Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle.

BACKGROUND: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. RESULTS: Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). CONCLUSIONS: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

BACKGROUND: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental×Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. RESULTS: A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value<0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. CONCLUSIONS: This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.

Evaluation of peripartum supplementation of methionine hydroxy analogue on beef cow-calf performance.

The objective was to evaluate the effects of peripartum supplementation of a methionine hydroxy analogue (MHA) to primiparous, spring-calving beef females on dam and progeny performance. Angus heifers (n = 60) were blocked by expected parturition date, stratified by body weight (BW) and body condition score (BCS), and randomized to 1 of 15 pens. Pens were randomly assigned to 1 of 3 dietary treatments: a basal diet supplemented with 0 (M0), 15 (M15), or 30 (M30) g/animal/d of MHA (provided as MFP feed supplement, Novus International Inc., St. Charles, MO). Diets were fed from 45 ±â€…13 (SD) d pre-calving through 81 ±â€…13 d postpartum (DPP), after which all cow-calf pairs were managed as a single group on pasture until weaning (199 ±â€…13 DPP). Dam BW, BCS, and blood samples were taken at 6 predetermined timepoints. Progeny data were collected at birth, 2 intermediate timepoints, and at weaning. Milk samples were collected for composition analysis at 7 ±â€…2 DPP and at 55 ±â€…5 DPP. Serial progesterone samples were analyzed to establish resumption of cyclicity, and ultrasonography was performed at 55 ±â€…5 DPP to evaluate ovarian function. Cows were bred via artificial insemination at 82 ±â€…13 DPP and subsequently exposed to bulls for a 55-d breeding season. Pen was the experimental unit, and preplanned orthogonal contrasts were tested (linear effect and M0 vs. M15 + M30). Dam BW and BCS were not affected by treatment (P ≥ 0.29) throughout the study. Week 1 milk fat concentration increased linearly (P = 0.05) and total solids tended to increase linearly (P = 0.07) as MHA increased; however, no other milk components were affected (P ≥ 0.16). Treatment did not affect (P ≥ 0.16) dam reproductive parameters or progeny growth from birth until weaning. Post-calving, circulating methionine equivalents tended to linearly increase (P = 0.10) with increasing MHA supplementation. At breeding, plasma urea N linearly decreased (P = 0.03) with increased supplementation of MHA, and plasma non-esterified fatty acids were less (P = 0.04) in MHA-supplemented dams compared with dams receiving no MHA. Maternal circulating glucose, glutathione peroxidase, and thiobarbituric acid-reactive substances were not affected (P ≥ 0.15) by treatment at any point. These data indicate that peripartum supplementation of MHA may increase milk fat composition shortly after calving, but MHA supplementation did not improve progeny growth or dam reproductive performance in the current study.

Effect of varying trace mineral supplementation of steers with or without hormone implants on growth and carcass characteristics.

To determine the effects of trace mineral (TM) supplementation and hormone implant strategy on growth and carcass characteristics of cattle, 72 Angus-cross steers (388 ± 17 kg) were blocked by body weight (six steers per pen) to a 2 × 3 factorial. Factors included growth-stimulating implant (GS): day 0 with Component TE-IS, reimplanted day 56 with Component TE-200 (IMP) or no implant (NoIMP), and TM supplementation (TM): no supplemental TM (CON), TM supplemented at national (NASEM, 2016). Nutrient requirements of beef cattle. 8th ed. Washington, DC: The National Academics Press) recommendations of 10 Cu, 30 Zn, 20 Mn, 0.10 Se, 0.15 Co, and 0.50 I (mg/kg; REC), or TM supplemented at feedlot consultant recommendations of 20 Cu, 100 Zn, 50 Mn, 0.30 Se, 0.20 Co, and 0.50 I (mg/kg; IND). Steers received a finishing diet for 124 d in GrowSafe bunks and were harvested on day 125. Data were analyzed in SAS as a 2 × 3 factorial with steer as the experimental unit (n = 12 per combination). Day -7 liver trace mineral concentrations were used as a covariate in analysis. There were no GS × TM effects for liver Zn, Mn, Se, or Co (P ≥ 0.11) on day 70 or 125. Implanted steers had lesser liver Cu and Mn on day 70 (P ≤ 0.05) and day 125 compared with NoIMP. There was a GS × TM interaction for liver Cu on day 125 (P = 0.05) where IMP/REC, IMP/IND, and NoIMP/REC had greater liver Cu than NoIMP/CON, which had greater liver Cu than IMP/CON. There was a TM effect for liver Cu on day 70 (P < 0.01) with IND having greater liver Cu than REC and CON. There was a TM effect (P ≤ 0.01) for liver Mn and Se on day 70 where IND had greater Mn and Se than CON, with REC being intermediate. There was a TM effect (P < 0.01) on liver Mn on day 125 where IND had greater liver Mn than CON and greater (P < 0.01) liver Se than CON and REC on day 125, whereas day 125 liver Se was greater in REC vs. CON. Implanted steers had greater (P < 0.01) dry matter intake (DMI), final body weight (BW), overall average daily gain (ADG), G:F, and hot carcass weight (HCW) than NoIMP. Overall DMI was affected by TM (P < 0.01) with REC and IND being greater than CON. There was a TM effect for carcass-adjusted final BW, ADG, and DMI (P ≥ 0.03) and a tendency for TM to affect adjusted G:F (P = 0.07). There was a TM effect (P = 0.03) for HCW where IND was greater than CON and REC. There was a GS × TM (P = 0.02) for ribeye area (REA); within IMP, CON were greater than IND, whereas REC were intermediate while NoIMP had smaller REA, regardless of TM supplementation. Additional research is needed to better determine trace mineral requirements of finishing beef steers for optimal performance.