Evaluation of genetic structure of pistachio through whole genome resequencing

Harun Karcı; Salih Kafkas

doi:10.31015/jaefs.2022.1.18

EN

Evaluation of genetic structure of pistachio through whole genome resequencing

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

Supporting Institution

Tübitak

Project Number

118O938

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Details

Primary Language

English

Subjects

Horticultural Production

Journal Section

Research Article

Authors

Harun Karcı ^*
0000-0002-9037-4764
Türkiye

Salih Kafkas This is me
0000-0002-9037-4764
Türkiye

Publication Date

March 15, 2022

Submission Date

January 4, 2022

Acceptance Date

March 14, 2022

Published in Issue

Year 2022 Volume: 6 Number: 1

DOI

https://doi.org/10.31015/jaefs.2022.1.18

IZ

https://izlik.org/JA79GT24JG

APA

Karcı, H., & Kafkas, S. (2022). Evaluation of genetic structure of pistachio through whole genome resequencing. International Journal of Agriculture Environment and Food Sciences, 6(1), 135-140. https://doi.org/10.31015/jaefs.2022.1.18

AMA

1.Karcı H, Kafkas S. Evaluation of genetic structure of pistachio through whole genome resequencing. int. j. agric. environ. food sci. 2022;6(1):135-140. doi:10.31015/jaefs.2022.1.18

Chicago

Karcı, Harun, and Salih Kafkas. 2022. “Evaluation of Genetic Structure of Pistachio through Whole Genome Resequencing”. International Journal of Agriculture Environment and Food Sciences 6 (1): 135-40. https://doi.org/10.31015/jaefs.2022.1.18.

EndNote

Karcı H, Kafkas S (March 1, 2022) Evaluation of genetic structure of pistachio through whole genome resequencing. International Journal of Agriculture Environment and Food Sciences 6 1 135–140.

IEEE

[1]H. Karcı and S. Kafkas, “Evaluation of genetic structure of pistachio through whole genome resequencing”, int. j. agric. environ. food sci., vol. 6, no. 1, pp. 135–140, Mar. 2022, doi: 10.31015/jaefs.2022.1.18.

ISNAD

Karcı, Harun - Kafkas, Salih. “Evaluation of Genetic Structure of Pistachio through Whole Genome Resequencing”. International Journal of Agriculture Environment and Food Sciences 6/1 (March 1, 2022): 135-140. https://doi.org/10.31015/jaefs.2022.1.18.

JAMA

1.Karcı H, Kafkas S. Evaluation of genetic structure of pistachio through whole genome resequencing. int. j. agric. environ. food sci. 2022;6:135–140.

MLA

Karcı, Harun, and Salih Kafkas. “Evaluation of Genetic Structure of Pistachio through Whole Genome Resequencing”. International Journal of Agriculture Environment and Food Sciences, vol. 6, no. 1, Mar. 2022, pp. 135-40, doi:10.31015/jaefs.2022.1.18.

Vancouver

1.Harun Karcı, Salih Kafkas. Evaluation of genetic structure of pistachio through whole genome resequencing. int. j. agric. environ. food sci. 2022 Mar. 1;6(1):135-40. doi:10.31015/jaefs.2022.1.18

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Evaluation of genetic structure of pistachio through whole genome resequencing

Evaluation of genetic structure of pistachio through whole genome resequencing

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