Selection signature and gene ontology for traits related to fat deposition in Afshari and Sunite fat-tailed sheep breeds

Tail in sheep is a valuable energy source. However, in modern intensive and semi-intensive sheep industry the lean-tailed sheep breeds have more desirable and marketable. Therefore, due to the negative effect of tail size on production efficiency, researchers are looking for methods to eliminate this trait. Identification of genes involved in the process of fat deposition in tail is necessary for reducing tail size in sheep. Several genomic methods such as genome-wide association and selection signature studies or gene expression analysis for describing a possible genetic background for deposition of fat in various fat-tail breeds have been used. The aim of this study was to identify effective genes in fat-tailed sheep breeds (Afshari and Sunite) compared to breeds without tail (Dorper and German Mutton) using selection signature and gene ontology methods.

In this study, genotype information of 366 sheep (37 Afshari, 69 Sunite, 99 Dorper and 161 German Mutton) genotyped with Illumina Ovine SNP50K BeadChip genome arrays, were used. The XP-EHH method using R software package version 1.9 was used to identify selection signature. Genomic version Oar_v4.0 database NCBI was used for detecting the genomic position of SNPs in sheep genome. Candidate genes were identified by SNPs located at 1% upper range of XP-EHH using Plink v1.9 software and gene list of Illumina in R. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with fat deposition traits in identified locations.

Based on the results of XP-EHH, 18 common genes were identified from comparing Afshari population with German Mutton and Dorper breeds, in which five genes (LOC114116389, LOC114118754, KCMF1, TCF7L1 and RASSF2) were associated with QTLs related to fat deposition including carcass fat percentage, internal fat amount and fat tail deposition. 15 common genes were also identified from comparing Sunite population with German Mutton and Dorper populations, in which two genes (SEMA5B and CDH9) were associated with QTLs related to fat deposition. The results of gene ontology showed that some of these genes play effective roles in signaling Wnt, growth, development and morphology of cells.

based on the results of selection signature using XP-EHH method in Afshari and Sunite breeds, RASSF2 gene was identified as a selection signature in Afshari breeds. This gene was also related to tail fat storage QTL, which was identified for the first time in this study. LOC11411689 and LOC114118754 genes related to carcass fat percentage QTL, KCMF1 and TCF7L1 genes related to the QTL of internal fat amount in Afshari breed were also identified. In addition, the SEMA5B gene associated with the QTL of carcass fat percentage and the CDH9 gene associated with of subcutaneous fat weight were identified in the Sunite breed. The results of this study could be used in sheep breeding programs to reduce fat deposition in tail, especially for Afshari breed.