Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows.

Beef × dairy crossbred cattle (n = 615) were used to evaluate the effect of preharvest indicator traits and genotypes on the accuracy of estimated breeding values (EBVs) of seedstock candidates for selection. Genotypes for 100,000 single nucleotide polymorphisms were provided by the American Simmental Association of purebred and crossbred seedstock animals (n = 2,632). Five hundred and ninety-five of the 615 beef × dairy cattle had carcass camera and ultrasound data. Phenotypes were not used for any of the seedstock animals even though some may have had performance and ultrasound data. We estimated the genomic relationship matrix among 3,247 animals including both phenotyped and unphenotyped animals. We computed genetic parameters among 37 traits using 666 bivariate restricted maximum likelihood analyses. The accuracy of EBV depends on heritability. For the sake of brevity, we report accuracy for marbling as a proxy for other traits with similar heritability. We focus on accuracy for marbling because marbling is the primary determinant of carcass value. We computed EBV for all 3,247 animals for marbling based on camera data postharvest using best linear unbiased prediction. We report evidence of overlap in causative genes among postharvest carcass traits; marbling, ribeye area, yield grade, fat thickness, and hot carcass weight (HCW) based on genetic correlations. Genetic correlations range from -0.73 to 0.89. Several live animal traits (frame size, body weight and ultrasound fat thickness and ribeye area) were genetically correlated with postharvest traits; including HCW, ribeye area, yield grade, fat thickness, and marbling. Genetic correlations between pre- and postharvest traits ranged from -0.53 to 0.95. Accuracy for marbling ranged from 0.64 to 0.80 for animals with marbling recorded, and from 0.09 to 0.60 for animals without marbling recorded. The accuracy of animals without phenotypes was related to the genomic relationship between animals with phenotype and those without. Live animal traits were useful for predicting economically important carcass traits based on genetic correlations. The accuracy of EBV for seedstock animals that were not phenotyped was low, but this is consistent with theory, and accuracy is expected to increase with the addition of genotypes and carcass data from beef × dairy animals.

Low-cost genotyping platforms and sexed-semen have enabled the production of high breeding value dairy replacement heifers from a fraction of the herd representing the most elite cows. The remainder of the cow herd can be bred to beef bulls using male-sexed-semen. Camera carcass data postharvest and ultrasound carcass estimates preharvest (live animals) on beef × dairy animals combined with genotypes and ultrasound on seedstock animals may provide an efficient scheme for selecting beef bulls to mate to dairy cows in the future to maximize carcass value of the progeny. Genotypes are needed to link carcass data from previously harvested to seedstock bull selection candidates because pedigree is typically not available for beef × dairy cattle. We report that live animal ultrasound carcass estimates are predictive of postharvest economically important carcass traits. The accuracy of genetic evaluation of selection candidates without recorded carcass traits was low but is expected to increase with more genotypes and phenotypes on beef × dairy cattle. Genotypes, ultrasound estimates, and camera carcass data on thousands of beef × dairy cattle could enable increased accuracy of selection with periodic infusion of new phenotypes from future generations.

Early detection of infectious bovine keratoconjunctivitis with artificial intelligence.

Artificial intelligence (AI) was developed to distinguish cattle by their muzzle patterns and identify early cases of disease, including infectious bovine keratoconjunctivitis (IBK). It was tested on 870 cattle in four locations, with 170 developing IBK. The AI identified 169 of the 170 cases prior to their identification by veterinarians, and another 17 cases that remained free of IBK signs (sensitivity = 99.4%, specificity = 97.6%). These results indicate the AI can detect emerging IBK cases by muzzle images very early in the disease process and be used as an intervention tool in the prevention of IBK outbreaks.

Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle.

Feed and water intake are two important aspects of cattle production that greatly impact the profitability, efficiency, and sustainability of producers. Feed and, to a lesser degree, water intake have been studied previously; however, there is little research on their associated animal behaviors and there is a lack of standardized phenotypes for these behaviors. Feed and water intakes obtained with an Insentec system (Hokofarm Group, The Netherlands) from 830 crossbred steers were used to compute five intake behaviors for both feed and water: daily sessions (DS), intake rate (IR), session size (SS), time per session (TS), and session interval (SI). Variance components and heritabilities were estimated for each trait. Heritabilities for feed intake behaviors were 0.50 ±â€…0.12, 0.63 ±â€…0.12, 0.40 ±â€…0.13, 0.35 ±â€…0.12, and 0.60 ±â€…0.12 for DS, IR, SS, TS, and SI, respectively. Heritabilities for water intake behaviors were 0.56 ±â€…0.11, 0.88 ±â€…0.07, 0.70 ±â€…0.11, 0.54 ±â€…0.12, and 0.80 ±â€…0.10 for NS, IR, SS, TS, and SI, respectively. Daily dry matter intake (DDMI) and daily water intake (DWI) had heritabilities of 0.57 ±â€…0.11 and 0.44 ±â€…0.11. Phenotypic correlations varied between pairs of traits (-0.83 to 0.82). Genetic correlations between DDMI and feed intake behaviors were moderate to high, while genetic correlations between DWI and water intake behaviors were low to moderate. Several significant single nucleotide polymorphisms (SNP) were identified for the feed and water intake behaviors. Genes and previously reported quantitative trait loci near significant SNPs were evaluated. The results indicated that feed and water intake behaviors are influenced by genetic factors and are heritable, providing one additional route to evaluate or manipulate feed and water intake.

Feed and water intake are important aspects of cattle production to understand because they impact producer profitability and sustainability. While feed intake and, to a lesser degree, water intake have previously been studied, the associated feeding and drinking behaviors are relatively unknown and lack standardized phenotypes. Using individual animal feed and water intake records, five behaviors were evaluated for feed and water intake from crossbred feedlot steers. The behaviors evaluated were daily sessions (no./d), session size (kg), time per session (s), intake rate (g/s), and session interval (min). The impact of season (winter vs. summer) and bunk management (ad libitum vs. slick) on feeding and drinking behaviors was evaluated. Heritability and variance components were estimated for all feeding and drinking behaviors. Pairwise phenotypic correlations between behaviors were discussed. The relationship between intake and feeding or drinking behaviors was evaluated with genetic correlations. A genome-wide association study identified several significant single nucleotide polymorphisms for feeding and drinking behaviors. The results indicate that feeding and drinking behaviors are heritable and may be one additional route to evaluate feed and water intake.

Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data.

A beef cattle population (n = 2,343) was used to assess the impact of variants identified from the imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post-weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (low, modifier, moderate, high) based on predicted functional impact and re-partitioned based on the consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models. Multiple analyses were conducted to compare the proportion of additive genetic variation explained by the different subsets individually and collectively, and these estimates were benchmarked against all LPS variants in a single GRM and array (e.g., GeneSeek Genomic Profiler 100K) genotypes. When all variants were included in a single GRM, heritability estimates for BWT and PWG were 0.43 ±â€…0.05 and 0.38 ±â€…0.05, respectively. Heritability estimates for BWT ranged from 0.10 to 0.42 dependent on which variant subsets were included. Similarly, estimates for PWG ranged from 0.05 to 0.38. Results showed that variants in the subsets modifier and G1 (untranslated region) yielded the highest heritability estimates and were similar to the inclusion of all variants, while estimates from GRM containing only variants in the categories High, G4 (non-coding transcript exon), and G6 (start and stop loss/gain) were the lowest. All variants combined provided similar heritability estimates to chip genotypes and provided minimal to no additional information when combined with chip data. This suggests that the chip single nucleotide polymorphisms and the variants from LPS predicted to be less consequential are in relatively high linkage disequilibrium with the underlying causal variants as a whole and sufficiently spread throughout the genome to capture larger proportions of additive genetic variation.

Animals from a crossbred beef cattle population were sequenced at low depth (i.e., 0.5×) and different subsets of selected imputed variants were investigated relative to their ability to explain variation in birth weight (BWT) and post-weaning gain (PWG). Variants were classified by both their predicted functional impact and by the consequence of the mutation and partitioned into subsets within these two criteria. When ~ 1 million variants were included in the same genomic relationship matrix, heritability estimates were similar to a 100k chip array. Heritability estimates for BWT ranged from 0.10 to 0.42 dependent on which variant subsets were included. Similarly, estimates for PWG ranged from 0.05 to 0.38. Differences in minor allele frequency were observed among subsets and these differences likely contributed to differences in heritability estimates. Results suggest that linkage disequilibrium between the variants categorized as being less consequential and underlying causal variants is high as indicated by the high percentage of variation explained.

Variance component estimation and genome-wide association of predicted methane production in crossbred beef steers.

Enteric methane is a potent greenhouse gas and represents an escape of energy from the ruminant digestive system. Additive genetic variation in methane production suggests that genetic selection offers an opportunity to diminish enteric methane emissions. Logistic and monetary difficulties in directly measuring methane emissions can make genetic evaluation on an indicator trait such as predicted methane production a more appealing option, and inclusion of genotyping data can result in greater genetic progress. Three predicted methane production traits were calculated for 830 crossbred steers fed in seven groups. The methane prediction equations used included mathematical models from Ellis et al. (2007), Mills et al. (2003), and IPCC (2019). Pearson correlations between the traits were all greater than 0.99, indicating that each prediction equation behaved similarly. Further, the Spearman correlations between the estimated breeding values for each trait were also 0.99, which suggests any of the predicted methane models could be used without substantially changing the ranking of the selection candidates. The heritabilities of Ellis, Mills, and IPCC predicted methane production were 0.60, 0.62, and 0.59, respectively. A genome-wide association study identified one single nucleotide polymorphism (SNP) that reached the threshold for significance for all of the traits on chromosome 7 related to oxidoreductase activity. Additionally, the SNP slightly below the significance threshold indicate genes related to collagen, intracellular microtubules, and DNA transcription may play a role in predicted methane production or its component traits.

Cattle produce methane, a greenhouse gas, as a byproduct of their digestion. It is possible to breed for animals which naturally produce less methane; however, measuring animals for methane production can be difficult or expensive and is required for effective selection. Therefore, an alternative solution is to use a mathematical model to predict methane production and select for animals with low predicted methane. The heritability of predicted methane production from each model ranged from 0.59 to 0.62. Animals were ranked nearly identical, regardless of model used. A genome-wide association study was also conducted to determine what loci may be related to predicted methane production. One significant locus was identified on chromosome 7 related to oxidoreductase activity. Other loci approaching significance showed that genes related to collagen production, intracellular microtubule binding, and DNA transcription may be related to predicted methane production. In particular, collagen turnover may have a relationship to predicted methane because it affects growth rate, which is driven by dry matter intake, which, in turn, is the primary driver of predicted methane production.

Heritability of beef cow metabolizable energy for maintenance.

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 d 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 midpoint 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/BW kg0.75 and had a heritability of 0.31 ± 0.11. Cows have a moderate heritability for maintenance suggesting an opportunity for selection.

Feed is one of the greatest costs of beef production. Most of the feed used annually by a cow is to maintain her body. A study was conducted measuring individual feed intake of mature pregnant cows. We have determined that the amount of energy that a cow uses to maintain her body is heritable suggesting that cows can be selected for differences in the energy required to maintain their bodies.

Use of overlapping DNA pools to discern genetic differences despite pooling error.

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 (PAFs) 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 PAFs for all 200 animals. Frozen lung tissue (0.01 g) from each animal was weighed into a tube containing a pool; there were two pools of 200 animals each and six 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 eight pools were then assayed for approximately 100,000 single nucleotide polymorphisms (SNP). PAF for each SNP and pool was based on the relative intensity of the two dyes used to detect the alleles rather than genotype calls which are not tractable from pooling data. Euclidean distances and genomic relationships among the PAFs for the eight 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 nonoverlapping pools indicated that nonoverlapping pool pairs did not share many related animals because genomic correlations were near zero for these pairs. On the other hand, one pair of nonoverlapping pools likely contained related animals between pools because the correlation was 0.21. Pools sharing 50% overlap ranged in genomic relationship between 0.21 and 0.39 (N = 12).

Genetic evaluation of seedstock cattle could benefit from commercial data. There are hidden relationships between commercial and seedstock sectors because many commercial producers buy bulls from the seedstock sector. Relationships are hidden because pedigree is not tracked in commercial populations. Single nucleotide polymorphism genotypes could reveal these hidden relationships; however, genotyping can be cost prohibitive. Cost of commercial data capture could be decreased by pooling DNA which is a method to genotype groups of animals to use their data in genetic evaluation; however, error from inexact pool formation can complicate interpretation. Results from pools of overlapping random unrelated animals mimic the results from pools sharing relatives with the same degree of shared genomes. For example, a pool of progeny and a pool of the dams of the pooled progeny would produce the same result as two pools sharing 50% overlap of random unrelated animals. We can estimate the relatedness between unknown pools even in the presence of pooling error if an unknown pool comparison is similar to an overlapping pool comparison. Knowing the relationship between seedstock cattle and pools of commercial cattle may allow commercial data to enhance genetic evaluation of seedstock animals.

Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle.

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.

This study investigated mitochondrial DNA copy number (mtDNA CN) as a potential genetic indicator of growth and carcass traits in a composite beef cattle population. Mitochondrial DNA CN was previously shown to be under genetic control. The current study estimated the genetic relationship of mtDNA CN with growth and carcass traits. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to whole-genome sequencing at a low depth that resulted in nuclear DNA and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuclear DNA coverages. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Genetic parameters were estimated from an animal model based on pedigree. Genetic correlation estimates of mtDNA CN with growth and carcass traits were low to moderate and mostly negative. These indicate that selection for lower mtDNA would be associated with an increase in birth weight, weaning weight, post-weaning gain, average daily dry-matter intake, mature cow weight, slaughter weight, and carcass weight. Therefore, the by-product of whole-genome sequencing at a low depth could be used as an indicator trait for growth and carcass traits in genetic evaluations, but the genetic relationships are not likely strong enough to prioritize mtDNA ahead of routinely used indicator traits.

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 growth-related 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.

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 < .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.

Influence of environmental factors and genetic variation on mitochondrial DNA copy number.

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.

Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle.

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 ±â€…0.05 to 0.55 ±â€…0.07 for MWT and from 0.12 ±â€…0.03 to 0.25 ±â€…0.04 for BCS and were lower with the repeatability model at 0.40 ±â€…0.02 and 0.11 ±â€…0.01 for MWT and BCS, respectively. Estimates of repeatability were high for MWT (0.67 ±â€…0.005) and low for BCS (0.22 ±â€…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 ±â€…0.09 to 0.68 ±â€…0.14. The direct heterosis estimates were 21.56 ±â€…3.53 kg (P ≤ 0.001) for MWT and 0.095 ±â€…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 ±â€…0.02 to 0.55 ±â€…0.07 for MWT and from 0.11 ±â€…0.01 to 0.25 ±â€…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 ±â€…0.09 to 0.68 ±â€…0.14. Heterosis effects were 21.56 ±â€…3.53 kg for MWT and 0.095 ±â€…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.

Hematology parameters as potential indicators of feed efficiency in pigs.

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.

Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation.

OBJECTIVE: Realimentation can compensate for weight loss from poor-quality feedstuffs or drought. Mature cows fluctuate in body weight throughout the year due to nutrient availability. The objective of this study was to determine whether cows that differ in weight gain during realimentation also differ in the abundance of transcripts for enzymes associated with energy utilization in skeletal muscle. Mature cows were subjected to feed restriction followed by ad libitum feed. Skeletal muscle transcriptome expression differences during the two feeding periods were determined from cows with greater (n = 6) and less (n = 6) weight gain during the ad libitum feeding period. RESULTS: A total of 567 differentially expressed genes (408 up- and 159 down-regulated) were identified for the comparison of restriction and ad libitum periods (PBonferroni < 0.05). These genes were over-represented in lysosome, aminoacyl-tRNA biosynthesis, and glutathione metabolism pathways. Validation of the expression of five of the genes was performed and four were confirmed. These data suggest that realimentation weight gain for all cows is partially controlled by protein turnover, but oxidative stress and cellular signaling pathways are also involved in the muscle tissue. This dataset provides insight into molecular mechanisms utilized by mature cows during realimentation after a period of low abundance feed.

Accuracy of GEBV of sires based on pooled allele frequency of their progeny.

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.

Breed and heterotic effects for mature weight in beef cattle.

Cow mature weight (MWT) is heritable and affects the costs and efficiency of a breeding operation. Cow weight is also influenced by the environment, and the relationship between the size and profitability of a cow varies depending on production system. Producers, therefore, need tools to incorporate MWT in their selection of cattle breeds and herd replacements. The objective of this study was to estimate breed and heterotic effects for MWT using weight-age data on crossbred cows. Cow's MWT at 6 yr was predicted from the estimated parameter values-asymptotic weight and maturation constant (k)-from the fit of the Brody function to their individual data. Values were obtained for 5,156 crossbred cows from the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation Program using 108,957 weight records collected from approximately weaning up to 6 yr of age. The cows were produced from crosses among 18 beef breeds. A bivariate animal model was fitted to the MWT and k obtained for each cow. The fixed effects were birth year-season contemporary group and covariates of direct and maternal breed fractions, direct and maternal heterosis, and age at final weighing. The random effects were direct additive and residual. A maternal additive random effect was also fitted for k. In a separate analysis from that used to estimate breed effects and (co)variances, cow MWT was regressed on sire yearling weight (YWT) Expected Progeny Differences by its addition as a covariate to the animal model fitted for MWT. That regression coefficient was then used to adjust breed solutions for sire selection in the USMARC herd. Direct heterosis was 15.3 ± 2.6 kg for MWT and 0.000118 ± 0.000029 d-1 for k. Maternal heterosis was -5.7 ± 3.0 kg for MWT and 0.000130 ± 0.000035 d-1 for k. Direct additive heritabilities were 0.56 ± 0.03 for MWT and 0.23 ± 0.03 for k. The maternal additive heritability for k was 0.11 ± 0.02. The direct additive correlation between MWT and k was negligible (0.08 ± 0.09). Adjusted for sire sampling, Angus was heaviest at maturity of the breeds compared. Deviations from Angus ranged from -8.9 kg (Charolais) to -136.7 kg (Braunvieh). Ordered by decreasing MWT, the breeds ranked Angus, Charolais, Hereford, Brahman, Salers, Santa Gertrudis, Simmental, Maine Anjou, Limousin, Red Angus, Brangus, Chiangus, Shorthorn, Gelbvieh, Beefmaster, and Braunvieh. These breed effects for MWT can inform breeding programs where cow size is considered a key component of the overall profitability.

Detection of bovine inflammatory cytokines IL-1ß, IL-6, and TNF-α with a multiplex electrochemiluminescent assay platform.

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-1ß, 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-1ß 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-1ß, 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.

Cytokine and Haptoglobin Profiles From Shipping Through Sickness and Recovery in Metaphylaxis- or Un-Treated 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-1ß, 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.

Genetic changes in beef cow traits following selection for calving ease.

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.