Dataset Information

Genome-wide association studies for sheep growth and meat production traits using Illumina OvineSNP50 BeadChip

ABSTRACT: Mear prodution is the most important trait for sheep. In this study, we performed a Genome-wide association study (GWAS) by using Illumina Ovine SNP50 BeadChip in 329 purebred sheep phenotyped for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers , chest girth and shin circumference). A total of 319 sheep and 48,198 SNPs were fitted using TASSEL 3.0 software as random effects in a mixed linear model. 36 chromosome-wise significant SNPs were identified for 7 traits and 10 of them reached genome-wide significance level consistently for post-weaning gain. Gene annotation was implemented based on the latest version3.1 ovine genome sequence (released October 2012), and meanwhile we referenced genomic information of human, bovine, mouse and rat. More than one-third SNPs (14 out of 36) were located within ovine genes , some other were located close to ovine genes (878bp-398165bp apart).

ORGANISM(S): Ovis aries

PROVIDER: GSE46231 | GEO | 2015/05/01

SECONDARY ACCESSION(S): PRJNA198484

REPOSITORIES: GEO

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Project description:Inherited rickets of Corriedale sheep is characterized by decreased growth rate, thoracic lordosis and angular limb deformities. Previous outcross and backcross studies suggest it is a simple autosomal recessive disorder. A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers. A homozygous region of 199 consecutive single-nucleotide polymorphism (SNP) loci was identified in all the affected sheep, covering a region of 10Mbp on ovine chromosome 6. Among 91 candidate genes in this region, exon 6 of the dentin matrix protein 1 gene (DMP1) was sequenced to reveal 9 SNPs including a nonsense mutation 253T/C which introduced a stop codon (R145X) and could truncate C-terminal amino acids. Genotyping by PCR-RFLP for this mutation showed that, all 17 affected sheep were “T T” genotypes and the 27 phenotypically normal sheep were either “C T” or “C C”. This locus is not in complete linkage disequilibrium with the other 8 SNPs that can all be ruled out as candidates. Previous research has shown that mutations in DMP1 gene are responsible for autosomal recessive hypophosphatemic rickets in humans. Dmp1_knockout mice also exhibit rickets phenotypes. We believe the R145X mutation to be responsible for the inherited rickets found in Corriedale sheep. A simple diagnostic test can be designed to identify carriers with the defective “T” alleles. Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers to define homozygous regions with consecutive single-nucleotide polymorphism (SNP) loci only existing in all the affected sheep. Fine mapping was conducted by screening coding regions and splicing regions on the positional candidate genes within the homozygous regions by using more sheep