Identification of SNP markers related to important traits for Iranian native sheep using selection signature

Authors

1 Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad

2 Animal Science department, Faculty of Agriculture, Ferdowsi University of Mashhad

3 Researcher Sveriges lantbruksuniversitet (SLU) Swedish University of Agricultural Sciences

Abstract

Background and objective
Identification of several genomic markers sequenced in farm animal enable us to study the structure of their genome. Samples from different parts of the world are usually used for sequencing genomic markers. Information on the sequence of specific markers of domestic animals of each geographical area will improve our knowledge about their genomic structure. The sequence of specific genome markers for Iranian native sheep were not yet identified. Present study aims to identify single-nucleotide polymorphism (SNPs) influencing important economic and physiological traits of Iranian domestic and wild sheep as candidate markers using selection signature.
Materials and methods
In order to identify significant genetic variants under selection in domestic and wild sheep, the whole genome sequence of 20 domestic (Ovis aries) and 14 wild sheep (Ovis orientalis) obtained from the Next Gene project was used. After doing quality control, variant under selection were detected using statistical methods consisting iHS and XP-EHH. Genetic variance for identified variants were estimated. The genetic variance of known variants in Merino, Suffolk, texel and Afshari were also estimated. The threshold for selecting variants based on iHS and XP-EHH methods were considerd to be 99.9% in domestic sheep and 99.9% and 0.001% in wild sheep, respectively. Finally, variants with genetic variances higher than 0.25, were identified and suggested as candidate markers.
Results
In present study, 170 genomic variants with iHS and XP-EHH values higher than 3.83 and 3.44 in domestic sheep and 150 genomic variants with iHS values higher than 3.05 and XP-EHH values lower than -4.43 in wild sheep were identified and suggested as candidate markers. Genetic variance of these variants were 0.27 to 0.50 and the genetic variance of known variants in Merino, Suffolk, Texel and Afshari were from 0.02 to 0.50. This comparison shows the importance of identified variants in Iranian domestic and wild sheep. Most of identified variants in domestic and wild sheep associated with economically important traits including carcass, milk and wool related traits. The ontology of genes related to identified variants showed that these variants are located near genes related to metabolic process of production and reproduction traits
Conclusion
Present results showed that there are many significant genetic variants associated with economic traits in domestic and wild Iranian sheep which are not included in the commercial sheep arrays available in the market. Identification of new SNPs related to economic traits in domestic and wild sheep may help to improve the studies related to genomic structure of Iranian sheep. These results together with similar studies could be efficiently used for producing SNP arrays designed for Iranian native sheep.

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Journal of Ruminant Research
Volume 11, Issue 4
January 2024
Pages 73-92

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