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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #399037
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle

Author
item WANG, TIANZHEN - Chinese Academy Of Agricultural Sciences
item NIU, QUNHAO - Chinese Academy Of Agricultural Sciences
item ZHANG, TIANLIU - Chinese Academy Of Agricultural Sciences
item ZHENG, XU - Chinese Academy Of Agricultural Sciences
item LI, HAIPENG - Chinese Academy Of Agricultural Sciences
item GAO, XUE - Chinese Academy Of Agricultural Sciences
item CHEN, YAN - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item LI, JUNYA - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: International Journal of Biological Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2022
Publication Date: 12/1/2022
Citation: Wang, T., Niu, Q., Zhang, T., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle. International Journal of Biological Sciences. 23(23):15055. https://doi.org/10.3390/ijms232315055.
DOI: https://doi.org/10.3390/ijms232315055

Interpretive Summary: Gene expression analyses will benefit our understanding of genetic bases for meat quality. We conducted a combined analysis of candidate genes and experimental validated two important genes (PON3 and PRIM2) for meat production in beef cattle. These results fill our knowledge gaps and will benefit livestock genetic improvement. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Meat production traits are of considerable economic importance for farm animals, which act as a major contributor to the world's food supply. Genome-wide association study (GWAS) has identified thousands of genetic variants associated with meat production traits in beef cattle. However, most of the identified variants are located in non-coding regions, and their functions are not effectively resolved. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) to detect candidate genes for meat production traits in beef cattle. The gene-based GWAS and eQTL analysis revealed 1780 GWAS genes and 1538 cis-specific genes, respectively. Among them, we identified 153 shared genes that may play important role in meat production. Notably, the identified cis-eQTL of PON3 and PRIM2 were significantly (P < 0.001) enriched in previous GWAS for carcass traits with several LD blocks. We constructed the eukaryotic expression vector pcDNA3.1 of PON3 and PRIM2, validated their effects by qPCR, CCK8 and EdU assays in bovine skeletal muscle satellite cells (BSCs). Our results showed that overexpression of PON3 and PRIM2 promoted the BSCs proliferation, increased the number of EdU-positive cells and expression of proliferation-related markers MYOD. In contrast, the expression levels of differentiation-related markers MYOG were significantly up-regulated in BSCs. During the differentiation of BSCs, PON3 and PRIM2 were significantly down-regulated. Our findings suggested that PON3 and PRIM2 may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanism of meat production traits in beef cattle.