Study of Genetic Diversity of Sheep Breeds in Afghanistan Using SNP Markers

The objective of present study is analyzing genetic diversity among three Arab, Baloch and Gadic breeds using selected markers. Mutual comparisons of each two breeds were conducted to detect and accurately analyze differences between breeds. . 45 blood samples were collected from three districts of Herat province (Shindand, Gulran and Obe) of three Afghan sheep breeds (Arabi, Baloch and Gadic). 10 µL of blood was collected via the jugular vein in Venoject tubes with EDTA (Ethylene Diamine Tetraacetic Acid) for prevention of blood coagulation and immediately stored in a refrigerator at 4 °C. DNA was extracted from blood using the GenElute™ Blood Genomic DNA Kit. DNA concentration was determined using NanoDrop (Spectrophotometer ND-1000). In this research haplotypic blocks analysis in experimental regions, the way of their erosions and LD graphs are drawn using Haploview v4.2 software. Required information as inputs for this software consisted of genotypic information of markers in experimental regions similarly; the statistics that are used for LD calculation are the same correlational coefficients between r2 and surrounding SNPs. A total of 15 Arabi, 15 Baloch and 15 Gadic sheep breed were genotyped at 53862 SNP loci with the Ovine SNP chip50K Bead chip (http://www.illumina.com). usually those SNP that had been assigned to the 26 autosomes and X chromosome was measured) Then for each SNP, minor allele frequency (MAF) (over all animals) less than 2% were removed and percentage of calls rate 95% (how many sheep the marker worked for) was removed (Teo YY, Fry AE, Clark TG, Tai ES, Seielstad M: On the usage of HWE for identifying genotyping errors. Annals of Human Genetics 2007, 71:701-703). Biodiversity is usually described in terms of three intimately connected levels, namely Species diversity, Genetic diversity, Ecosystem diversity. Considering excess of heterozygosity within studied breeds, one can conclude that these breeds are not threatening in terms of heterozygosity decline and can be considered as an appropriate genetic reserve for different husbandry and eugenic purposes in Afghanistan. Furthermore high heterozygosity in studied chromosomes in Arab, Baloch and Gadic breeds suggest high diversity within population in spite of carrying out eugenic activities on livestock due to managerial plans which has managed to reduce the consistency level and keep the diversity in acceptable level.

Keywords:

Genetic diversity , sheep breed , LD graph , SNP , Afghanistan , Heterozygosity.