Genome-wide SNP Discovery for Variety Identification in a Collection of Cultivated Peach

다국어 초록 (Multilingual Abstract)

Peach (Prunus persica L.) is a major fruit crop species in the Rosaceae family including apple, pear, and strawberry. With its nutritional and economic value, breeders have made many efforts to develop new cultivars. Molecular markers can facilitate variety identification to protect breeder’s intellectual property rights. In this study, we conducted genotyping by sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in 48 peach cultivars. This peach collection consisted of 36 cultivars from the Republic of Korea (ROK), eight from Japan, and four from the United State. The illumine HiSeq X sequencing of GBS library generated 72.6 Gb of trimmed read sequences representing 273x coverage for a peach reference genome assembly (227 Mb). A total of 38,616 confident SNPs was identified from GBS and these SNP were unevenly distributed on eight chromosomes. The number of SNPs per chromosome ranged from 2,840 (chromosome 5) to 6,836 (chromosome 2). Of these, a subset of 344 SNPs was filtered based on ≤ 15% of heterozygote rate, ≥ 0.3 of polymorphism information content, and physical map position on each chromosome. In this subset, 83 and 261 SNPs were derived from coding and non-coding sequences, respectively. The Nei’s genetic distances were calculated among 48 peach cultivars using these SNP markers. The resulting dendrogram showed that all of these cultivars were distinguished, suggesting that the 344 markers are a useful resource to develop molecular tools for variety identification in peach.