Robert L. Weaber

Genome-wide association analysis for feed efficiency in Angus cattle

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41 028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.

Evaluation of physiological and blood serum differences in heat-tolerant (Romosinuano) and heat-susceptible (Angus) Bos taurus cattle during controlled heat challenge.

A study was performed to evaluate differences in thermoregulatory ability of 2 Bos taurus breeds with known differences in heat tolerance. Nine Angus (AG; 304 +/- 7 kg of BW) and 9 Romosinuano (RO; 285 +/- 7.5 kg of BW) steers were transported to the Brody Environmental Center at the University of Missouri. Steers were housed for 18 d at thermoneutrality (TN; 21 degrees C) before initiation of heat stress (HS), which consisted of daily cyclic air temperature (26 degrees C, night; 36 degrees C, day) for 14 d. Rectal temperature and respiration rate were measured 6 times daily throughout the study. Sweat rates at shaved skin sites were recorded on specific days. Blood samples were taken once per week. Angus steers maintained rectal temperature 0.5 degrees C greater than RO at TN (P < 0.001). Likewise, respiration and sweat rates were greater (P < 0.001) in AG than RO at TN (P < 0.05). Rectal temperature increased during HS for both breeds with AG maintaining greater temperatures (P < 0.001). Both breeds increased respiration rate during HS, with AG steers exhibiting the greater rate (P < 0.001). Sweat rate increased more than 4-fold during HS (P < 0.001), followed by reduction after 7 d. Even after HS acclimation, AG exhibited the greater sweat rate (P < 0.001). Breed differences for serum leptin, creatinine, and cholesterol were found throughout the study with AG being greater than RO. Although there were no breed differences (P = 0.21) at TN, only AG steers exhibited a HS-induced increase (P < 0.05) in prolactin, creatinine, and cholesterol concentrations to suggest that an increase in rectal temperature is required for this effect. Use of rectal temperature along with endocrine markers, such as prolactin, may aid in the identification of B. taurus sensitivity to heat.

Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle.

BackgroundMolecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population.ResultsResults were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle.ConclusionsThis research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

Summary We performed a genome-wide association study for Warner–Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within μ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31–0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.

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

BackgroundThe 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 50xa0K and 770xa0K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmentalu2009×u2009Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake.ResultsA 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 23xa0Mb 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 38xa0Mb and BTA 7 at 93xa0Mb 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.ConclusionsThis 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.

Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

Determinants of bovine thermal response to heat and solar radiation exposures in a field environment

Continuous exposure of cattle to summer heat in the absence of shade results in significant hyperthermia and impairs growth and general health. Reliable predictors of heat strain are needed to identify this condition. A 12-day study was conducted during a moderate summer heat period using 12 Angus x Simmental (Bos taurus) steers (533u2009±u200912xa0kg average body weight) to identify animal and ambient determinations of core body temperature (Tcore) and respiration rate (RR) responses to heat stress. Steers were provided standard diet and water ad libitum, and implanted intraperitoneally with telemetric transmitters to monitor Tcore hourly. Visual count of flank movement at 0800 and 1500xa0hours was used for RR. Dataloggers recorded air temperature (Ta), and black globe temperatures (Tbg) hourly to assess radiant heat load. Analysis was across four periods and 2 consecutive days averaged within each period. Average Ta and Tbg increased progressively from 21.7 to 30.3°C and 25.3 to 34.0°C, respectively, from the first to fourth periods. A model utilizing a quadratic function of Ta explained the most variation in Tcore (R2u2009=u20090.56). A delay in response from 1 to 3xa0h did not significantly improve R2 for this relationship. Measurements at 0800 and 1500xa0hours alone are sufficient to predict heat strain. Daily minimum core body temperature and initial 2-h rise in Ta were predictors of maximum core temperature and RR. Further studies using continuous monitoring are needed to expand prediction of heat stress impact under different conditions.

The Economic Value of Improvements in Beef Tenderness by Genetic Marker Selection

A genetic simulation model is combined with an economic model of the U.S. beef industry to determine how consumer demand shifts, resulting from bull and heifer selection strategies that improve steak tenderness, affect economic profitability at four points in the beef supply chain. The results indicate that a selection strategy in which bulls in the upper 30% of genetic merit are selected each year would result in increased profitability of

Parâmetros e tendência genética de peso de bovinos criados á pasto no Brasil

9.60/head for feeder cattle and

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

1.23/head for fed cattle in 20 years. The net present value of the genetic improvement program is estimated to produce economic benefits of