Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

Abstract

Improvement in feed conversion efficiency can improve the sustainability of beef cattle production, but genomic selection for feed efficiency affects many underlying molecular networks and physiological traits. This study describes the differences between steer progeny of two influential Angus bulls with divergent genomic predictions for residual feed intake (RFI). Eight steer progeny of each sire were phenotyped for growth and feed intake from 8 mo. of age (average BW 254 kg, with a mean difference between sire groups of 4.8 kg) until slaughter at 14–16 mo. of age (average BW 534 kg, sire group difference of 28.8 kg). Terminal samples from pituitary gland, skeletal muscle, liver, adipose, and duodenum were collected from each steer for transcriptome sequencing. Gene expression networks were derived using partial correlation and information theory (PCIT), including differentially expressed (DE) genes, tissue specific (TS) genes, transcription factors (TF), and genes associated with RFI from a genome-wide association study (GWAS). Relative to progeny of the high RFI sire, progeny of the low RFI sire had -0.56 kg/d finishing period RFI (P = 0.05), -1.08 finishing period feed conversion ratio (P = 0.01), +3.3 kg^0.75 finishing period metabolic mid-weight (MMW; P = 0.04), +28.8 kg final body weight (P = 0.01), -12.9 feed bunk visits per day (P = 0.02) with +0.60 min/visit duration (P = 0.01), and +0.0045 carcass specific gravity (weight in air/weight in air—weight in water, a predictor of carcass fat content; P = 0.03). RNA-seq identified 633 DE genes between sire groups among 17,016 expressed genes. PCIT analysis identified >115,000 significant co-expression correlations between genes and 25 TF hubs, i.e. controllers of clusters of DE, TS, and GWAS SNP genes. Pathway analysis suggests low RFI bull progeny possess heightened gut inflammation and reduced fat deposition. This multi-omics analysis shows how differences in RFI genomic breeding values can impact other traits and gene co-expression networks.

Liver morphometrics and metabolic blood profile across divergent phenotypes for feed efficiency in the bovine

“…Additionally, albumin is solely produced in hepatocytes and is a relatively abundant and large molecule [39] and understanding that the machinery associated with albumin synthesis and secretion represents a large portion of the cytoplasm of hepatocytes [40]. We suggest that the myriad of liver functional differences (i.e., [31, 32]) influencing feed efficiency could be related to the processes involved with production, storage and secretion of albumin by the hepatocytes, which ultimately could influence the histomorphometric differences observed herein. We hypothesize that the secretion of this protein may be enhanced in inefficient animals, resulting in a lower accumulation of albumin in the hepatocytes and partially explaining the diminished cell size in response to lower feed efficiency.…”

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

“…Purinergic receptors have been identified as important drivers of immune responses in cattle 39 . Selection on immune genes and pathways is likely driven by the increased production efficiency of healthy calves 41,42 . Shared selection on SLC2A5 and BIRC5 point towards biological pathways involved in sensing carbohydrate, hexose, and monosaccharide stimuli (Benjamini-Hochberg adjusted p-values = 0.01).…”

Differential expression of genes related to gain and intake in the liver of beef cattle

“…Weber et al [7] found differentially expressed genes involved in lipid metabolism and inflammation were down-regulated in the livers of low RFI Angus bull progeny. In 2011 Chen [8] found that low RFI bulls tended to have an up-regulation of genes related to the extracellular matrix and a down-regulation of genes involved in xenobiotic metabolism.…”