Abstract
Single nucleotide polymorphisms (SNPs) associated with average daily gain (ADG) and dry matter intake (DMI), two major components of feed efficiency in cattle, were identified in a genome-wide association study (GWAS). Uni- and multi-SNP models were used to describe feed efficiency in a training data set and the results were confirmed in a validation data set. Results from the univariate and bivariate analyses of ADG and DMI, adjusted by the feedlot beef steer maintenance requirements, were compared. The bivariate uni-SNP analysis identified (P-value <0.0001) 11 SNPs, meanwhile the univariate analyses of ADG and DMI identified 8 and 9 SNPs, respectively. Among the six SNPs confirmed in the validation data set, five SNPs were mapped to KDELC2, PHOX2A, and TMEM40. Findings from the uni-SNP models were used to develop highly accurate predictive multi-SNP models in the training data set. Despite the substantially smaller size of the validation data set, the training multi-SNP models had slightly lower predictive ability when applied to the validation data set. Six Gene Ontology molecular functions related to ion transport activity were enriched (P-value <0.001) among the genes associated with the detected SNPs. The findings from this study demonstrate the complementary value of the uni- and multi-SNP models, and univariate and bivariate GWAS analyses. The identified SNPs can be used for genome-enabled improvement of feed efficiency in feedlot beef cattle, and can aid in the design of empirical studies to further confirm the associations.
Highlights
Optimization of feed efficiency in livestock production demands the consideration of the system inputs and outputs
The positive genetic correlation supports the hypothesis that SNP alleles that have positive association with Average daily gain (ADG) and negative association with Dry matter intake (DMI) could be identified and could assist with genome-based improvement feed efficiency in beef cattle
The bivariate analysis detected the highest number of SNPs (11 SNPs) followed by the univariate analyses of DMI (9 SNPs) and ADG (8 SNPs)
Summary
Optimization of feed efficiency in livestock production demands the consideration of the system inputs and outputs. In feedlot beef cattle enterprises, feed consumption dominates the input (and costs) and weight gain dominates the output (and return). The cost of feed represents 62% to 84% of the total costs in a beef cattle production unit [1]. Dry matter intake (DMI) per day and animal is a frequently used indicator of feed consumption. 70 to 75% of the total energy feed intake is spent on maintenance functions (e.g. body temperature, digestion) in beef cattle [2]. Metabolic body weight (MBW) per animal, computed as BW0.73, is an accepted indicator of maintenance requirements
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