Whole genome association of SNP with newborn calf cannon bone length

Abstract

The objective of this study was to describe associations between 34,957 SNP genotypes and newborn calf cannon bone length in a crossbred Bos indicus–Bos taurus F2 population. Cannon bone length was measured on 463 newborn F2 Nelore–Angus calves from full-sibling families. All models included birth year–season of birth combinations and family as fixed effects. Two Bayesian association analyses were conducted; in those the estimated proportion of SNP loci not contributing to trait variance was 0.998. The proportion of Markov Chain Monte Carlo iterates in which 1Mb windows of SNP loci had detectable genetic variance was used as evidence of association; the largest of these ranged from 0.2 to 0.7 in the Bayesian analyses and included windows on BTA14 and BTA24. Single marker regression analysis identified 363 SNP loci associated with cannon bone length; the majority of these (323) were on BTA14. Separately, a preselected group of 860 SNP loci was evaluated, chosen based upon proximity to 38 genes with known influence on endochondral bone growth. Significant associations were detected for 18 loci in that analysis. Representative loci were chosen from linked SNP within those 18 to comprise the final set of 8 loci with detected association. Stepwise regression was utilized to select a subset of these that best accounted for variation in cannon bone length. Four markers in the physical regions of genes coding Vitamin D3 Receptor (VDR) and IGF-I receptor (IGF1R) as linear and linear×linear covariates explained 0.06 of the phenotypic variation in cannon bone length. This procedure using a preselected set of genes, however, resulted in omission of the large association on BTA14 detected in the other analyses. The identified chromosomal regions were consistent with others previously identified with genes influencing stature-type traits in cattle (e.g., PLAG1). No advantage of analyzing actual cannon bone length or breeding values was evident; many of the same regions were identified by both, but associations unique to one or the other were also detected.