Weighted single‐step genome‐wide association study and pathway analyses for feed efficiency traits in Nellore cattle

Abstract

The aim was to conduct a weighted single‐step genome‐wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein‐coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p‐value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int‐1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE‐related traits.

Gene networks for three feed efficiency criteria reveal shared and specific biological processes

“…Glucagon reduces glucose utilisation in adipose tissue, stimulates lipolysis and increases gluconeogenesis. This pathway was also highlighted in Nellore cattle [ 53 ] and the ADCY2 gene was identified in both our study and [ 53 ].…”

“…Linked to this protease, the thrombin signalling pathway was also enriched in a study that performed Ingenuity Pathway Analysis [ 37 ]. Moreover, the thrombin receptor signalling pathway was reported in [ 53 ] and two of the genes, F2RL2 and IQGAP2 , detected in [ 53 ], were found in our study. Both the RG and FE networks also enriched several processes related to the vascular system, such as renin secretion, hematopoietic progenitor cell differentiation, smoothened signalling pathway and platelet activation (see Fig.…”

Genomics of seasonal hair shedding and ecoregion-specific growth to identify environmentally-adapted beef cattle

“…For the direct effect of weaning weight, associations were mostly shared across S3.2); KCNIP4 and SLIT2 on BTA6 [17,129]; FBXO32 and ATAD2 on BTA14 [130,131]; METTL15 on BTA15 [132]). In all 3 regions, QTL enrichment analyses identified known large-effect growth QTL including those near ARRDC3, ERGIC1 and BNIP1 ( [133,134]; Table S3.2).…”

The search for genetic functional variants of feed efficiency in Nelore cattle

“…We also unravel the metabolic pathways related to FE in Nellore cattle showing an increased bacterial load in low feed efficient animals which is in part responsible for the hepatic lesions and inflammation in these animals [16]. Previously, some QTL's for feed efficiency in Nellore beef cattle were found by conventional GWAS [17][18][19][20][21], however only attempts to find causal variants were done.…”

“…The relationship matrix used in the analyses was calculated based on pedigree information from 19,507 animals, provided by the Nelore Brazil Breeding Program, coordinated by the National Association of Breeders and Researchers. More information regarding the set of animals used in this study can be found elsewhere[18].3.2.6.2. Genomic informationPhenotypic and genotypic records from the Nelore Brazil breeding program coordinated by the National Association of Farmers and Researchers (Associação Nacional de Criadores e Pesquisadores -ANCP, Ribeirão Preto-SP, Brazil) were used for this study.…”