Genome-wide association study of temperament and tenderness using different Bayesian approaches in a Nellore–Angus crossbred population
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Genomic prediction models using Bayesian inference determine marker associations based on available data. The objective of this study was to evaluate marker associations for two traits using different Bayesian models applied to a crossbred population. Nellore-Angus F2, F3 and half-sibling calves were used with records for overall temperament at weaning (TEMP; a subjective scoring system on a 1-9 scale, where 1 is docile or calm and 9 is wild or unruly; n=769) and Warner-Bratzler shear force (WBSF; a measure of tenderness; n=387). After quality control filtering, there were 34,913 SNP markers distributed across the genome available for use (excluding the Y chromosome). An unknown proportion of these markers (designated as π) were assumed not to contribute to the variation in these traits. Bayesian methods employed were BayesC to estimate the ideal π (i.e., value that used as few markers as possible while maintaining heritability, designated as π~). For WBSF or TEMP, π~=0.995 or 0.997, respectively. Then BayesB (using π~) or BayesC (using π=0 or π~) were fitted to estimate SNP marker effects. Markers were mapped to genes closest to their placement on Bos taurus UMD 3.1 assembly and grouped into 1Mb windows to identify associated regions, where association was determined based on the posterior probability of association of that window being greater than 0.75. No regions associated with either trait were found using π~, but with π=0, 37 and 147 regions were found to account for more variation than expected under an infinitesimal model for TEMP and WBSF, respectively. Genes from windows identified as associated were used to conduct enrichment analyses. Significant ontology terms related to sodium ion transport and activity, especially voltage-gated channel activity were identified for TEMP, which could be identifying genetic differences between nervous system response to environment and stress stimuli in this population. For WBSF, significant ontology terms related to activity of serine peptidases were identified, but little is known about their true role in muscle tenderness, although they are known to be expressed in muscle. © 2013 Elsevier B.V.
author list (cited authors)
Hanna, L., Garrick, D. J., Gill, C. A., Herring, A. D., Riggs, P. K., Miller, R. K., Sanders, J. O., & Riley, D. G.