a critically valuable source of genetic diversity for plant breeding efforts. Our ability to make optimal use of such resources for crop improvement is facilitated by genetic characterization. Therefore, one of the objectives of the CucCAP project, “CucCAP: Leveraging applied genomics to improve disease resistance in cucurbit crops”, is to characterize genetic diversity within the U.S. cucurbit plant introduction (PI) collections and develop sequence-informed functional panels for genetic and phenotypic analyses. To this end, we have performed genotyping-by-sequencing (GBS) analysis of the USDA PI collections of the four major cucurbit crops: watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cucumis sativus), and squash (Cucurbita pepo and C. moschata). A total of 1,234 cucumber, 2,077 melon, 1,365 watermelon, 850 C. pepo and 314 C. moschata accessions were genotyped. A total of 1.57, 1.71 and 0.88 billion GBS reads were obtained for cucumber, melon and watermelon, respectively. From these reads, 76.9, 54.2 and 34.6 million unique tags were obtained, of which 593,678, 743,545 and 388,298 tags with at least 10 reads were used for SNP calling for cucumber, melon and watermelon, respectively. A total of 114,338, 89,377 and 62,258 SNPs were called in cucumber, melon and watermelon, respectively, and 23,828, 27,846 and 25,930 SNPs were obtained by applying criteria of missing data rate < 0.5 and minor allele frequency (MAF) > 0.01. The SNPs were well distributed across the genomes with average density of one SNP per 10.6, 14.6, and 15.7 kb for cucumber, melon and watermelon, respectively. Using these SNP data, we have performed population structure and principal component analysis (PCA), and constructed a neighbor-joining trees to infer phylogenetic relationships among the accessions. These analyses are being used to establish functional panels of 300-400 accessions per crop representing ~99% of the genetic diversity along with key disease resistance, fruit quality, horticultural and agronomic traits.