Dataset Information

Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks.

ABSTRACT: With continuously increasing living standards and health requirements of consumers, meat quality is becoming an important consideration while buying meat products. To date, no genome-wide association study (GWAS) for copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) has been conducted to reveal the genetic effects on meat quality in ducks. This study analyzed the phenotypic correlation and heritability of fat, water, collagen, and protein content of duck breast muscle. To identify the candidate variants for meat quality, we performed a GWAS using 273 ducks from an F2 population. The results of the SNP GWAS showed that the BARHL2, COPS7B, and CCDC50 genes were associated with fat content; BLM, WDR76, and EOMES with water content; CAMTA1, FGD5, GRM7, and RAPGEF5 with collagen production; and RIMS2, HNRNPU, and SPTBN1 with protein content. Additionally, 3, 7, 1, and 3 CNVs were associated with fat, water, collagen, and protein content, respectively, in duck breast muscle. The genes identified in this study can serve as markers for meat quality. Furthermore, our findings may help devise effective breeding plans and selection strategies to improve meat quality.

SUBMITTER: Guo Q

PROVIDER: S-EPMC9222319 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks.

Guo Qixin Q Huang Lan L Bai Hao H Wang Zhixiu Z Bi Yulin Y Chen Guohong G Jiang Yong Y Chang Guobin G

Genes 20220531 6

With continuously increasing living standards and health requirements of consumers, meat quality is becoming an important consideration while buying meat products. To date, no genome-wide association study (GWAS) for copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) has been conducted to reveal the genetic effects on meat quality in ducks. This study analyzed the phenotypic correlation and heritability of fat, water, collagen, and protein content of duck breast muscle. To id ...[more]

PMID: 35741748

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Project description:There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8x10(-57)), CCL4L1 (p = 3.9x10(-21)), IL18 (p = 6.8x10(-13)), LPA (p = 4.4x10(-10)), GGT1 (p = 1.5x10(-7)), SHBG (p = 3.1x10(-7)), CRP (p = 6.4x10(-6)) and IL1RN (p = 7.3x10(-6)) genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA), variation in gene copy number (CCL4L1) and altered transcription (GGT1). We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha) levels (p = 6.8x10(-40)), but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis locations. The identification of protein quantitative trait loci (pQTLs) may be a powerful complementary method of improving our understanding of disease pathways.

Dataset Information

Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks.

Publications

Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks.

Similar Datasets

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