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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 #409661

Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis

Author
item HU, ZHENBIN - OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION (ORISE)
item BOSCHIERO, CLARISSA - UNIVERSITY OF MARYLAND
item Li, Congjun - Cj
item CONNOR, ERIN - UNIVERSITY OF DELAWARE
item Baldwin, Ransom - Randy
item Liu, Ge - George

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2023
Publication Date: 11/24/2023
Citation: Hu, Z., Boschiero, C., Li, C., Connor, E.E., Baldwin, R.L., Liu, G. 2023. Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis. Genes. 14(12):2121. https://doi.org/10.3390/genes14122121.
DOI: https://doi.org/10.3390/genes14122121

Interpretive Summary: Feed efficiency is important for the animal industry. We analyzed DNA methylation and gene expression in 48 Holstein cows with different feed efficiency. These results fill our knowledge gaps and provide the foundation for incorporating new epigenetics insights into the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Feed costs for dairy cattle production can amount to up to 75 percent of the total overhead cost of raising cows for milk production. Meanwhile, the livestock production industry is considered to be a significant contributor to global climate change due to the production of greenhouse gas emissions such as methane. Indeed, the genetic basis of feed efficiency is of great interest to the animal research community. Here, we explore the epigenetic basis of feed efficiency in order to provide base knowledge for the development of genomic tools for feed efficiency improvement in cattle. The methylation level of 37,554 CpG sites was quantified using a mammalian methylation array (HorvathMammalMethylChip40) for 48 Holstein cows with extreme Residual Feed Intake (RFI). We identified 421 CpG sites related to 287 genes that are associated with RFI. Several of them were previously validated genes for feeding or digestion issues. AUTS2 is associated with feeding problems in humans, while GPD2 (Glycerol-3-Phosphate Dehydrogenase 2) encodes a protein on the inner mitochondrial membrane, which can regulate glucose utilization and fatty acid and triglyceride synthesis. The extensive expression and co-expression of these genes across diverse tissues indicated the complex regulation of feed efficiencies in cattle. Our study provides insight into the epigenetic basis of RFI and gene resources for cow feed efficiency improvement.