Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle
Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carcass yield traits in beef cattle. However, their functions are...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-12-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/23/15055 |
| Summary: | Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carcass yield traits in beef cattle. However, their functions are not effectively illustrated. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) analysis to detect candidate genes for carcass yield traits and validate their effects on bovine skeletal muscle satellite cells (BSCs). The gene-based GWAS and cis-eQTL analysis revealed 1780 GWAS and 1538 cis-expression genes. Among them, we identified 153 shared genes that may play important roles in carcass yield traits. Notably, the identified cis-eQTLs of <i>PON3</i> and <i>PRIM2</i> were significantly (<i>p</i> < 0.001) enriched in previous GWAS loci for carcass traits. Furthermore, overexpression of <i>PON3</i> and <i>PRIM2</i> promoted the BSCs’ proliferation, increased the expression of <i>MYOD</i> and downregulated the expression of <i>MYOG</i>, which indicated that these genes may inhibit myogenic differentiation. In contrast, <i>PON3</i> and <i>PRIM2</i> were significantly downregulated during the differentiation of BSCs. These findings suggested that <i>PON3</i> and <i>PRIM2</i> may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanisms of carcass yield traits in beef cattle. |
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| ISSN: | 1661-6596 1422-0067 |