Genome-wide association analyses for growth and feed efficiency traits in beef cattle1

Abstract

A genome-wide association study using the Illumina 50K BeadChip included 38,745 SNP on 29 BTA analyzed on 751 animals, including 33 purebreds and 718 crossbred cattle. Genotypes and 6 production traits: birth weight (BWT), weaning weight (WWT), ADG, DMI, midtest metabolic BW (MMWT), and residual feed intake (RFI), were used to estimate effects of individual SNP on the traits. At the genome-wide level false discovery rate (FDR < 10%), 41 and 5 SNP were found significantly associated with BWT and WWT, respectively. Thirty-three of them were located on BTA6. At a less stringent significance level (P < 0.001), 277 and 27 SNP were in association with single traits and multiple traits, respectively. Seventy-three SNP on BTA6 and were mostly associated with BW-related traits, and heavily located around 30 to 50Mb. Markers that significantly affected multiple traits appeared to impact them in same direction. In terms of the size of SNP effect, the significant SNP (P < 0.001) explained between 0.26 and 8.06% of the phenotypic variation in the traits. Pairs of traits with low genetic correlation, such as ADG vs. RFI or DMI vs. BWT, appeared to be controlled by 2 groups of SNP; 1 of them affected the traits in same direction, the other worked in opposite direction. This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting growth and feed efficiency traits in beef cattle.

Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers

“…This same study also reported QTL for mature body weight and mature height slightly further downstream at 53 Mb on the UMD 3.1 genome assembly. In addition, several other SNPs in a GWAS at BTA15:42.7-42.8 Mb were associated with birth weight in a study by Lu et al (2013). Thus there is additional evidence that a gene(s) in this region contributes to GN in cattle.…”

Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves

“…There were 14, 8, and 9 SNP loci detected as associated with birth weight at the p < 0.001, < 0.01, and < 0.05 levels respectively (Table S1); corresponding numbers in Bos taurus studies were 35, 91, and 339 (Snelling et al , 2010), and 105, 527, and 2,095 (Lu et al , 2013). The majority of detected loci (30 of 31) were from BTA14:16.3 to 28.4 Mb.…”

Livestock and the promise of genomics

“…Associated benefits from the Canadian Cattle Project include the identification of causal mutations and an understanding of how different forms of genetic variation such as indels, copy number variants, and nonadditive variation can be used for genetic improvement in cattle (Lu et al 2013). Consequently, the project aims to deliver immediate benefits for breeders and also lays the foundation for the next generation of technologies, including improved capability for ensuring the environmental sustainability of beef and dairy cattle production.…”