A genome‐wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries)

Abstract

Genome-wide association studies (GWASs) have been widely applied in livestock to identify genes associated with traits of economic interest. Here, we conducted the first GWAS of the supernumerary nipple phenotype in Wadi sheep, a native Chinese sheep breed, based on Ovine Infinium HD SNP BeadChip genotypes in a total of 144 ewes (75 cases with four teats, including two normal and two supernumerary teats, and 69 control cases with two teats). We detected 63 significant SNPs at the chromosome-wise threshold. Additionally, one candidate region (chr1: 170.723-170.734 Mb) was identified by haplotype-based association tests, with one SNP (rs413490006) surrounding functional genes BBX and CD47 on chromosome 1 being commonly identified as significant by the two mentioned analyses. Moreover, Gene Ontology enrichment for the significant SNPs identified by the GWAS analysis was functionally clustered into the categories of receptor activity and synaptic membrane. In addition, pathway mapping revealed four promising pathways (Wnt, oxytocin, MAPK and axon guidance) involved in the development of the supernumerary nipple phenotype. Our results provide novel and important insights into the genetic mechanisms underlying the phenotype of supernumerary nipples in mammals, including humans. These findings may be useful for future breeding and genetics in sheep and other livestock.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

“…5c) as well-characterized functional genes for the polycerate and polled phenotypes in sheep 29 . For the number of nipples, most of the significant GWAS signals were located in genes associated with breast cancer, including five genes (LRP1B, GRM3, MACROD2, SETBP1, and GPC3) reported previously 30 .…”

Genome‐wide association study reveals novel genes for the ear size in sheep (Ovis aries)

“…SNPs or individuals meeting any of the following criteria were removed from further analyses: (i) no chromosomal or physical location, (ii) minor allele frequency less than 0.05, (iii) individual call rate less than 0.95, (iv) missing genotype frequency for SNPs more than 0.05 and (v) P ‐value for Hardy‐Weinberg equilibrium less than 0.001 (Peng et al . ). Also, we implemented sex screening using the ‘check‐sex’ option in plink v1.07.…”

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

“…The availability of several forms of DNA variants, such as single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), has played an important role in phenotypic variation studies. Most genetic and genome-wide association studies (GWAS) have investigated the associations between SNPs as genetic variants and complex and economically important traits, with the aim of identifying subsets of markers able to explain traits [1–5]. CNVs are polymorphic genomic regions, including deletions, duplications and insertions that involve DNA segment ranging from 1 kb to several Mb, that vary compared to a reference genome [6].…”