Dataset Information

Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep.

ABSTRACT: Despite their economic value, sheep remain relatively poorly studied animals in terms of the number of known loci and genes associated with commercially important traits. This gap in our knowledge can be filled in by performing new genome-wide association studies (GWAS) or by re-analyzing previously documented data using novel powerful statistical methods. This study is focused on the search for new loci associated with meat productivity and carcass traits in sheep. With a multivariate approach applied to publicly available GWAS results, we identified eight novel loci associated with the meat productivity and carcass traits in sheep. Using an in silico follow-up approach, we prioritized 13 genes in these loci. One of eight novel loci near the FAM3C and WNT16 genes has been replicated in an independent sample of Russian sheep populations (N = 108). The novel loci were added to our regularly updated database increasing the number of known loci to more than 140.

SUBMITTER: Zlobin AS

PROVIDER: S-EPMC8002146 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep.

Zlobin Alexander S AS Nikulin Pavel S PS Volkova Natalia A NA Zinovieva Natalia A NA Iolchiev Baylar S BS Bagirov Vugar A VA Borodin Pavel M PM Aksenovich Tatiana I TI Tsepilov Yakov A YA

Genes 20210304 3

Despite their economic value, sheep remain relatively poorly studied animals in terms of the number of known loci and genes associated with commercially important traits. This gap in our knowledge can be filled in by performing new genome-wide association studies (GWAS) or by re-analyzing previously documented data using novel powerful statistical methods. This study is focused on the search for new loci associated with meat productivity and carcass traits in sheep. With a multivariate approach ...[more]

PMID: 33806625

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Project description:BackgroundVariants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles.ResultsWhereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles.ConclusionsWe detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

Dataset Information

Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep.

Publications

Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep.

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