Dataset Information

Exclusion of Candidate Genes within Thrombin Signaling Pathway in Association with Atypical Equine Thrombasthenia in Thoroughbreds

ABSTRACT: Exclusion of Candidate Genes within Thrombin Signaling Pathway in Association with Atypical Equine Thrombasthenia in Thoroughbreds

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Equus Caballus

SUBMITTER: University of California Davis

PROVIDER: PRJEB33757 | EVA | 2019-08-02

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	AKT1_cc_eff_header_rename.accessioned.vcf.gz	Vcf
	AKT1_cc_eff_header_rename.vcf.gz	Vcf
	AKT1_cc_eff_header_rename.vcf.gz.tbi	Vcf
	AKT2_cc_eff_header_rename.accessioned.vcf.gz	Vcf
	AKT2_cc_eff_header_rename.vcf.gz	Vcf

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Project description:Boar taint is an unpleasant odour and flavour of the meat from some uncastrated male pigs primarily caused by elevated levels of androstenone and skatole in adipose tissue. Androstenone is produced in the same biochemical pathway as testosterone and estrogens, which represents a particular challenge when selecting against high levels of androstenone in the breeding programme, without simultaneously decreasing levels of other steroids. Detection of single nucleotide polymorphisms (SNPs) associated with compounds affecting boar taint is important both for gaining a better understanding of the complex regulation of the trait and for the purpose of identifying markers that can be used to improve the gain of breeding. The beneficial SNPs to be used in breeding would have the combinational effects of reducing levels of boar taint without affecting fertility of the animals. The aim of this study was to detect SNPs in boar taint candidate genes and to perform association studies for both single SNPs and haplotypes with levels of boar taint compounds and phenotypes related to reproduction.An association study involving 275 SNPs in 121 genes and compounds related to boar taint and reproduction were carried out in Duroc and Norwegian Landrace boars. Phenotypes investigated were levels of androstenone, skatole and indole in adipose tissue, levels of androstenone, testosterone, estrone sulphate and 17beta-estradiol in plasma, and length of bulbo urethralis gland. The SNPs were genotyped in more than 2800 individuals and several SNPs were found to be significantly (LRT > 5.4) associated with the different phenotypes. Genes with significant SNPs in either of the traits investigated include cytochrome P450 members CYP2E1, CYP21, CYP2D6 and CYP2C49, steroid 5alpha-reductase SRD5A2, nuclear receptor NGFIB, catenin CTNND1, BRCA1 associated protein BAP1 and hyaluronoglucosaminidase HYAL2. Haplotype analysis provided additional evidence for an effect of CYP2E1 on levels of skatole and indole, and for BAP1, HYAL2 and SRD5A2 on levels of androstenone.The findings in this study indicate that polymorphisms in CYP2E1, CYP21, CYP2D6, CYP2C49, NGFIB and CTNND1 might be used to reduce levels of boar taint without affecting levels of testosterone, estrone sulphate, 17beta-estradiol or length of bulbo urethralis gland.

Dataset Information

Exclusion of Candidate Genes within Thrombin Signaling Pathway in Association with Atypical Equine Thrombasthenia in Thoroughbreds

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