Mean EPDs Reported by Different Breeds

Expected progeny differences (EPDs) have been the primary tool for genetic improvement of beef cattle for over 40 years beginning with evaluations of growth traits. Since that time, EPDs have been added for several other production traits such as calving ease, stayability, carcass merit and conformation. Most recently, several breed associations have derived economic indices from their EPDs to increase profit under different management and breeding systems. It is useful for producers to compare the EPDs of potential breeding animals with their breed average. The current EPDs from the most recent genetic evaluations of 26 breeds are presented in this report. Mean EPDs for growth traits are shown in Table 1 (26 breeds), for other production traits in Table 2 (20 breeds), and for carcass and composition traits in Table 3 (21 breeds). Several breeds also have EPDs and indices that are unique to their breed; these EPDs are presented in Table 4

Mean EPDs Reported by Different Breeds

Expected progeny differences (EPDs) have been the primary tool for genetic improvement of beef cattle for over 40 years beginning with evaluations of growth traits. Since that time, EPDs have been added for several other production traits such as calving ease, stayability, carcass merit and conformation. Most recently, several breed associations have derived economic indices from their EPDs to increase profit under different management and breeding systems. It is useful for producers to compare the EPDs of potential breeding animals with their breed average. The current EPDs from the most recent genetic evaluations of 26 breeds are presented in this report. Mean EPDs for growth traits are shown in Table 1 (26 breeds), for other production traits in Table 2 (20 breeds), and for carcass and composition traits in Table 3 (21 breeds). Several breeds also have EPDs and indices that are unique to their breed; these EPDs are presented in Table 4

Managing the risk of comparing estimated breeding values across flocks or herds through connectedness: a review and application

Comparing predicted breeding values (BV) among animals in different management units (e.g. flocks, herds) is challenging if units have different genetic means. Unbiased estimates of differences in BV may be obtained by assigning base animals to genetic groups according to their unit of origin, but units must be connected to estimate group effects. If many small groups exist, error of BV prediction may be increased. Alternatively, genetic groups can be excluded from the statistical model, which may bias BV predictions. If adequate genetic connections exist among units, bias is reduced. Several measures of connectedness have been proposed, but their relationships to potential bias in BV predictions are not well defined. This study compares alternative strategies to connect small units and assesses the ability of different connectedness statistics to quantify potential bias in BV prediction. Connections established using common sires across units were most effective in reducing bias. The coefficient of determination of the mean difference in predicted BV was a perfect indicator of potential bias remaining when comparing individuals in separate units. However, this measure is difficult to calculate; correlated measures such as prediction errors of differences in unit means and correlations among prediction errors are suggested as practical alternatives

Using pooled data for genomic prediction in a bivariate framework with missing data

Pooling samples to derive group genotypes can enable the economically efficient use of commercial animals within genetic evaluations. To test a multivariate framework for genetic evaluations using pooled data, simulation was used to mimic a beef cattle population including two moderately heritable traits with varying genetic correlations, genotypes and pedigree data. There were 15 generations (n = 32,000; random selection and mating), and the last generation was subjected to genotyping through pooling. Missing records were induced in two ways: (a) sequential culling and (b) random missing records. Gaps in genotyping were also explored whereby genotyping occurred through generation 13 or 14. Pools of 1, 20, 50 and 100 animals were constructed randomly or by minimizing phenotypic variation. The EBV was estimated using a bivariate single-step genomic best linear unbiased prediction model. Pools of 20 animals constructed by minimizing phenotypic variation generally led to accuracies that were not different than using individual progeny data. Gaps in genotyping led to significantly different EBV accuracies (p \u3c .05) for sires and dams born in the generation nearest the pools. Pooling of any size generally led to larger accuracies than no information from generation 15 regardless of the way missing records arose, the percentage of records available or the genetic correlation. Pooling to aid in the use of commercial data in genetic evaluations can be utilized in multivariate cases with varying relationships between the traits and in the presence of systematic and randomly missing phenotypes

Breeding Sustainable Beef Cows: Reducing Weight and Increasing Productivity

Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions. Cumulative weight weaned reflects reproductive performance and avoidance of premature culling for characteristics related to animal health, welfare, and worker safety. Both traits were evaluated with random regression models with records from a crossbred population representing 18 breeds that conduct US national cattle evaluations. The genomic REML analyses included additive and dominance components, with relationships among 22,776 animals constructed from genotypes of 181,286 potentially functional variants imputed from a low-pass sequence. Projected to 8 years of age, the additive heritability estimate for CW was 0.57 and 0.11 for WtW. Dominance heritability was 0.02 for CW and 0.19 for WtW. Many variants with significant associations with CW were within previously described quantitative trait loci (QTL) for growthrelated production, meat, and carcass traits. Significant additive WtW variants were covered by QTL for traits related to reproduction and structural soundness. All breeds contributed to groups of cows with high and low total genetic values (additive + dominance effects) for both traits. The high WtW cows and cows above the WtW mean but below the CW mean had larger heterosis values and fewer bases in runs of homozygosity. The high additive heritability of CW and dominance effects on WtW indicate that breeding to improve beef cow sustainability should involve selection to reduce CW and mate selection to maintain heterosis and reduce runs of homozygosity. Simple Summary: Improving the sustainability of beef cows involves reducing feed costs and enteric methane emissions and increasing calf production while addressing concerns including animal health and welfare and worker safety. Reducing cow weight can favorably impact feed costs and methane emissions. Cumulative weight weaned observed throughout a cow’s productive life directly addresses calf production and indirectly addresses other concerns—cumulative production is higher for cows who wean healthy calves and avoid culling because of reproductive failure, unsoundness, and dangerous behavior. Using functional variant genotypes imputed from the low-coverage whole genome sequence, this examination of cow weight and cumulative weight weaned in a herd of crossbred cattle resulted in additive heritability estimates of 0.57 for cow weight and 0.11 for weight weaned by 8-year-old cows. Corresponding dominance heritability estimates were 0.02 for cow weight and 0.19 for weight weaned. All breeds were represented by cows projected to have high and low cow weights and weight weaned. Heterosis was higher and genomic inbreeding, measured by runs of homozygosity, was lower among high-weight weaned cows. These results suggest selection should be effective in reducing cow weight. Selection to increase weight weaned will be slow but can be hastened with crossbreeding. Especially when pedigree is not available to estimate heterosis, runs of homozygosity may be a useful indicator of heterosis and a predictor of cumulative productivity. Beef cow sustainability can be improved with appropriate crossbreeding and selection, and may be accelerated by incorporating functional variants associated with sustainability-related traits

Characterization of the aldo-keto reductase 1C gene cluster on pig chromosome 10: possible associations with reproductive traits

BACKGROUND: The rate of pubertal development and weaning to estrus interval are correlated and affect reproductive efficiency of swine. Quantitative trait loci (QTL) for age of puberty, nipple number and ovulation rate have been identified in Meishan crosses on pig chromosome 10q (SSC10) near the telomere, which is homologous to human chromosome 10p15 and contains an aldo-keto reductase (AKR) gene cluster with at least six family members. AKRs are tissue-specific hydroxysteroid dehydrogenases that interconvert weak steroid hormones to their more potent counterparts and regulate processes involved in development, homeostasis and reproduction. Because of their location in the swine genome and their implication in reproductive physiology, this gene cluster was characterized and evaluated for effects on reproductive traits in swine. RESULTS: Screening the porcine CHORI-242 BAC library with a full-length AKR1C4 cDNA identified 7 positive clones and sample sequencing of 5 BAC clones revealed 5 distinct AKR1C genes (AKR1CL2 and AKR1C1 through 4), which mapped to 126–128 cM on SSC10. Using the IMpRH(7000rad )and IMNpRH2(12000rad )radiation hybrid panels, these 5 genes mapped between microsatellite markers SWR67 and SW2067. Comparison of sequence data with the porcine BAC fingerprint map show that the cluster of genes resides in a 300 kb region. Twelve SNPs were genotyped in gilts observed for age at first estrus and ovulation rate from the F8 and F10 generations of one-quarter Meishan descendants of the USMARC resource population. Age at puberty, nipple number and ovulation rate data were analyzed for association with genotypes by MTDFREML using an animal model. One SNP, a phenylalanine to isoleucine substitution in AKR1C2, was associated with age of puberty (p = 0.07) and possibly ovulation rate (p = 0.102). Two SNP in AKR1C4 were significantly associated with nipple number (p ≤ 0.03) and another possibly associated with age at puberty (p = 0.09). CONCLUSION: AKR1C genotypes were associated with nipple number as well as possible effects on age at puberty and ovulation rate. The estimated effects of AKR1C genotypes on these traits suggest that the SNPs are in incomplete linkage disequilibrium with the causal mutations that affect reproductive traits in swine. Further investigations are necessary to identify these mutations and understand how these AKR1C genes affect these important reproductive traits. The nucleotide sequence data reported have been submitted to GenBank and assigned accession numbers [GenBank:DQ474064–DQ474068, GenBank:DQ494488–DQ494490 and GenBank:DQ487182–DQ487184]

Evaluating a New Shade for Feedlot Cattle Performance and Heat Stress

Heat stress in cattle results in decreased feed intake, lower daily gain, and potentially death in susceptible animals under intense conditions. A study was carried out during the summer of 2013 at the USDA-ARS U.S. Meat Animal Research Center feedlot evaluating the impact of shade on environmental conditions and cattle performance. A novel two-tiered shade was used in half of the 14 pens, each holding 30 animals. The shades were designed to reduce solar heat load by 40% to 60% and to provide traveling shade across the pen, providing varied amounts of shade area as well as varied solar reduction potential. The objective of this study was to determine if the shade was effective at improving performance (evaluated as average daily gain, feed intake, and feed to gain ratio) and reducing environmental conditions that cause heat stress. A group of mixed-breed cattle with varied genetics including both and were selected, penned on the basis of sex, and blocked by color. Production parameters of pen feed usage were measured daily, and individual body weights were taken monthly. Environmental conditions including air temperature, relative humidity, wind speed, ground temperature, and black globe temperature with and without shade were measured. Solar load on the pens was reduced when shade was provided, with both ground temperature and black globe temperature showing reductions. Cattle showed nominally better performance; however, no significant differences were found in gain or feed intake. Panting scores were significantly lower with shade provided; slopes of cattle respiration rate versus ambient temperature were significantly lower with shade during the afternoon period

Longitudinal study of humoral immunity to bovine coronavirus, virus shedding, and treatment for bovine respiratory disease in pre-weaned beef calves

Background: Bovine coronavirus (BCV) is associated with respiratory infections in cattle of all ages; however, a temporal study to evaluate the effect of BCV immunity on virus shedding and bovine respiratory disease (BRD) incidence in pre-weaned beef calves has not been reported. Thus, we report here a prospective study in three herds of crossbred beef calves (n = 817) with endemic BCV. Serial blood samples for measurement of serum anti-BCV antibody titers and nasal swabs for detection of BCV and other common viral and bacterial BRD pathogens were collected from all calves or subsets of calves at predetermined times from birth through weaning. The calves were monitored for BRD and those that developed signs of respiratory disease were sampled for diagnostic testing. To discover additional risk factors that could have influenced BRD development, sequence analysis of the BCV strain(s) circulating in each herd, and the prevalence of common opportunistic bacterial pathogens in the upper respiratory tract of sick and apparently healthy cattle were also evaluated. Results: Two hundred forty-eight of the 817 study calves (30.4%) were treated for BRD prior to weaning; 246 of those were from a single herd involved in two outbreaks of BRD leading to mass treatment of all calves in that group. Molecular diagnostic testing found BCV and Histophilus somni in nasal swabs taken at the time of BRD treatment. Between herd analyses revealed anti-BCV serum antibody abundance did not associate with the incidence of BRD or BCV shedding, though these measurements may have been hindered by the long periods between sample collections. Analysis of the BCV spike gene hypervariable region revealed four polymorphisms in 15 isolates from the three herds, making strain variation unlikely to account for differences in treatment rates between herds. Persistent or recurrent shedding episodes of BCV occurred in some animals treated for BRD. Conclusion: Co-detection of BCV and H. somni at the time of the disease outbreak suggests that these pathogens contributed to disease pathogenesis. Developing appropriate control measures for respiratory BCV infections may help decrease the incidence of pre-weaning BRD. The role of antibodies in protection must still be further defined

Longitudinal study of humoral immunity to bovine coronavirus, virus shedding, and treatment for bovine respiratory disease in pre-weaned beef calves

Background: Bovine coronavirus (BCV) is associated with respiratory infections in cattle of all ages; however, a temporal study to evaluate the effect of BCV immunity on virus shedding and bovine respiratory disease (BRD) incidence in pre-weaned beef calves has not been reported. Thus, we report here a prospective study in three herds of crossbred beef calves (n = 817) with endemic BCV. Serial blood samples for measurement of serum anti-BCV antibody titers and nasal swabs for detection of BCV and other common viral and bacterial BRD pathogens were collected from all calves or subsets of calves at predetermined times from birth through weaning. The calves were monitored for BRD and those that developed signs of respiratory disease were sampled for diagnostic testing. To discover additional risk factors that could have influenced BRD development, sequence analysis of the BCV strain(s) circulating in each herd, and the prevalence of common opportunistic bacterial pathogens in the upper respiratory tract of sick and apparently healthy cattle were also evaluated. Results: Two hundred forty-eight of the 817 study calves (30.4%) were treated for BRD prior to weaning; 246 of those were from a single herd involved in two outbreaks of BRD leading to mass treatment of all calves in that group. Molecular diagnostic testing found BCV and Histophilus somni in nasal swabs taken at the time of BRD treatment. Between herd analyses revealed anti-BCV serum antibody abundance did not associate with the incidence of BRD or BCV shedding, though these measurements may have been hindered by the long periods between sample collections. Analysis of the BCV spike gene hypervariable region revealed four polymorphisms in 15 isolates from the three herds, making strain variation unlikely to account for differences in treatment rates between herds. Persistent or recurrent shedding episodes of BCV occurred in some animals treated for BRD. Conclusion: Co-detection of BCV and H. somni at the time of the disease outbreak suggests that these pathogens contributed to disease pathogenesis. Developing appropriate control measures for respiratory BCV infections may help decrease the incidence of pre-weaning BRD. The role of antibodies in protection must still be further defined

Genome-wide association study for feed efficiency traits using SNP and haplotype models

Feed costs comprise the majority of variable expenses in beef cattle systems making feed efficiency an important economic consideration within the beef industry. Due to the expense of recording individual feed-intake phenotypes, a genomic-enabled approach could be advantageous toward improving this economically relevant trait complex. A genome-wide association study (GWAS) was performed using 748 crossbred steers and heifers representing seven sire breeds with phenotypes for ADG and ADFI. Animals were genotyped with the BovineSNP50v2 BeadChip containing approximately 54,000 SNP. Both traits were analyzed using univariate SNPbased (BayesC) and haplotype-based (BayesIM) models and jointly using BayesIM to perform a bivariate GWAS. For BayesIM, a hidden Markov model (HMM) of haplotype segments of variable length was built where haplotypes were mapped to clusters based on local similarity. The estimated HMM was then used to assign haplotype cluster genotypes, instead of SNP genotypes, as latent covariates in a Bayesian mixture model. The number of haplotype clusters at each location was assumed to be either 8 (BayesIM8) or 16 (BayesIM16). A total of three univariate analyses for each trait and two bivariate analyses were performed. Posterior SD (PSD) for ADG were 0.28 (0.08), 0.37 (0.11), 0.37 (0.11), 0.35 (0.11), and 0.35 (0.12) for BayesC, BayesIM8, BayesIM16, BayesIM8 bivariate, and BayesIM16 bivariate, respectively. ADFI PSD were 0.30 (0.07), 0.44 (0.13), 0.42 (0.12), 0.38 (0.10), and 0.38 (0.10) for the same models. The top 1% of 1-Mb windows that explained the largest fraction of genetic variation in common between univariate SNP and haplotype models ranged from 24% to 40% and from 20% to 32% for ADG and ADFI, respectively. Spearmen rank correlations between molecular breeding values from SNP and haplotype-based models in the training data were similar for both traits (\u3e0.96) suggesting that either model would lead to similar rankings of animals, although resolution of potential QTL appeared to be greater for BayesIM