Development of New Microsatellite Marker in ‘Whangkeumbae’ Pear through Next Generation Sequencing

The microsatellite, or SSRs are known for being highly polymorphic, codominantly inherited, a large number of alleles per locus, suitable for automation, abundant and evenly distributed in the genome. Recently developed next generation sequencing platforms offer opportunities for high-throughput, inexpensive genome sequencing and rapid marker development. In Korea, Pear (Pyrus spp., X=17) is one of the important fruit and three basic species, P. ussuriensis, P. pyrifolia and P. fauriei, are known as Korean native. As a starting of Korean pear genome project (supported by Biogreen 21 program of Rural Development Administration, Korea), selection of new microsatellite were conducted to apply core collection management and reference map construction. The objectives of this study were to develop polymorphic genomic microsatellite from 'Whangkeumbae' genomic sequences generated by next generation sequencing technology and to evaluate the utility of the microsatellite for genetic diversity of P. pyrifolia and P. ussuriensis. In total 50 primer pairs were designed from sequences generated by Roche’s 454 GS FLX. Of 50 microsatellite markers, 38 were polymorphic in 'Whangkeumbae', 'Minibae', and six progenies. These selected 38 microsatellite markers and their alleles information might be available for identification of the genotype among pear cultivars, mapping, MAS, QTL and breeding for important traits in Korean pear.