Genetics and Genomics Journal Cover Design Service (GWAS)

Journal of Genetics and Genomics

3 February 2023

Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows

Hailiang Zhang^a,1, Siyuan Mi^a,1, Luiz F. Brito^b, Lirong Hu^a, Lei Wang^a, Longgang Ma^a, Qing Xu^c, Gang Guo^d, Ying Yu^a,*, Yachun Wang^a,*

10.1016/j.jgg.2023.01.011

The main objectives of this study are to identify key candidate genes regulating subcutaneous fat deposition in high-producing dairy cows by integrating genomic and transcriptomic datasets. A total of 1654 genotyped Holstein cows are used to perform a genome-wide association study (GWAS) aiming to identify genes associated with subcutaneous fat deposition. Subsequently, weighted gene co-expression network analyses (WGCNA) are conducted based on RNA-sequencing data of 34 cows and cow yield deviations of subcutaneous fat deposition. Lastly, differentially expressed (DE) mRNA, lncRNA, and differentially alternative splicing genes are obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition. Integrating all findings, the NID2, STARD3, UFC1, DEDD, PPP1R1B, and USP21 genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows.