Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array

Abstract

BackgroundFatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying important traits in cattle. In this study, we performed GWAS using high density SNP array to analyze the association between SNPs and fatty acids and evaluated the accuracy of genomic prediction for fatty acids in Chinese Simmental cattle.ResultsUsing the BayesB method, we identified 35 and 7 regions in Chinese Simmental cattle that displayed significant associations with individual fatty acids and fatty acid groups, respectively. We further obtained several candidate genes which may be involved in fatty acid biosynthesis including elongation of very long chain fatty acids protein 5 (ELOVL5), fatty acid synthase (FASN), caspase 2 (CASP2) and thyroglobulin (TG). Specifically, we obtained strong evidence of association signals for one SNP located at 51.3 Mb for FASN using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approaches. Also, region-based association test identified multiple SNPs within FASN and ELOVL5 for C14:0. In addition, our result revealed that the effectiveness of genomic prediction for fatty acid composition using BayesB was slightly superior over GBLUP in Chinese Simmental cattle.ConclusionsWe identified several significantly associated regions and loci which can be considered as potential candidate markers for genomics-assisted breeding programs. Using multiple methods, our results revealed that FASN and ELOVL5 are associated with fatty acids with strong evidence. Our finding also suggested that it is feasible to perform genomic selection for fatty acids in Chinese Simmental cattle.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3847-7) contains supplementary material, which is available to authorized users.

Genomic selection of milk fatty acid composition in Sarda dairy sheep: Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy

“…Other studies in sheep underlined the higher accuracy of genomic methods compared with the pedigree-based approach for milk and meat production traits (Daetwyler et al, 2012;Legarra et al, 2014;Baloche et al, 2014). Moreover, GS studies carried out in beef cattle on muscle FA composition reported for some of FA also investigated in this study a similar pattern of GEBV accuracy (Chen et al, 2015;Chiaia et al, 2017;Zhu et al, 2017).…”

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Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression

“…The accumulation of fatty acids in muscle is a dynamic process that is regulated by multiple biological processes, including lipogenesis, fatty acid uptake and fatty acid βoxidation [17][18][19][20]. Large efforts have been made to identify the genes and gene networks associated with fatty acid composition traits in pigs and cattle [21][22][23]. In addition, several works have aimed to understand the lipid deposition in breast muscle of poultry using approaches such as transcriptomic, proteomic and metabolomic analysis.…”

Genome-wide association study for milk production traits in a Brazilian Holstein population

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