Development of SNP markers using genotyping-by-sequencing for cultivar identification in rose (Rosa hybrida)

Abstract

In this study, we developed single nucleotide polymorphism (SNP) markers to identify cultivars of the polyploid Rosa hybrida using genotyping-by-sequencing (GBS). Sequences obtained from GBS libraries of the genomes of 79 rose cultivars were aligned to contigs created by de novo assembly, and these contigs ranged from 200 to 2,591 bp, with an average of 305 bp per contig. We selected 1,778 SNPs from 13,488 putative SNPs. SNP markers that were present in more than 70% of the 79 cultivars were selected and evaluated, both on the basis of polymorphism information content values and level of heterozygosity, and 20 SNP markers were ultimately selected for high- throughput analysis. From these 20 SNP markers, 4 were successfully converted to markers for DNA chip assays. High resolution melting analysis was carried out to further distinguish rose genotypes. Using a set of seven SNP markers, we identified 70.9% of the 79 rose cultivars, and 87.5% of the 16 new cultivars developed in Goyang City. This paper is the first to report the development of a SNP marker set to identify Rosa hybrida cultivars by GBS.