Genome-Wide Scanning for Signatures of Selection Revealed Karakul Sheep Breed in Compared to other Iranian Breeds
محورهای موضوعی : Genetics and BreedingA. Mirzapour-Abibagloo 1 , N. Hedayat 2 , R. Khalkhali-Evrigh 3 , R. Seyedsharifi 4 , H. Abdi-Benemar 5 , R. Hassanzadeh 6 , A. Tanveer Hussain 7
1 - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
2 - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
3 - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
4 - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
5 - Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
6 - Department of Engineering Mathematics, Faculty of New Technologies, University of Mohaghegh Ardabili, Ardabil, Iran
7 - Department of Biological Sciences, Virtual University of Pakistan, Islamabad, Pakistan
کلید واژه: Karakul sheep, pigmentation, signature of selection, whole-genome sequencing,
چکیده مقاله :
Karakul (KAR) is one of the resistant sheep breeds to harsh desert conditions, which is also known for its excelent lamb pelt quality. This study was performed to identify the signature of selections in the KAR breed using whole-genome sequencing data (WGS) compared with five other Iranian native sheep. Three methods, including population differentiation index (Fst), nucleotide diversity (π), and cross-population extended haplotype homozygosity (XP-EHH) applied to detect the genomic signature of selection. Data analysis leads to identifying 38 shared genes among three methods as positively selected genes for the KAR breed. The most of mentioned genes were associated with coat color (KIT, DVL3, YPEL3, ERBB4, ZNF451, and CTSO), fat and energy metabolism (GDPD3, STARD13, ZNF106, MAPK3, RGS6, PHYH, AP2M1, SPAG9, DNAH9, NDUFAF6, and ARSK), muscle function (MYOCD and MCTP1), growth (CPNE4), altitude adaptation (DNAH9 and SERGEF), and reproduction (TBX6, PHYH, SPAG9, and ARSK). Based on our results, these candidate genes may have a positive effect on the adaptation of the KAR breed to a desert environment.
Karakul (KAR) is one of the resistant sheep breeds to harsh desert conditions, which is also known for its excelent lamb pelt quality. This study was performed to identify the signature of selections in the KAR breed using whole-genome sequencing data (WGS) compared with five other Iranian native sheep. Three methods, including population differentiation index (Fst), nucleotide diversity (π), and cross-population extended haplotype homozygosity (XP-EHH) applied to detect the genomic signature of selection. Data analysis leads to identifying 38 shared genes among three methods as positively selected genes for the KAR breed. The most of mentioned genes were associated with coat color (KIT, DVL3, YPEL3, ERBB4, ZNF451, and CTSO), fat and energy metabolism (GDPD3, STARD13, ZNF106, MAPK3, RGS6, PHYH, AP2M1, SPAG9, DNAH9, NDUFAF6, and ARSK), muscle function (MYOCD and MCTP1), growth (CPNE4), altitude adaptation (DNAH9 and SERGEF), and reproduction (TBX6, PHYH, SPAG9, and ARSK). Based on our results, these candidate genes may have a positive effect on the adaptation of the KAR breed to a desert environment.
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