Genome-wide association study and pathway analysis for identifying the genes ‎associated with coat color in Lori-Bakhtiari sheep breed

Document Type : Research Paper

Authors

1 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Environmental Science, ‎Arak University, Arak, Iran

2 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Environmental Science, Arak University, Arak, ‎Iran

Abstract

Coat color is one of the important economic traits in sheep and it can be used for breed identification and characterization as well. The aim of the present study was to perform genome wide association study (GWAS) and pathway analysis based on gene set enrichment analysis for identifying the loci associated with coat color in Lori-Bakhtiari sheep breed. The GWAS was carried out using PLINK v. 1.90. The gene enrichment analysis was performed by goseq R package in R v.3.6.1 with the aim of identifying functional clusters and biological pathways of the genes in selected candidate regions and finally, for bioinformatics analysis we used online databases and softwares of GO, Metacyc, KEEG, Reactome and panther. In this study significant SNP markers were identified on chromosomes 1, 2, 6, 9, 10, and 16 that overlapped with EDNRB, PDGFRA, TCF25, and TYRP1 genes. According to pathway analysis, four GO pathways were associated with the coat color trait (P˂0.05). Among these pathways, regulation of protein tyrosine kinase activity, regulation of protein kinase A signaling and activation of protein kinase activity biological pathways, were previously reported to have an important role on the melanocyte development and coat pigmentation. Considering that the genomic regions identified in the current study have been confirmed to be associated with coat color in sheep and other species in previous reports, as well as the identification of some novel putative regions, the identified candidate genes in our study could be further studied and eventually used in genetic selection for coat color in sheep.

Keywords

References

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Iranian Journal of animal Science
Volume 53, Issue 3
December 2022
Pages 153-160

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History

  • Receive Date: 06 September 2021
  • Revise Date: 11 November 2021
  • Accept Date: 08 March 2022

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