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.
Highlights
The largest variable costs in beef cattle production are feed and land [1]
Sire breeding values predict progeny of the low residual feed intake (RFI) sire to exhibit reduced intake with similar ADG relative to progeny of the high RFI sire, which was observed in the growing phase but not in the finishing phase
Larger finishing and carcass weights were observed in the progeny of the low RFI sire, as might be predicted from the higher pedigreebased breeding values of that sire for weaning weight (WW), yearling weight (YW), and mature weight (MW)
Summary
The largest variable costs in beef cattle production are feed and land [1]. Feed costs can be reduced by improving feed conversion efficiency without sacrificing production traits; one option for this is to consider residual feed intake (RFI; [2]). The heritability of RFI has been estimated to be as high as 42% in growing beef cattle [3], suggesting it has a strong genetic component and would respond to selective breeding While it is too expensive for all bull testing centers and feedlots to measure individual feed intake in order to calculate RFI, reference populations of animals possessing both RFI phenotypes and high density SNP genotypes have been used to generate predictions of total genetic merit [4] for RFI in major cattle breeds [5,6,7]. These genomic predictions can be a selection tool in the absence of direct phenotypic data
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