In silico polymorphism analysis for the development of simple sequence repeat markers in pistachio

Pistacia vera L. is one of the most important nut crops. There are a limited number of simple sequence repeat (SSR) markers in the literature for pistachio. The short Illumina DNA sequences of three cultivars ('Siirt', 'Ohadi' and 'Bagyolu') in P. vera and one genotype belongs to P. atlantica (Pa-18) were produced by next-generation sequencing, and a total of 750 polymorphic loci were detected in silico and the primers were designed. Seventy-nine (10.5%) did not have amplification product and they were discarded. The remaining loci were subjected to PCR and then capillary electrophoresis for polymorphism in 18 pistachio cultivars as well as in six P. atlantica genotypes. Fifty-three SSR loci produced complex patterns, and were unable to score. Among the remaining (618) SSR primer pairs, seven had multilocus amplifications, and in total 625 SSR loci were produced from 618 SSR primer pairs. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.