Detection of mutations using bioinformatic tools in next generation re-sequencing data and determination of loci linked to nut traits by association mapping in pistachio

Pistachio (Pistacia vera L.) is one of the most important nut crops in Turkey. It is very important to take place early selection because the juvenile period of pistachio is very long. In the present study, it was aimed to detect loci linked by nut traits in pistachio using the genome wide associated mapping. A total of 150 pistachio cultivars and genotypes have been characterized with their harvest date and 25 pomological nut characters, in their kernels during two years. At the same time, it was obtained whole genome resequencing data of 150 pistachio genotypes at 15x coverage (10 Gb). The reads from a total of 150 pistachio cultivars and genotypes were mapped to the genome of the Siirt cultivar, and the total number of SNPs was calculated as 21,794,564 and the total number of InDels was calculated as 6,123,840. The total number of loci (SNP+InDel) was calculated as 27,918,404 and they were filtred according to missing data rate 5% and minor allele frequency (MAF=0.05). A total of 2,685,844 SNP markers were obtained for mapping and it was calculated that there is an average of approximately 230 bases of one SNP based on its distribution to the pistachio genome. The population structure of pistachio cultivars and genotypes by using the obtained markers in the study was determined by the ADMIXTURE program, and the possible population number was determined as K=10. A total of 113 highly associated loci were identified in nine fruit traits by association mapping. In addition, the correlation among loci was determined by Linkage Disequilibrium analysis and the mean r2 value was calculated as high as 0.60 in the 100 kb genome. As a result of genome annotation, related loci were determined to be highest in intergenic regions and least in UTR3, UTR5 and upstream:downstream regions. As a result of the functional annotations of the variants in the exonic regions, it was determined that the pistachio.v30011260 gene, which is related to the splitting rate trait, takes part in the biological process from cell division to the separation of sister chromatids. The results of this study can be used in marker assisted selection in future studies in pistachio breeding.