Abstract
Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10−5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
Highlights
Feed can account for more than 75% of variable costs of beef enterprises[1]
As well as single nucleotide polymorphisms (SNPs) that are used for the genomic selection programme, the International Dairy and Beef (IDB) chip contains SNPs for parentage verification and SNPs included for research purposes only[13]
genome-wide association studies (GWAS) results generated for residual feed intake (RFI) by meta-analysis are plotted in GWAS and meta-analysis for average daily gain (ADG)
Summary
Feed can account for more than 75% of variable costs of beef enterprises[1]. selection of cattle that efficiently convert feed to carcass growth would improve farm profits due to reducing expenditure on feed while maintaining protein output[2]. Identification of genetic markers for RFI and component traits, such as FI and average daily gain (ADG), and their incorporation into genomic assisted breeding programmes would enable more rapid and cost effective selection of feed efficient cattle[8]. As well as single nucleotide polymorphisms (SNPs) that are used for the genomic selection programme, the IDB chip contains SNPs for parentage verification and SNPs included for research purposes only[13] This includes a selected subset of SNPs associated with RFI in cattle populations outside of Ireland[15,16,17,18,19,20,21] which have been added to the IDB chip for research purposes to validate their use as biomarkers of RFI and associated traits in Irish beef cattle (n = 102, Supplementary Table S1). This breed heterogeneity coupled with the challenges in obtaining sufficient numbers of RFI phenotypes for GWAS are primary reasons for the difficulty in applying GWAS on a large-scale basis for RFI to beef cattle in Ireland and most other beef producing nations
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