Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle

Abstract

BackgroundIdentification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet management. In this study, 81 and 83 fatty acid traits were measured in subcutaneous adipose (SQ) and longissimus lumborum muscle (LL), respectively, from 1366 purebred and crossbred beef steers and heifers that were genotyped on the Illumina BovineSNP50 Beadchip. The objective was to conduct genome-wide association studies (GWAS) for the fatty acid traits and to evaluate the accuracy of genomic prediction for fatty acid composition using genomic best linear unbiased prediction (GBLUP) and Bayesian methods.ResultsIn total, 302 and 360 significant SNPs spanning all autosomal chromosomes were identified to be associated with fatty acid composition in SQ and LL tissues, respectively. Proportions of total genetic variance explained by individual significant SNPs ranged from 0.03 to 11.06 % in SQ, and from 0.005 to 24.28 % in the LL muscle. Markers with relatively large effects were located near fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), and thyroid hormone responsive (THRSP) genes. For the majority of the fatty acid traits studied, the accuracy of genomic prediction was relatively low (<0.40). Relatively high accuracies (> = 0.50) were achieved for 10:0, 12:0, 14:0, 15:0, 16:0, 9c-14:1, 12c-16:1, 13c-18:1, and health index (HI) in LL, and for 12:0, 14:0, 15:0, 10 t,12c-18:2, and 11 t,13c + 11c,13 t-18:2 in SQ. The Bayesian method performed similarly as GBLUP for most of the traits but substantially better for traits that were affected by SNPs of large effects as identified by GWAS.ConclusionsFatty acid composition in beef is influenced by a few host genes with major effects and many genes of smaller effects. With the current training population size and marker density, genomic prediction has the potential to predict the breeding values of fatty acid composition in beef cattle at a moderate to relatively high accuracy for fatty acids that have moderate to high heritability.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0290-0) 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).…”

“…In dairy sheep, the molecular basis of FA has been investigated by candidate gene (Crisà et al, 2010;Moioli et al, 2012), and QTL detection approaches. Genomic selection studies for FA compositions are limited to beef cattle (Uemoto et al, 2011;Chen et al, 2015;Zhu et al, 2017) and meat sheep (Rovadoscki et al, 2018). One of the main advantages of GS over traditional selection is that, once a reference population with both phenotypic and genotypic records has been settled, breeding values of animals without their own phenotypes can be predicted with a reasonable accuracy (Meuwissen et al, 2001;Hayes et al, 2009).…”

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

“…Of the five major enriched molecular and cellular biological functions, lipid metabolism was common to all the four traits, with synthesis of lipids including triglycerides appearing as a very important subfunction or process. Lipid metabolism has also been identified as an enriched molecular process for feed efficiency traits in beef cattle in several transcriptome studies [63][64][65]. In finishing beef cattle, deposition of fat requires more energy than protein because protein synthesis is energetically more efficient than fat synthesis [12,66].…”

A genetic analysis of meat compositions in Japanese Black cattle: Genetic parameters and sex influence

“…For example, carnosine, anserine and taurine have been suggested to be associated with health benefits (Hipkiss, 2009;Huxtable, 1992). Whereas genetic parameters for fatty acid compositions in beef have been reported relatively frequently (Chen et al, 2015;Inoue, Kobayashi, Shoji, & Kato, 2011;Nogi, Honda, Mukai, Okagaki, & Oyama, 2011;Onogi et al, 2015;Saatchi et al, 2013), reports on genetic parameters for other meat components, such as free amino acids and peptides, have been still limited (Mateescu et al, 2012;Sakuma et al, 2016). Thus, our first aim was to investigate genetic parameters for 51 meat components, including free amino acids, peptides and fatty acid compositions in a large Japanese Black cattle population.…”

“…Although sex differences in genetic variance are generally small in economic traits, large differences occasionally have been reported in the growth and carcase traits (Garrick, Pollak, Quaas, & Van Vleck, 1989;St alhammar & Philipsson, 1997). Genetic analyses of meat compositions are usually conducted in one sex (Inoue et al, 2011;Sevane et al, 2013) or treat sex as fixed effect (Chen et al, 2015;Nogi et al, 2011;Onogi et al, 2015;Saatchi et al, 2013;Sakuma et al, 2016). Hence, sex differences in genetic parameters and gene-sex interactions remain unstudied in any breed.…”