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

Pistachio (Pistacia vera L.) is one of the commercially important cultivated nut tree species in Turkey. Pistachio nuts have many beneficial properties to human health and are widely used in the food industry. Cultivar breeding programs in pistachio take a long time, huge labor, high cost, and large land areas due to the alternate bearing and the long juvenile period of pistachio. Molecular breeding approaches are widely used to shorten long-term breeding programs in pistachio. In this study, we aimed to (i) 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'), and (ii) perform QTL analysis in leaf, shoot, and inflorescence traits in pistachio. To obtain the SNP markers, the DArT-Seq & TRADE; genotyping-by-sequencing method was used. A total of 1407 SNPs were mapped in the 'Ohadi' female, whereas the 'Pa-18' male map consisted of a total of 2518 SNP markers. The total length of the 'Ohadi' map was 1122.2 cm with an average length of 74.8 cM, while the 'Pa-18' map was 1307.2 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. The 'Ohadi' map had an average of 93.8 markers per linkage group (LG), 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. While the detected QTLs can be used for marker-assisted breeding and genetic studies, the generated SNP-based genetic linkage maps in this study will be used for QTL analysis of other important agronomic traits in pistachio.