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Genotyping pools of commercial cattle and individual seedstock animals may reveal hidden relationships between sectors enabling use of commercial data for genetic evaluation. However, commercial data capture may be compromised by inexact pool formation. We aimed to estimate the concordance between distances or genomic covariance among pooling allele frequencies (PAF) of DNA pools comprised of 100 animals with 0 or 50 % overlap of animals in common between pools. Cattle lung samples were collected from a commercial beef processing plant on a single day. Six pools of 100 animals each were constructed so that overlap between pools was 0 or 50 %. Two pools of all 200 animals were constructed to estimate PAF for all 200 animals. Frozen lung tissue (0.01 g) from each animal was weighed into a tube containing a pool; there were 2 pools of 200 animals each and 6 pools of 100 animals each. Every contribution of an individual animal was an independent measurement to insure independence of pooling errors. Lung samples were kept on dried ice during the pooling process to keep them from thawing. The 8 pools were then assayed for approximately 100,000 single nucleotide polymorphisms (SNP). Pooling allele frequency for each SNP and pool was based on the relative intensity of the 2 dyes used to detect the alleles rather than genotype calls which are not tractable from pooling data. Euclidean distances and genomic relationships among the PAF for the 8 pools were estimated and distances were tested for concordance with pool overlap using permutation-based analysis of distance. Distances among pools were concordant with the planned overlap of animals shared between pools (P = 0.0024); pool overlap accounted for 70 % of the variation and pooling error accounted for 30 %. Pools containing 100 animals with no overlap were the most distant from one another and pools with 50% overlap were the least distant. This work shows that we can discern differences in distance between pairs of overlapping DNA pools sharing 0 and 50 % of the animals. Genomic correlations among non-overlapping pools indicated that non-overlapping pool pairs did not share many related animals because genomic correlations were near zero for these pairs. On the other hand, one pair of non-overlapping pools likely contained related animals between pools because the correlation was 0.21. Pools sharing 50 % overlap ranged in genomic relationship between 0.21 to 0.39 (n=12).

Most of the metabolizable energy that a cow uses during a production year is for maintenance; however, less is known about the heritability of maintenance compared to other traits that can be measured directly. Feed intake is a heritable trait in the mature cow and most of the feed consumed is used for maintenance. We hypothesized that maintenance energy was a heritable trait. Individual feed intake was measured for 84 or 85 days on 5-yr-old pregnant cows (n = 887) from a pedigreed population of cattle that represent prominent breeds in the United States. Phenotypic mean (± SD) values were 654 ± 68 kg for cow body weight, 0.21 ± 0.24 kg/d for average daily gain, and 175 ± 17 d for mid-point fetal age. Dry matter intake averaged (± SD) 10.84 ± 1.41 kg/d. Metabolizable energy for maintenance was estimated by subtracting the metabolizable energy used for conceptus growth and tissue accretion from metabolizable energy intake. Metabolizable energy for maintenance averaged (± SD) 139 ± 18 ME kcal·d -1/BW kg 0.75 and had a heritability of 0.31 ± 0.11. Cows have a moderate heritability for maintenance suggesting an opportunity for selection.

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P-value ≤0.08) to be associated with birth weight and weaning weight. There was no association (P-value >0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were −0.30 ± 0.16 with birth weight, −0.31 ± 0.16 with weaning weight, −0.15 ± 0.14 with post-weaning gain, −0.11 ± 0.19 with average daily dry-matter intake, −0.04 ± 0.22 with average daily gain, −0.29 ± 0.13 with mature cow weight, −0.11 ± 0.13 with slaughter weight, −0.14 ± 0.13 with carcass weight, −0.07 ± 0.14 with carcass backfat, 0.14 ± 0.14 with carcass marbling, and −0.06 ± 0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits.

IntroductionRespiratory disease incidence is intimately associated with an animal’s commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. In addition, viral pathogens affect the immune system and appear to play an integral role in the overall incidence of bovine respiratory disease (BRD); so, an understanding of the interaction of the bacterial and viral pathogens in the upper respiratory tract (URT) may help us to understand the impact of these pathogens on development of BRD. For this research, the overall goal was to characterize bacterial and viral populations in the URT of nursing beef calves at initial vaccination and at the time of a BRD outbreak.MethodsNasal swabs from the URT were collected at initial vaccination (average 45 days of age) and again at the time of the BRD outbreak (average 126 days of age). DNA and RNA were extracted from nasal swabs to evaluate bacterial and viral populations in the URT. Whole blood was also collected at the time of the BRD outbreak for determination of complete blood counts. To evaluate the microbiome, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. To evaluate the viral pathogens, multiplex reverse transcription real-time polymerase chain reaction and next-generation sequencing (Illumina NextSeq) was completed.ResultsOverall, evaluation of these samples revealed that at the time of the BRD outbreak, all calves were nasally shedding bovine coronavirus and a large percentage had a coinfection with Mycoplasma sp., with Mycoplasma bovirhinis being the predominant species. Neither bovine coronavirus nor Mycoplasma sp. were present at high abundance at the earlier timepoint of initial vaccination. When comparing bacterial population diversity between the two sampling timepoints, alpha diversity was significantly greater at initial vaccination compared to the BRD outbreak (P-value DiscussionAnalysis of the respiratory microflora in the URT during initial vaccination and a BRD outbreak will provide insight into the distribution of bacterial and viral populations in nursing beef calves.

Genotypes generated from common single nucleotide polymorphisms (SNP) chips have been the sole source of genomic information for current beef cattle genetic evaluations. More recently, the development of low-pass whole-genome sequencing (LPS) followed by imputation to full sequence and variant calls has provided an alternative option to generate genotypes for inclusion into genetic evaluations. The objective of this study was to estimate the genotype concordance between SNP chip and LPS genotypes. Ear samples, via tissue sampling units, were obtained from 226 individuals. A subset of 109 individuals also had blood samples collected. Samples were sent to GeneSeek (Neogen company, Lincoln, NE) for genotyping (100K or 50K) and LPS and imputation was performed by Gencove. A total of 33,451 and 78,032 SNP overlapping between SNP panel and LPS for ear and blood samples, respectively, were used for further analyses. Genotype concordance was performed by counting the number of matching genotypes per SNP between (1) SNP chip vs. LPS in ear and blood samples, and (2) LPS in blood vs. LPS in ear samples. The average concordances between SNP chip vs. LPS in ear and blood samples were 0.97±0.04 and 0.98±0.06, respectively. The average concordance between LPS in blood vs. ear samples was 0.97±0.03. In conclusion, the concordance was high regardless of the tissue type, and, at least in these data, differences in resulting genetic predictions would not be expected between the use of genotypes derived from SNP chips or LPS. Additional work is warranted to determine sensitivity to relationships between target animals and the reference set used for imputation. The USDA is an equal opportunity provider and employer.

Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.Mitochondrial DNA copy number (mtDNA CN) is related to mitochondrial function and thus may be indicative of energy efficiency. This study investigated the genetic and non-genetic factors associated with mtDNA CN in a beef cattle population of 2,371 animals using whole-genome sequencing at low depth. Blood, leucocyte, and semen samples were subjected to whole-genome sequencing, resulting in mtDNA and nuclear DNA to estimate mtDNA CN. Findings revealed that 11% to 31% of the variation in mtDNA CN is under genetic control. Non-genetic effects of tissue type, age, and sex were significantly associated with mtDNA CN. Semen samples had the lowest mtDNA CN, followed by blood and leucocyte samples. Younger and older ages were associated with a greater mtDNA CN than intermediate ages. Females had greater mtDNA CN than males. Heterosis and breed composition were not significantly associated with mtDNA CN. These results suggest that mtDNA CN is heritable and would respond favorably to genetic selection.

A better understanding regarding the mechanisms by which the rumen processes feed may assist us in identifying animals with superior feed efficiency. Studies to evaluate the gene expression of rumen tissue have previously been performed to analyze their relationship with feed efficiency. Continuing this research is critical to determine whether the expression of the genes identified is associated with feed efficiency in additional populations of beef cattle to ensure that they are robust across breed and environment. A previous rumen-transcriptome study on Hereford × Angus steers identified 122 differentially expressed genes (PFDR

Summary Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, and 25% Tarentaise. A total of 248 animals were used in this study: CGC (n = 79), Red Angus (n = 61), Charolais (n = 79), and Tarentaise (n = 29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations, runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.Composite breeds are commonly used in the U.S. beef industry since they provide producers with benefits such as breed complementarity and retained heterosis. However, cattle composite genomes are not well characterized. Therefore, in this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed composite (50% Red Angus, 25% Charolais, and 25% Tarentaise). The analysis showed an increase in the proportion of Tarentaise to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38%. Furthermore, new genome segments formed around the sixth generation. These changes show that progenitor breed proportions are not stable over generations and that either direct or natural selection plays a role in modifying the proportions. The increase in Tarentaise proportion suggests useful attributes to the composite in a cool semi-arid environment.

Understanding the genetic relationship between mature cow weight (MWT) and body condition score (BCS) is useful to implement selection programs focused on cow efficiency. The objectives of this study were to estimate genetic parameters, heterosis, and breed effects for MWT and BCS. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS on 6,138 and 6,131 cows, respectively, from the Germplasm Evaluation program, a crossbred beef population at the U.S. Meat Animal Research Center. Pedigree was available for 48,013 individuals. Univariate animal models were used to estimate heritabilities for each trait by parity. Bivariate animal models were used to estimate genetic correlations between parities within a trait and between traits within parities. Bivariate repeatability animal models were used to estimate genetic correlations between traits across parities. Estimates of heritability for different parities ranged from 0.43 ± 0.05 to 0.55 ± 0.07 for MWT and from 0.12 ± 0.03 to 0.25 ± 0.04 for BCS and were lower with the repeatability model at 0.40 ± 0.02 and 0.11 ± 0.01 for MWT and BCS, respectively. Estimates of repeatability were high for MWT (0.67 ± 0.005) and low for BCS (0.22 ± 0.006). Estimates of genetic correlation for MWT and BCS between parities were, in general, high, especially between consecutive parities. Estimates of genetic correlation between MWT and BCS were positive and moderate, ranging from 0.32 ± 0.09 to 0.68 ± 0.14. The direct heterosis estimates were 21.56 ± 3.53 kg (P ≤ 0.001) for MWT and 0.095 ± 0.034 (P ≤ 0.001) for BCS. Ordered by decreasing MWT, the breeds ranked Brahman, Charolais, Angus, Simmental, Salers, Hereford, Santa Gertrudis, Chiangus, Brangus, Red Angus, Shorthorn, Maine-Anjou, Gelbvieh, Beefmaster, Limousin, and Braunvieh. Ordered by decreasing BCS, the breeds ranked Brahman, Red Angus, Charolais, Angus, Hereford, Brangus, Beefmaster, Chiangus, Salers, Simmental, Maine-Anjou, Limousin, Santa Gertrudis, Shorthorn, Gelbvieh, and Braunvieh. Estimates of breed differences for MWT were also adjusted for BCS (AMWT), and in general, AMWT depicted smaller differences between breeds with some degree of re-ranking (r = 0.59). These results suggest that MWT and BCS are at least moderately genetically correlated and that they would respond favorably to selection. Estimates of breed differences and heterotic effects could be used to parameterize multibreed genetic evaluations for indicators of cow maintenance energy requirements.The current study estimated the genetic relationship between mature cow weight (MWT) and body condition score (BCS), heterosis, and breed effects for these traits in a crossbred beef population. In total, 25,035 and 24,522 overlapping records were available for MWT and BCS, respectively. Pedigree was available for 48,013 individuals. Heritability and genetic correlations were estimated within a trait between parities, between traits within parities, and between traits across parities. Estimates of heritability ranged from 0.40 ± 0.02 to 0.55 ± 0.07 for MWT and from 0.11 ± 0.01 to 0.25 ± 0.04 for BCS. Genetic correlations within a trait and between parities were, in general, high. Estimates of genetic correlation between MWT and BCS were positive and moderate, ranging from 0.32 ± 0.09 to 0.68 ± 0.14. Heterosis effects were 21.56 ± 3.53 kg for MWT and 0.095 ± 0.034 for BCS. For both traits, Brahman and Braunvieh were associated with the highest and lowest breed effects, respectively. These results suggest that MWT and BCS would respond favorably to selection and are moderately genetically correlated. Breed differences and heterotic effects could be used to parameterize multibreed genetic evaluations for indicators of cow maintenance energy requirements.

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 .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.

The identification of an inexpensive, indirect measure of feed efficiency in swine could be a useful tool to help identify animals with improved phenotypes to supplement expensive phenotypes including individual feed intakes. The purpose of this study was to determine whether hematology parameters in pigs at the beginning and end of a feed efficiency study, or changes in those values over the study, were associated with average daily gain (ADG), average daily feed intake (ADFI), or gain-to-feed (G:F). Whole blood samples were taken at days 0 and 42 from pigs (n = 178) that were monitored for individual feed intakes and body weight gain during a 6-week study. Blood samples were analyzed for blood cell parameters including white blood cell (WBC), neutrophil, lymphocyte, monocyte, eosinophil and basophil counts, red blood cell (RBC) counts, hemoglobin, hematocrit, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC), platelet count, and mean platelet volume (MPV). Feed efficiency parameters were predicted using an ANOVA model including fixed effects of farrowing group and pen (sex constant) and individual hematology parameters at day 0, day 42 or their change as covariates. At day 0, platelet count was positively associated with ADFI (P < 0.05) and negatively associated with G:F (P < 0.1), and lymphocyte count was positively associated with ADFI (P < 0.05). At day 42, neutrophil, RBC counts, hemoglobin and hematocrit were associated with ADFI (P < 10−3). Over the course of the study, changes in RBC measurements including RBC, hemoglobin, MCV, MCH, and MCHC (P < 10−4) which may improve oxygen carrying capacity, were associated with ADG and ADFI. The change in hematocrit over the course of the study was the only parameter that was associated with all three measures of feed efficiency (P < 0.05). Changes in RBC parameters, especially hematocrit, may be useful measurements to supplement feed efficiency phenotypes in swine.

Despite decreasing genotyping costs, in some cases individually genotyping animals is not economically feasible (e.g., in small ruminants). An alternative is to pool DNA, using the pooled allele frequency (PAF) to garner information on performance. Still, the use of PAF for prediction (estimation of genomic breeding values; GEBVs) has been limited. Two potential sources of error on accuracy of GEBV of sires, obtained from PAF of their progeny themselves lacking pedigree information, were tested: (i) pool construction error (unequal contribution of DNA from animals in pools), and (ii) technical error (variability when reading the array). Pooling design (random, extremes, K-means), pool size (5, 10, 25, 50, and 100 individuals), and selection scenario (random, phenotypic) also were considered. These factors were tested by simulating a sheep population. Accuracy of GEBV—the correlation between true and estimated values—was not substantially affected by pool construction or technical error, or selection scenario. A significant interaction, however, between pool size and design was found. Still, regardless of design, mean accuracy was higher for pools of 10 or less individuals. Mean accuracy of GEBV was 0.174 (SE 0.001) for random pooling, and 0.704 (SE 0.004) and 0.696 (SE 0.004) for extreme and K-means pooling, respectively. Non-random pooling resulted in moderate accuracy of GEBV. Overall, pooled genotypes can be used in conjunction with individual genotypes of sires for moderately accurate predictions of their genetic merit with little effect of pool construction or technical error.

Phenotypes are necessary for genomic evaluations and management. Sometimes genomics can be used to measure phenotypes when other methods are difficult or expensive. Prolificacy of bulls used in multiple-bull pastures for commercial beef production is an example. A retrospective study of 79 bulls aged 2-year-old and older used 141 times in 4-5 pastures across 4 years was used to estimate repeatability from variance components. Traits available before each season’s use were tested for predictive ability. Sires were matched to calves using individual genotypes and evaluating exclusions. A lower cost method of measuring prolificacy was simulated for 5 pastures using the bulls’ genotypes and pooled genotypes to estimate average allele frequencies of calves and of cows. Repeatability of prolificacy was 0.62 ± 0.09. A combination of age-class and scrotal circumference accounted for less than 5 % of variation. Simulated estimation of prolificacy by pooling DNA of calves was accurate. Adding pooling of cow DNA or actual genotypes both increased accuracy about the same. Knowing a bull’s prior prolificacy would help predict future prolificacy for management purposes and could be used in genomic evaluations and research with coordination of breeders and commercial beef producers.

Interest in reducing labour costs due to shearing has led to development of breed types that shed their wool naturally. Selection at young ages can facilitate response. Reliability of predictions of adult from lamb wool shedding (WS) is thus key in the design of breeding programmes to increase shedding. Our objectives were to estimate heritabilities and genetic relationships between WS measured once in lambs and repeatedly in ewes and to assess the accuracy of lamb WS EBV to predict ewe WS EBV based on a multi-trait threshold or a repeatability model. Data were 4,971 lamb and 3,335 ewe WS records on a Romanov, White Dorper and Katahdin composite flock. For the multivariate model, WS heritability ranged from 0.47 ± 0.03 in lambs to 0.59 ± 0.04 at 1 year of age. For the repeatability model, WS in adult ewes was moderately heritable (0.50 ± 0.03) and repeatable (0.60 ± 0.02). Genetic correlations were 0.72 ± 0.04, 0.65 ± 0.05, 0.50 ± 0.09 and 0.51 ± 0.09 between lamb WS and 1st through 4th record, respectively. Given the moderately high heritability and high correlations between WS performance in lambs and ewes, selecting animals early in life would effectively increase WS in crossbred flocks.

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. Electronic supplementary material The online version of this article (10.1186/s12917-019-1887-8) contains supplementary material, which is available to authorized users.

Disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. An understanding of the animal's resident respiratory pathogens, in the upper nasal cavity prior to weaning, may help us to understand the impact of these pathogens on incidence of respiratory disease. For this research, the overall goal was to characterize bacterial populations associated with calves at an early age and through time periods prior to weaning in 3 herds at the U.S. Meat Animal Research Center. Nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 40 d of age), preconditioning (approximately 130 d of age), and weaning (approximately 150 d of age) in 2015 and 2016. DNA was extracted from nasal swabs and combined into 2 pools of 10 animals for each sampling time point, in each herd, for a total of 6 pools at each sampling time point and 18 pools for all sampling time points within each year. To evaluate and compare the microbiome of each pooled sample, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Alpha and beta diversity were also measured. Overall, microbial communities were different between combinations of sampling year, herd location, and sampling time prior to weaning as shown by beta diversity. Analysis of these specific respiratory pathogens prior to weaning will present a clearer picture of the distribution of microbial populations in animals prior to weaning and not exhibiting clinical signs of respiratory disease. Therefore, evaluation of the animal's resident bacterial populations in the upper nasal cavity during different phases of the beef production system may help us to understand the impact of the microbiome on incidence of respiratory disease in cattle.

Cow mature weight (MWT) has increased in the past 30 yr. Larger cows cost more to maintain, but their efficiency—and thus profitability—depends on the production environment. Incorporating MWT effectively into selection and mating decisions requires understanding of growth to maturity. The objective of this study was to describe growth to maturity in crossbred beef cattle using Brody, spline, and quadratic functions. Parameter estimates utilized data on crossbred cows from cycle VII and continuous sampling phases of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center. The MWT were estimated at 6 yr from the fitted parameters obtained from the Brody (BMWT), spline (SMWT), and quadratic (QMWT) functions. These were defined as BMWT, SMWT, and QMWT for the Brody, spline, and quadratic functions, respectively. Key parameters from the Brody function were BMWT and maturing constant. The spline was fitted as piecewise linear where the two linear functions joined at a knot. Key parameters were knot position and SMWT. For the quadratic model, the main parameter considered was QMWT. Data were scaled for fitting such that 180 d was the y-intercept with the average weight at 180 d (214.3 kg) subtracted from all weights. Weights were re-expressed by adding 214.3 kg after analysis. Once data were edited, with outliers removed, there were parameter estimates for 5,156, 5,041, and 4,905 cows for the Brody, spline, and quadratic functions, respectively. The average maturing constant (SD) was 0.0023 d(−1) (0.0008 d(−1)). The mean MWT estimates (SD) from the Brody, spline, and quadratic functions were 650.0 kg (64.0 kg), 707.3 kg (79.8 kg), and 597.8 kg (116.7 kg), respectively. The spline function had the highest average R(2) value when fit to individual cows’ data. However, the Brody function produced more consistent MWT estimates regardless of the timeframe of data available and produced the fewest extreme MWT. For the spline and quadratic functions, weights through 4 and 5 yr of age, respectively, were needed before consistent estimates of MWT were obtained. Of the three functions fitted, the Brody was best suited for estimating MWT at a later age in crossbred beef cattle.

Fifty-six head of cattle, 28 animals with bovine respiratory disease complex (BRDC), and 28 healthy animals that were matched by treatment, sale barn of origin, day, and interactions among these variables, were identified from a population of 180 animals (60 each purchased at three sale barns located in Missouri, Tennessee, and Kentucky) enrolled in a study comparing animals receiving metaphylaxis to saline-treated controls. Cattle were transported to a feedlot in KS and assigned to treatment group. Blood samples were collected at Day 0 (at sale barn), Day 1, Day 9, and Day 28 (at KS feedlot), and transported to the US Meat Animal Research Center in Clay Center, NE where plasma was harvested and stored at −80°C until assayed for the cytokines IFN-γ, IL-1β, IL-6, and TNF-α, and the acute stress protein haptoglobin (HPT). Our objectives were to determine if cytokine and haptoglobin profiles differed between control and metaphylaxis treatment groups over time, and if profiles differed between animals presenting with BRDC and those that remained healthy. There was no difference between the treated animals and their non-treated counterparts for any of the analytes measured. Sale barn of origin tended to affect TNF-α concentration. Differences for all analytes changed over days, and on specific days was associated with state of origin and treatment. The Treatment by Day by Case interaction was significant for HPT. The analyte most associated with BRDC was HPT on D9, possibly indicating that many of the cattle were not exposed to respiratory pathogens prior to entering the feedlot.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison–cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

One approach to reducing calving difficulty is to select heifers with higher breeding value for calving ease. Calving ease is often associated with lower birth weight and that may result in other possible effects on lifetime productivity. Females from experimental select and control calving ease lines within each of the seven populations were compared. Random samples of 720 heifers from lines selected for better calving ease breeding values and 190 heifers from control lines selected for average birth weights were followed through four parities. Select and control lines within the same population were selected to achieve similar yearling weight breeding values. Weights of sampled heifers in select lines were 2.6 kg (P < 0.01) lighter at birth but not different from control lines at weaning. Select lines had significantly shorter hip height, lighter mature weight, and greater calving success at second parity. Their calves were born significantly earlier with lighter weights and less assistance. Significant interactions with parity showed fewer calves assisted and greater calf survival to weaning as heifers but negligible differences with control lines in later parities. Steer progeny sampled from these dams in select lines (n = 204) were not different from steers in control lines (n = 91) for hot carcass weight but had significantly greater fat depth. Two production systems were compared considering the seven populations as replicates. The systems differed in selection history of females (select and control lines) and the use of bulls within their lines as young cows, but used the same bulls in both lines as older cows. Cows were culled after single unsuccessful breeding and kept for up to four parities. Select line cows tended (P ≤ 0.10) to wean more calves and stay in the herd longer. They were assisted significantly fewer times at calving and had greater calf weight gain to weaning when evaluated over their herd life. Mature weights were lighter in select lines, but marketable cow weight from the systems was nearly identical. Control lines did have more marketable young cow weight and select lines older cow weight. Weaned calf weight per heifer starting the system was significantly greater for the select heifer system due to greater survival of calves from heifers and greater calving success at second parity. No important unfavorable effects of genetic differences in calving ease were identified in this experiment.

The Agricultural Research Service (ARS) Beef Grand Challenge is a cooperative, multidisciplinary effort evaluating differences in performance of genetic lines across production environments representative of different geographical regions. Weaned spring-born calves (n = 120 per location), representing natural service matings to Angus, Hereford, Simmental, Charolais, or indicus-composite (Beefmaster or Brangus) bulls from the U.S. Meat Animal Research Center Germplasm Evaluation program in south central Nebraska, are sent to wheat pasture (central Oklahoma) and winter range (eastern Montana), and weaned fall-born calves (n=40 per location) are sent to summer grazing on shortgrass prairie (northeastern Colorado) and southern mixed-grass rangeland (western Oklahoma). All cattle are fed a finishing ration representative of the region that approximately matches energy content across locations. Each calving season has a matching counterpart of calves that remain in Nebraska on a calf-fed drylot program (receiving ration followed by longer finishing ration). Breeds and sires are represented equally, to the extent possible, at each location. To detect differences in breed effects at each location and average over yearly variation, the study is being replicated for 4 years. Weights, stress measures, carcass composition (marbling, yield grade, quality grade, etc.), steak tenderness and steak fatty acid composition are collected from each location. Additionally, rumen metagenomic composition, metagenomic samples, preharvest food safety samples, and feed intake measures are collected at some locations. Grazing impacts and supplemental range feeding are also being evaluated. One year of sampling has been completed, with numeric differences observed for marbling and tenderness as well as growth performance among locations. Statistical differences will be evaluated when replicate years are collected. The USDA is an equal opportunity provider and employer.

Economically relevant traits (ERT) are routinely collected within commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, which would be costly; pooling DNA and phenotypic data provides a cost-effective solution. A simulated beef cattle population consisting of 15 generations was genotyped with approximately 50k markers (841 quantitative trait loci were located across the genome) and phenotyped for a moderately heritable trait. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step GBLUP model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when no gap between genotyped parents and pooled offspring occurred. The EBV accuracies resulting from pools were greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. Pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared to individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to EBV accuracies that were statistically different than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible, although differences exist depending on pool size and pool formation strategy. The USDA is an equal opportunity employer.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison–Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.

Commercially available bovine-specific assays are limited in number, and multiplex assays for this species are rare. Our objective was to develop a multiplex assay for the bovine inflammatory cytokines IL-1β, IL-6, and TNF-α using the Meso Scale Discovery U-PLEX platform. "Do-It-Yourself" ELISA kits that contained polyclonal antibodies, both unlabeled and biotinylated, and the specific recombinant bovine cytokine standard, were purchased for each of these three cytokines. The biotinylated antibodies were coupled to linkers that bind to specific locations within each well of the U-PLEX plate. Unique linkers were used for each of the cytokines. The unlabeled antibodies were conjugated with electrochemiluminescent labels to serve as detection antibodies. Each cytokine assay was optimized individually prior to performing an optimization on the multiplex assay containing reagents for all three cytokines. To calculate cytokine concentrations, standard curves were developed using the recombinant cytokines and were run concurrently on each plate. Standard curves for IL-1β and TNF-α were run at concentrations ranging from 0 to 50,000 pg/mL, and for IL-6 from 0 to 10,000 pg/mL. The average lowest level of detection concentration measured by the standard curves were 5.3 pg/mL, 0.92 pg/mL, and 22.34 pg/mL for IL-1β, IL-6, and TNF-α respectively, as determined by data from seven plates containing bovine plasma samples from a combination of healthy and diseased cattle. The U-PLEX platform was a viable means to develop custom analyte- and species-specific multiplex assays using privately developed or purchased sets of commercially available reagents.

Economically relevant traits are routinely collected within the commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, but this would be costly; therefore, pooling DNA and phenotypic data provide a cost-effective solution. Pedigree, phenotypic, and genomic data were simulated for a beef cattle population consisting of 15 generations. Genotypes mimicked a 50k marker panel (841 quantitative trait loci were located across the genome, approximately once per 3 Mb) and the phenotype was moderately heritable. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step genomic best linear unbiased prediction model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation within pools), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when there was no gap between genotyped parents and pooled offspring. The EBV accuracies resulting from pools were usually greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. A pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared with individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to statistical differences in EBV accuracy than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Largest numerical increases in EBV accuracy resulting from pooling compared with no data from generation 15 were seen with sires with prior low EBV accuracy (those born in generation 14). Pooling of any size led to larger EBV accuracies of the pools than individual data when minimizing phenotypic variation. Resulting EBV for the pools could be used to inform management decisions of those pools. Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible although differences exist depending on pool size and pool formation strategy.

In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.

Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is improved through reduced unassigned reads by including a survey of near-full-length sequences specific to the target environment, using a niche of interest represented by the upper respiratory tract (URT) of cattle. We created a custom Bovine URT database from these longer sequences for assignment of shorter, less expensive reads in comparisons of the upper respiratory tract among individual animals. This process improves the ability to detect changes in the microbial populations of a given environment, and the accuracy of defining the content of that environment at increasingly higher taxonomic resolution.

The cow herd consumes approximately 70% of the annual feed resources. To date, most genetic evaluations of feed intake in beef cattle have been made in growing animals and little information is available for mature cows. Genetic evaluations in mature cows have predominately been confined to lactating dairy cows and the relationship between feed intake as growing heifers and mature cows has not been addressed. It was the purpose of this study to estimate the heritability of feed intake when measured as growing heifers and mature cows and determine the genetic correlation between these measurements. Individual feed intake and BW gain were measured on 687 heifers and 622 5-yr-old cows. The heritability of average daily DMI (ADDMI) estimated in heifers was 0.84 ± 0.12 and 0.53 ± 0.12 in cows. The heritability of ADG estimated in heifers was 0.53 ± 0.12 and 0.34 ± 0.11 in cows. The genetic correlation between heifer and cow ADDMI was 0.84 ± 0.09. The genetic correlation between heifer and cow ADG was 0.73 ± 019. Heritability of residual feed intake in heifers was 0.25 ± 0.11 and 0.16 ± 0.10 in cows. Heritability for residual gain in heifers was 0.21 ± 0.11 and 0.14 ± 0.10 in cows. Feed intake and ADG are heritable and genetically correlated between heifers and cows. Selection for decreased feed intake and ADG in growing animals will probably have the same directional effects on mature cows.

Mature weight of beef cows in the United States has been increasing as a correlated response to selection for calf growth. Unfavorable genetic correlations between cow weight and various measures of female fertility, stayability, and lifetime production suggest declining cow productivity might also be expected as a correlated response to growth selection. National cattle evaluations, however, show increasing trends for stayability and sustained fertility. Random regression (RR) models were employed to further examine genetic relationships among cow weight and productivity, and to assess cumulative productivity traits observed throughout cows' productive lives. Records were from 13,707 females born in the Germplasm Evaluation (GPE) project and mated to calve first as 2-yr olds. Weights observed at pregnancy testing (n = 65,086) and calf production from each exposure to breeding (n = 71,583) were included in uni- and bivariate RR analyses. Production following each breeding season was added to previous production to obtain cumulative production records for each season that the female was exposed to breeding. Zero was added if the cow failed to produce after a breeding season. The number of pregnancies, calves born and calves weaned, as well as age and weight of weaned calves, were accumulated. Projected age-specific heritability (h2) estimates for cumulative production were low (

Steers (n = 868) were raised, feedlot-finished with ad libitum access to a high-energy diet and harvested to determine if there is genomic control of fatty acid profile traits in beef breeds common to the United States. Cattle included purebred and crossbred progeny of Angus, Red Angus, Hereford, Shorthorn, Simmental, Charolais, Limousin, Gelbvieh, Maine Anjou, Chiangus, Braunvieh, Salers, Brahman, Brangus, Santa Gertrudis, and Beefmaster as well as three composite lines. Either directly or through imputation, genotypes were determined for > 133,000 functional single nucleotide polymorphisms (SNP). At approximately 38 h postmortem, a 2.54-cm-thick longissimus steak was obtained from the 13th rib region of the left side of each carcass. At 14 d postmortem, steaks were cooked and subsequently longissimus was pulverized in liquid nitrogen. Fatty acid profile was determined by gas chromatography and mass spectrometry. A genome-wide association study was conducted for fatty acid profile traits expressed as a deviation from the contemporary group mean using the Mixed Linear Model Analysis of SNP & Variation Suite 8.8.3 (Golden Helix) and Pre-computed Kinship Matrix using the GBLUP Genomic Relationship Matrix. A SNP in coiled coil domain containing 57 (CCDC57; Chromosome 19 at 51,349,695) affected the percentage of C14:0 (P < 10–46), short-chain fatty acids (P < 10–36), and saturated fatty acids (P < 10–17). Also, a SNP in thyroid hormone responsive (THRSP; Chromosome 29 at 18,090,403) affected the percentage of C14:0 (P < 10–16) and short-chain fatty acids (P < 10-10). The percentage of polyunsaturated fatty acids was affected by SNP in myostatin (Chromosome 2 at 6,213,980; P < 10–15). These results show that fatty acid profile of beef can be changed through genetic selection but, it is not clear if the level of change will be great enough to impact human health.