Genome‐wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed

Abstract

Microtia is a congenital deformity of the outer ear with phenotypes varying from a small auricle to total absence (anotia). The genetic basis is still poorly understood, and very few studies have been performed in sheep. Valle del Belice sheep is a breed showing microtia. The aim of this study was to identify the potential genomic regions involved in microtia in sheep. A total of 40 individuals, 20 with microtia and 20 normal, were genotyped with the Illumina OvineSNP50 BeadChip. The comparison among the results from a genome-wide association study, Fisher's exact test and F analysis revealed a single strong association signal: rs419889303 on chromosome 1, located within intron 3 of the CLRN1 gene. Our study suggests for the first time that this novel candidate gene is responsible for microtia in sheep. Additional analysis based on the sequencing would help confirm our findings and allow for the proposal of a precise genetic basis for microtia in sheep.

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

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“…The F ST case-control analysis was performed using the -fst functionality in PLINK 1.9 [11], by comparing single markers between the PW and PB. Relevant F ST differences were defined considering the SNPs falling in and above the 99.98th percentile distribution [3,4].…”

“…Local animal genetic resources might indeed be characterized by specific heritable phenotypes potentially relevant for current or future use in breeding programs [1]. Several studies showed that local populations can be useful for the investigation of the genetic factors underlying those unique phenotypes related to their diversity [2][3][4].…”

A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

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Duplication in ECR near HMX1 and a SNP in GATA6 Genes Regulate Microtia in Awassi Sheep

“…Moreover, available reports on the etiology and inheritance of microtia in different sheep breeds are controversial. Using GWAS or local sequence alignment techniques, microtia was reported to be associated with mutations in GATA6 (GATA binding protein 6) in Awassi sheep [ 3 ], DCC (deleted in colorectal carcinoma) in Duolang sheep [ 4 ], CLRN1 (Clarin 1) in Valle del Belice [ 5 ] and a duplication within an evolutionary conserved region ( ECR ) near HMX1 (H6 family home-box 1) in Altay sheep [ 6 ]. Following these debatable reports in the underlying genetic causes behind the microtia phenotype in different sheep breeds, this study aims at identifying the possible mutation(s) behind the inheritance of microtia in the Awassi breed.…”