Evaluation of genetic structure of pistachio through whole genome resequencing

Authors : Harun KARCI, Salih KAFKAS

Pages : 135-140

Doi:10.31015/jaefs.2022.1.18

View : 29 | Download : 11

Publication Date : 2022-03-15

Article Type : Research Paper

Abstract :Pistachio insert ignore into journalissuearticles values(Pistacia vera L.); is the only edible and cultivated species. Pistachio is the only economically importance and dioecious species in the genus Pistacia. There are basic problems in pistachio breeding such as dioecious flower structure, long juvenile period and alternate bearing. These problems can be overcome not with classical breeding methods, but with modern molecular breeding methods. In this study, very high numbers of single nucleotide polymorphism insert ignore into journalissuearticles values(SNP);, insertion/deletion insert ignore into journalissuearticles values(InDel);, structural variants insert ignore into journalissuearticles values(SV); and copy number variation insert ignore into journalissuearticles values(CNV); were determined by using the next generation sequencing data of the pistachio genotype obtained with 15x sequencing coverage. A total of 1,785,235 SNP, 260,683 InDel, 5,227 SV and 1,914 CNV variants identified in PvF217 pistachio genotype. The variant density was calculated as one variant per 292 base. The distribution of the obtained variants to the Siirt reference genome was obtained. In addition, all variants were annotated to the reference genome and exonic and genomic variants were described using Annovar. These data will be used to consist of a molecular database in pistachio breeding for DNA fingerprinting, discovering unique cultivar specific alleles and to identify quantitative trait loci related to important nut traits.
Keywords : Pistachio, resequencing, genome, SNP