Developing new microsatellite markers in walnut (Juglans regia L.) from Juglans nigra genomic GA enriched library

Abstract

We attempted to develop new polymorphic SSR primer pairs in walnut using sequences derived from Juglans nigra L. genomic enriched library with GA repeat. The designed 94 SSR primer pairs were subjected to gradient PCR in 12 walnut cultivars to determine their optimum annealing temperatures and to determine whether they produce bands. Then, the primer pairs which had amplification in agarose gel were analyzed in capillary electrophoresis to determine their allele sizes. According to the gradient PCR and capillary electrophoresis results, 60.6% of the SSR primer pairs did not amplify any bands in agarose gel. Rest of the 37 primer pairs produced bands and their annealing temperatures and allele sizes were determined. From the amplified primer pairs, 18 of them were monomorphic, while 19 of them were polymorphic. As a result, 20.2% polymorphism was obtained from 94 SSR primer pairs tested in this study which had lower ratio when compared to the literature

Keywords

• SSR, walnut, polymorphism, PCR