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ARS Home » Plains Area » Miles City, Montana » Livestock and Range Research Laboratory » Research » Publications at this Location » Publication #412504
Research Project: Identifying and Mitigating Factors that Limit Beef Production Efficiency

Location: Livestock and Range Research Laboratory

Title: Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle

Author
item ZHU, BO - Chinese Academy Of Agricultural Sciences
item WANG, TIANZHEN - Chinese Academy Of Agricultural Sciences
item NIU, QUNHAO - Chinese Academy Of Agricultural Sciences
item WANG, ZEZHAO - Chinese Academy Of Agricultural Sciences
item Hay, El Hamidi
item XU, LEI - Chinese Academy Of Agricultural Sciences
item CHEN, YAN - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item GAO, XUE - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item CAO, YANG - Chinese Academy Of Agricultural Sciences
item XHAO, YUMING - Chinese Academy Of Agricultural Sciences
item LI, JUNYA - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2025
Publication Date: 2/10/2025
Citation: Zhu, B., Wang, T., Niu, Q., Wang, Z., Hay, E.A., Xu, L., Chen, Y., Zhang, L., Gao, X., Gao, H., Cao, Y., Xhao, Y., Li, J., Xu, L. 2025. Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle. Communications Biology. 8. Article 208. https://doi.org/10.1038/s42003-025-07604-z.
DOI: https://doi.org/10.1038/s42003-025-07604-z

Interpretive Summary: In this study, we investigated the fat composition of muscle in Chinese Simmental cattle to better understand meat quality. Using a genetic analysis called Genome-wide Association Study (GWAS) with imputed SNPs, we explored the genetic factors influencing fatty acids. Over 7,500 SNPs were identified, each associated with different fatty acids, including some linked to specific genes. We uncovered novel variants and potential genes related to fatty acid traits and most notably FASN candidate gene. This research contributes to our understanding of the genetic aspects of fatty acids in beef cattle, helping in future selection programs for improved meat quality.

Technical Abstract: Background Fatty acid composition of muscle is an important indicator for meat quality. Genome-wide association study (GWAS) analysis using imputed SNPs can provide an alternative way to comprehensively understand the genetic bases underlying these traits in cattle. To obtain the candidate causal variants for fatty acids (FAs), we first evaluated the accuracy of imputation from high-density SNP array to sequencing dataset, and then performed GWAS to explore the association between imputed SNPs and fatty acids in Chinese Simmental cattle. Results We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 1252 Simmental cattle using both Beagle and Minimac software. The accuracy of imputation varied considerably across chromosomes and deceased at genome regions where SNPs have low MAF. We observed the correlation between imputed and true genotypes ranged from 0.898 to 0.952. Using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach, we identified a total of 7,509 SNPs associated with sixteen fatty acid composition in Step I association based on imputed sequencing dataset (approximately 10.6 million SNPs). In this study, a total of 2,791 non-redundant variants were identified for FAs, and among them, 68 SNPs can be found in the Bovine HD panel, while 2,723 novel SNPs were detected from imputed SNPs. Of these 7,509 significant SNPs, 1864 SNPs were identified for saturated fatty acids, 1750 SNPs for monounsaturated fatty acids, and 3895 SNPs for polyunsaturated fatty acids. Then, we further identified 95 candidate SNPs (P> 9.39E-8) for 11 fatty acid composition including C14:0, C20:0, C24:0, C14:1, C18:3a, C20:1, C20:2, C24:4, C22:6 DHA, CLA_C9_T11, CLA_C12_T10 using step II association analysis. We observed 95 SNPs were overlapped with five candidate genes (CCDC57, FASN, HDAC11, ALG14 and ZMAT4). Notably, we found one SNP at 48.6 Mb on BTA3 showing significant association for multiple traits (C20_0, C20_2, C20_4, CLA_C9_T11 and CLA_T10_C12), which was within ALG14. We also detected one 130 kb region located at 51.2 Mb on BTA19 for C14:0, this region was overlapped with CCDC57. Moreover, we found 12 candidate SNPs with MAF between 0.01 and 0.02, which were annotated as missense variants that cause amino acid changes in proteins. These SNPs were found overlapped with several genes including BCAS1, MYBL1, TANGO6, MCMDC2, DCT, FSHB, CSF2RB and RRS1. Conclusions Our results revealed several novel variants for FAs by using the imputed whole genome sequence data. Our finding will contribute the understanding of genetic architecture for FAs, and further promote the identifications of candidate regions and causal variants for selection program in beef cattle.