Construction of high-density genetic linkage map and QTL analysis using an interspecific F1 population in pistachio

Pistachio (Pistacia vera L.) is one of the commercially most important cultivated fruit tree species around the world including Turkey due to its edible nuts having beneficial properties to human health as well as commercial importance in the industry. Cultivar breeding programs in pistachio take a long time, huge labor, high cost, and large land areas due to the alternate bearing and long juvenile period of pistachio. To mitigate such constraints in the breeding programs, the molecular approach is necessary to apply. Therefore, this study aimed (i) to construct the first SNP-based high-density genetic linkage maps using an interspecific F1 population derived from a cross between P. vera cv. 'Ohadi' and P. atlantica cv. 'Pa-18' ('Ohadi x Pa-18'), (ii) to perform QTL analysis in leaf, shoot and inflorescence traits in pistachio. To obtain the SNP markers, DArT-SeqTM genotyping-by-sequencing method was used. A total of 1,407 SNPs was mapped in the 'Ohadi' female, whereas the 'Pa-18' male map consisted of a total of 2,518 SNPs markers. The total length of the 'Ohadi' map was 1,122.2 cM with an average length of 74.8 cM, while the 'Pa-18' map was 1,307.2 cM in length with an average length of 87.1 cM. The marker density was 1.2 and 1.9 markers per cM in 'Ohadi' and 'Pa-18' linkage maps, respectively. 'Ohadi' map had an average of 93.8 markers per linkage group, while the 'Pa-18' map had an average of 167.9 markers per linkage group. A total of four significant QTLs that are related to terminal leaflet base, leaf width, tree vigor, and inflorescence rachis length were detected in three linkage groups in the 'Ohadi' genetic linkage map. The data generated in this study will be very useful and framework for further QTL analysis, molecular breeding, and genetic studies in the future for pistachio.