Evaluation of genetic structure of pistachio through whole genome resequencing


KARCI H., KAFKAS S.

International Journal of Agriculture, Environment and Food Sciences, vol.6, no.1, pp.135-140, 2022 (Peer-Reviewed Journal) identifier

Abstract

Abstract Pistachio (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 (SNP), insertion/deletion (InDel), structural variants (SV) and copy number variation (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