Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries )

Song-Song Xu; Lei Gao; Min Shen; Fenghua Lyu

doi:10.3389/fgene.2021.738879

Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries )

Front Genet. 2021 Nov 18:12:738879. doi: 10.3389/fgene.2021.738879. eCollection 2021.

Authors

Song-Song Xu^{1

2}, Lei Gao³, Min Shen³, Fenghua Lyu¹

Affiliations

¹ College of Animal Science and Technology, China Agricultural University, Beijing, China.
² Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Shenzhen Branch, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
³ State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China.

Abstract

Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise F _ST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.

Keywords: artificial selection; genetic improvement; genome-wide SNPs; phenotypic traits; sheep.