Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species

- Four enriched genomic libraries were constructed to develop SSR markers in pistachio.
- Of designed 84 primer pairs from sequenced 228 clones, 59 had amplifications and 47 were polymorphic.
- A higher number and frequency of SSRs was obtained from di-nucleotide-enriched libraries than tri-nucleotide libraries.
- 54 loci were transferable to at least one of eight tested Pistacia species.
- The SSR loci in tri-nucleotide enriched libraries had higher transferability than di-nucleotide ones.

Pistachio (Pistacia vera L.) is the only commercially grown species within the genus Pistacia and there are a limited number of simple sequence repeat (SSR) markers in the literature for Pistacia species. Therefore, genomic libraries enriched with CA, GA, AAC and AAG repeats were constructed using genomic DNA of P. vera cv. Siirt to develop SSR markers for pistachio and to determine their transferability in eight Pistacia species. A total of 228 clones were sequenced by selecting 57 clones from each library; 68 were duplicates, whereas 94 contained repeats. Eighty-four primer pairs were designed, 59 generated PCR products, and 47 were polymorphic within seven diverse pistachio cultivars. The number of alleles ranged from two to nine among 47 polymorphic loci with an average of 3.6. The GA-enriched library was the best, whereas the AAC library was the worst among the four libraries in terms of perfect repeats, number of alleles, polymorphism, and informativeness. A higher number and frequency of SSRs was obtained from di-nucleotide-enriched libraries than tri-nucleotide libraries. Testing of 59 SSR primer pairs in eight Pistacia species showed that 54 loci were transferable to at least one of the tested Pistacia species. P. atlantica had the highest number of transferable loci (51 loci), followed by P. integerrima (47 loci). The SSR loci in tri-nucleotide (72.7%) enriched libraries had higher transferability than di-nucleotide (54.7%) ones. The SSR markers developed in this study provide valuable tools for genetic studies in pistachio and related species, such as germplasm characterization, fingerprinting of individuals, population genetics, genetic mapping and marker assisted selection, as well as integrating genetic linkage maps.