High-Throughput SSR Marker Development in Korean Pear Using Next-Generation Sequencing

SSRs are co-dominant and typically neutral inheritance showing high degree of polymorphism, abundance in genomes, and suitability for automation. In Korea, there are three basic species, P. ussuriensis, P. pyrifolia and P. fauriei, which are known as Korean native. Genetic relationship among Korean pear cultivars compared with their parents were also identified that they are closely related P. pyrifolia, P. ussuriensis and/or hybrid between two species. Genetic resources, including molecular markers, to study pears are severely lacking. Recently developed NGS (Next Generation Sequencing) platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objective of this study was to develop polymorphic SSR markers in ‘Whangkeumbae’ and ‘Minibae’, which were chosen as the representative cultivars of P. pyrifolia and P. ussuriensis × pyrifolia in each among Korean pears, using genomic sequences generated by NGS technology. In this study, more than 169.8 million and 145.8 million sequencing reads were obtained from NGS of ‘Whangkeumbae’ and ‘Minibae’. ‘Whangkeumbae’ and ‘Minibae’ contained 75,837 and 75,733 SSR motif with dinucleotide (87.67 % and 87.77 %), motifs as the most abundant repeat type followed by tri- (9.60 % and 9.53%), tetra- (2.23% and 2.22%), penta- (0.34% and 0.33 %), and hexa-(0.17% and 0.14 %) respectively. Totally, 1,284 polymorphic SSRs were developed by comparing of ‘Whangkeumbaee’ and ‘Minibae’ SSR primers. This study shows the utility of the NGS technology to efficiently discover a large number of microsatellite markers and these SSR primers can provide valuable information on the genome study in Pyrus spp.