Development of novel SSR markers by next generation sequencing and constructon of the first SSR linkage referance maps in Pistachio

There are a limited number of simple sequence repeat (SSR) markers in the literature for Pistacia species. Therefore, this study aims to develop novel polymorphic SSR markers in silico by next generation sequencing (NGS) and to construct the first SSR-based genetic linkage maps in pistachio. About 10x coverage of Illumina sequences were obtained from three Pistacia vera L. cultivars (Siirt, Ohadi and Bagyolu) and one monoecious P. atlantica Desf. genotype (Pa-18) to find polymorphic SSR loci in silico among them. A total of 750 polymorphic SSR loci were detected and 79 (10.5%) did not have amplification in SSR-PCR reactions. The remaining loci were tested for polymorphism by capillary electrophoresis in 18 pistachio cultivars in six P. atlantica genotypes. Fifty-three SSR loci produced complex patterns, and they were discarded. A total of 625 SSR loci were produced from 618 SSR primer pairs. The novel SSRs in this study as well as SSRs in the literature were used to construct the first SSR based genetic linkage map of pistachio using Siirt x Bağyolu F1 population. The parental, consensus and reference genetic maps were constructed. The consensus map included 385 SSR markers along with 15 chromosomes and 70.9% of them were common markers. The LG length changed between 61.3 cM (LG8) and 131.0 cM (LG12) with a total length of 1,511.2 cM. The avarage distance between the markers was 3.9 cM, and the marker density was 0.25. The novel SSR markers and constructed genetic linkage maps in this study will be reference for further genetic linkage mapping and genetic characterization studies in pistachio.