Genome-wide association study of concentrations of iron and other minerals in longissimus muscle of Angus cattle1

Abstract

The objective of this study was to characterize variation and identify SNP and chromosomal regions associated with mineral concentrations in LM of Angus beef cattle. Samples of LM from 2,285 Angus cattle were obtained, and concentrations of 7 minerals, including iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Genomic DNA extracted from the ground beef sample used for mineral composition was genotyped with the Bovine SNP50 Infinium II BeadChip, and effects of SNP on each trait were estimated using the Bayes-Cπ module of GenSel software. Pedigree-based estimates of heritabilities and corresponding genetic variances indicate iron was the only mineral concentration that could be considered a good candidate for manipulation by genomic selection. The amount of variation that could be accounted for by SNP genotypes was concordant with pedigree-based heritabilities and varied from very low for potassium and sodium (<0.09) to medium high (0.37) for iron. Although significant chromosomal regions were identified for all minerals analyzed in this study, further study focused on iron. Seven regions on 6 chromosomes (1, 2, 7, 10, 15, and 28) were identified to have a major effect on the iron content of LM in Angus cattle. The accuracy of direct genomic values (DGV) for iron concentration was estimated using a 5-fold cross-validation strategy. The accuracy of DGV estimated as the genetic correlation between DGV and the phenotype (iron concentration) adjusted for contemporary groups was 0.59. A bivariate animal model was used to estimate genetic correlations between iron concentrations and a reduced set of economically important carcass traits: HCW, rib eye area, calculated USDA yield grade, percent KPH, and marbling score. The genetic correlations between iron concentration and HCW, percentage KPH, marbling score, and rib eye area were small (-0.19 to 0.15) and nonsignificant. Although still weak (0.22), a positive significant genetic correlation was identified between iron content and USDA calculated yield grade. Beef is a major contributor of iron and zinc in the human diet, and this study found that iron content might be effectively manipulated through marker-assisted selection programs, without compromising other carcass and palatability traits.

Genome wide association study of cholesterol and poly- and monounsaturated fatty acids, protein, and mineral content of beef from crossbred cattle

“…Mateescu et al (2013a) estimated the heritability based on pedigree information and phenotypic data to be 0.48, 0.00, and 0.15 for LTL iron, potassium, and sodium, respectively. The proportions of phenotypic variation explained by the BovineSNP50 assay were 0.37, 0.03, and 0.09 for iron, potassium and sodium, respectively (Mateescu et al, 2013b). These results are in general agreement with the findings of the current study for the traits of iron and sodium.…”

“…This is supported by Wiener et al (2009) who showed a significant effect of the myostatin mutation in South Devon cattle for both PUFA and MUFA concentrations. Outside of the myostatin mutation, Mateescu et al (2013b) reported 16 SNP in a single Mb region (103-104 Mb) on BTA2 to explain 1.33% of the phenotypic variation of iron content, although the region reported by Mateescu et al (2013b) does not overlap with the regions reported in the current study.…”

“…Considerable attention has been placed on improving the nutritional value of beef and the development of products that are beneficial to human health and disease prevention (Scollan et al, 2006). It has been illustrated that animal nutritional regime differences can alter the nutrient profile of beef (Realini, Duckett, Brito, Rizza, & De Mattos, 2004) and that genetic factors can also play a role (De Smet et al, 2004;Mateescu et al, 2013a;Mateescu et al, 2013b). Identification of genetic variants that would allow producers to select for optimum nutritional values with respect to fatty acids, minerals, and vitamins, without sacrificing performance or product quality, could ultimately increase value and consumer satisfaction of beef.…”

Detection of quantitative trait loci for mineral content of Nelore longissimus dorsi muscle

“…The estimates of additive genetic and residual variance from the BayesC analyses were then used to run the BayesB analyses [18] to estimate SNP effects. The parameter π was set to 0.9995 such that the number of SNP effects to be estimated was less than the number of animals with data (449 364 × (1 - π) = 224 SNPs), as suggested by Mateescu et al [9]. The BayesB analysis fits separate variances for each SNP in the model, which allows large-effect SNPs to be estimated without excessively regressing their effects towards 0.…”

“…Furthermore, it has been shown that mineral content in tissues is in part genetically determined and heritable [8,9] and that the genes involved may act via receptor, transporter and chaperone proteins [1]. …”