Genome‐wide association studies pathway‐based meta‐analysis for residual feed intake in beef cattle

Abstract

Genome-wide association studies (GWASes) have been performed to search for genomic regions associated with residual feed intake (RFI); however inconsistent results have been obtained. A meta-analysis may improve these results by decreasing the false-positive rate. Additionally, pathway analysis is a powerful tool that complements GWASes, as it enables identification of gene sets involved in the same pathway that explain the studied phenotype. Because there are no reports on GWAS pathways-based meta-analyses for RFI in beef cattle, we used several GWAS results to search for significant pathways that may explain the genetic mechanism underlying this trait. We used an efficient permutation hypothesis test that takes into account the linkage disequilibrium patterns between SNPs and the functional feasibility of the identified genes over the whole genome. One significant pathway (valine, leucine and isoleucine degradation) related to RFI was found. The three genes in this pathway-methylcrotonoyl-CoA carboxylase 1 (MCCC1), aldehyde oxidase 1 (AOX1) and propionyl-CoA carboxylase alpha subunit (PCCA)-were found in three different studies. This same pathway was also reported in a transcriptome analysis from two cattle populations divergently selected for high and low RFI. We conclude that a GWAS pathway-based metaanalysis can be an appropriate method to uncover biological insights into RFI by combining useful information from different studies.

Transcriptome Analysis of Ice Plant Growth-Promoting Endophytic Bacterium Halomonas sp. Strain MC1 to Identify the Genes Involved in Salt Tolerance

“…A total of 66 genes in MC1 strain were allocated to the valine, leucine, and isoleucine degradation pathway (Table 3). This pathway is highly related to residual feed intake [50]. A previous researcher has reported similar results and pointed out that leucine and isoleucine degradation occurs when Staphylococcus aureus is subjected to methicillin treatment in the presence of glucose [51].…”

Genetic mechanisms underlying feed utilization and implementation of genomic selection for improved feed efficiency in dairy cattle

“…In this context, genome-wide association studies (GWAS) and transcriptomics using RNA-sequencing (RNA-Seq) technology have contributed to the identification of functional candidate genes and genetic variants [e.g., SNPs, copy number of variations (CNVs), and insertions and deletions; Cánovas et al 2010;Wickramasinghe et al 2014]. In beef cattle, GWAS and transcriptomics studies using RNA-Seq have enabled the identification of key regulators of biological processes and pathways linked to feed efficiency variability, including lipid and protein metabolism, ion transport, protein and amino acid glycosylation, as well as valine, leucine, and isoleucine degradation (Rolf et al 2012;Abo-Ismail et al 2014;Olivieri et al 2016;Duarte et al 2019).…”

Comparing Alternative Single-Step GBLUP Approaches and Training Population Designs for Genomic Evaluation of Crossbred Animals

“…In other words, it does not indicate the complete inheritance mode of the trait, but the proportion of the total genetic variance explained by the simulated QTLs. The number of QTLs (198) was defined based on a systematic review performed for RFI in beef cattle (Duarte et al, 2019). In addition, simulations considering 4,500 QTLs were also performed, assuming that not all QTLs for RFI are currently known.…”