Development of SSR markers by next generation sequencing in pistacia, genetic linkage mapping and QTL analysis using an inter-specific F1 population

Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia. Genome survey sequences of pistachio was obtained at 40x depth by next generation sequencing to understand genome structure. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds in the P. vera cv. Siirt genome. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 pistachio cultivars and 20 wild Pistacia genotypes. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The SSR-based genetic linkage map was constructed using an inter-specific F1 population derived from P. vera L. 'Siirt' and monoecious Pistacia atlantica Desf. (Pa-18 genotype). A total of 388 SSR markers were mapped. The length of consensus map was 1,492 cM along with 15 linkage groups with an average marker distance of 3.7 cM. Sex-linked markers in the literature were also mapped with the SSR markers in LG1. Phenotypic data were collected during 2015 and 2016 growing season for five traits: leaf length (LL), leaf width (LW), number of leaflet (NLF), young shoot color (YSC), and leaf color (LC). QTL analysis were performed for the five traits using the the 'Siirt' and 'Pa-18' SSR-based genetic maps and 17 QTLs were identified. The novel SSR markers, linkage maps, and QTLs reported in this study will be useful resources for future genetic linkage maps and QTL analysis, and for identification of important genes in Pistacia as well as genome sequencing projects.