March 28, 2018

Interpretive Summary: Development and Validation of a Small SNP Panel for Feed Efficiency in Beef Cattle

Interpretive Summary: Development and validation of a small SNP panel for feed efficiency in beef cattle

By Anne Zinn

In a recent study published in the February 2018 edition of the Journal of Animal Science, a research time at the University of Alberta developed and validated a cost-effective small single nucleotide polymorphism (SNP) marker panel for genetic improvement of feed efficiency in beef cattle. 

Part of improving beef cattle production is selecting beef cattle with feed efficiency or low residual feed take. Benefits include reduced feed intake without compromising growth or product quality and reducing the environmental footprint, which can lead to increased profits for producers. This means it is important to identify efficient animals and utilize them for breeding and productions purposes.  Measuring individual feed efficiency can be expensive and time-consuming; using genomics offers a potential alternative with the ability to immediately predict feed efficiency at a young age. Therefore, the objective of this study was to develop and validate a customized, cost-effective SNP panel for genetic improvement of feed efficiency. 

To begin, previous association studies were analyzed and a comprehensive literature search was performed to identify genes or SNPs associated with feed efficiency traits and its components. These SNPs were then screened for their functional impact and allele frequency in Angus and Hereford breeds and association analyses were performed on genotypes of 159 SNPs for 871 Angus, Hereford, and Angus-Hereford crossbred cattle. 

A total of 63 SNPs within 43 genes showed a significant association with at least one trait. Results showed that the minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI), minor alleles of SNPs within MK167 gene were associated with increasing effects on RFI, and the minor allele of 137400016 SNP within CNTR was associated with increasing average daily gain. Additionally, the SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects while other SNPs located in SMARCAL1, ANXa2, CACNA1G, and PHYHIPL genes showed additive effects of RFI. The gene enrichment analysis indicated that glad development, ion, and cation transport are important mechanisms contributing to variations in feed efficiency traits and revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTER, OSMR, and GHR genes, which could be useful for genetic selection for feed efficiency. 

The results of this study can be used in practice by the beef industry to increase feed efficiency, reduce waste, and need to be taken into consideration in any cross breeding system to optimize useful allele combinations. This small SNP panel can be used to generate molecular breeding values for feed efficiency at a relatively low cost. Results of this study suggest further testing in other populations, including a wider variety of crossbreed cattle, is warranted to continue making improvements in the beef cattle industry. 

The full title of this paper is, "Development and validation of a small SNP panel for feed efficiency in beef cattle," and can be found here.