Dataset Information

A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs.

ABSTRACT: Brown coat colour has been described in Chinese-Tibetan, Kele, and Dahe pigs. Here, we report the identification of a causal mutation underlying the brown colouration. We performed a genome-wide association study (GWAS) on Tibetan and Kele pigs, and found that brown colours in Chinese breeds are controlled by a single locus on pig chromosome 1. By using a haplotype-sharing analysis, we refined the critical region to a 1.5-Mb interval that encompasses only one pigmentation gene: tyrosinase-related protein 1 (TYRP1). Mutation screens of sequence variants in the coding region of TYRP1 revealed a strong candidate causative mutation (c.1484_1489del). The protein-altering deletion showed complete association with the brown colouration across Chinese-Tibetan, Kele, and Dahe breeds by occurring exclusively in brown pigs (n=121) and lacking in all non-brown-coated pigs (n=745) from 27 different breeds. The findings provide the compelling evidence that brown colours in Chinese indigenous pigs are caused by the same ancestral mutation in TYRP1. To our knowledge, this study gives the first description of GWAS identifying causal mutation for a monogenic trait in the domestic pig.

SUBMITTER: Ren J

PROVIDER: S-EPMC3186233 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs.

Ren J J Mao H H Zhang Z Z Xiao S S Ding N N Huang L L

Heredity 20101027 5

Brown coat colour has been described in Chinese-Tibetan, Kele, and Dahe pigs. Here, we report the identification of a causal mutation underlying the brown colouration. We performed a genome-wide association study (GWAS) on Tibetan and Kele pigs, and found that brown colours in Chinese breeds are controlled by a single locus on pig chromosome 1. By using a haplotype-sharing analysis, we refined the critical region to a 1.5-Mb interval that encompasses only one pigmentation gene: tyrosinase-relate ...[more]

PMID: 20978532

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Project description:BackgroundSemen quality and insemination success are monitored in artificial insemination bulls to ensure high male fertility rates. Only ejaculates that fulfill minimum quality requirements are processed and eventually used for artificial inseminations. We examined 70,990 ejaculates from 1343 Brown Swiss bulls to identify bulls from which all ejaculates were rejected due to low semen quality. This procedure identified a bull that produced 12 ejaculates with an aberrantly small number of sperm (0.2 ± 0.2 × 109 sperm per mL) which were mostly immotile due to multiple morphological abnormalities.ResultsThe genome of this bull was sequenced at a 12× coverage to investigate a possible genetic cause. Comparing the sequence variant genotypes of this bull with those from 397 fertile bulls revealed a 1-bp deletion in the coding sequence of the QRICH2 gene which encodes the glutamine rich 2 protein, as a compelling candidate causal variant. This 1-bp deletion causes a frameshift in translation and a premature termination codon (ENSBTAP00000018337.1:p.Cys1644AlafsTer52). The analysis of testis transcriptomes from 76 bulls showed that the transcript with the premature termination codon is subject to nonsense-mediated mRNA decay. The 1-bp deletion resides in a 675-kb haplotype that includes 181 single nucleotide polymorphisms (SNPs) from the Illumina BovineHD Bead chip. This haplotype segregates at a frequency of 5% in the Brown Swiss cattle population. Our analysis also identified another bull that carried the 1-bp deletion in the homozygous state. Semen analyses from the second bull confirmed low sperm concentration and immotile sperm with multiple morphological abnormalities that primarily affect the sperm flagellum and, to a lesser extent, the sperm head.ConclusionsA recessive loss-of-function allele of the bovine QRICH2 gene likely causes low sperm concentration and immotile sperm with multiple morphological abnormalities. Routine sperm analyses unambiguously identify homozygous bulls for this allele. A direct gene test can be implemented to monitor the frequency of the undesired allele in cattle populations.

Dataset Information

A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs.

Publications

A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs.

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