Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle

Genome-Wide Association Analysis Identifies the PMEL Gene Affecting Coat Color and Birth Weight in Simmental × Holstein

Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, PMEL_1, rs134930689, rs383170073, rs109924971, and rs109146332), and these were in RNF41, ZC3H10, ERBB3, PMEL, and OR10A7 on BTA5. Interestingly, rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, and PMEL_1 showed strong linkage disequilibrium (r2 > 0.8) and were significantly associated with coat color. Notably, Hypotrichosis_PMel17 and PMEL_1 were located in the gene PMEL (p = 2.22 × 10-18). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with Hypotrichosis_PMel17 and PMEL_1 genotypes was significantly greater than that of homozygous individuals (0.01 < p < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (p < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, PMEL appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight.

Animal board invited review: Practical applications of genomic information in livestock

Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic evaluations exploit genome-wide genotype information to improve the accuracy of predicting an animal's (and by extension its progeny's) genetic merit. Genomic data also provide a huge resource for research, albeit the outcome from this research, if successful, should eventually be realised through one of the ten applications already mentioned. The process for generating a genotype all the way from sample procurement to identifying erroneous genotypes is described, as are the steps that should be considered when developing a bespoke genotyping panel for practical application.

Genomic Analysis of Heterosis in an Angus × Hereford Cattle Population

Crossbreeding is widely used in the beef cattle industry to exploit its several benefits. This study evaluated the effects of heterozygosity on growth traits in an Angus × Hereford cross-population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1530 animals comprising of pure Line 1 Hereford, Angus and Angus × Line 1 Hereford cross. Growth phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Significant effects of genomic heterozygosity on growth traits were detected. These effects were 0.03 kg (0.006), 5.13 kg (0.04), 6.02 kg (0.08) on birth weight, weaning weight and yearling weight, respectively. Genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 6, 21, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

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.

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.

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 ± 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.

Evaluation of growth and efficiency-related traits of different levels of Boer x Central Highland crossbred goats

The growth and efficiency-related traits of the Boer x Central Highland goats raised semi-intensively were evaluated. Besides, genetic and non-genetic factors affecting growth and efficiency-related traits were identified. Data were collected over a period of nine years in a flock of Boer crossbred goats and analyzed using general linear model procedure of SAS. The overall least-squares mean live weight at birth, 3-, 6-, 9- and 12 months of age were 2.52 ± 0.01, 9.81 ± 0.13, 13.8 ± 0.15, 17.8 ± 0.19, and 20.5 ± 0.29 kg, respectively. The average weight gains from birth to 3 months, 3 to 6, 6 to 9 and 9–12 months of age were 80.3, 37.5, 41.9, and 31.2 g day⁻¹, respectively. Boer blood level, birth type, season and year of kidding had a significant effect on growth traits. The overall least-squares mean of Kleiber ratio from birth to 3 months, 3–6 months, 6–9 months, and 9 month to yearling age were 13.99 ± 0.11, 5.23 ± 0.14, 4.66 ± 0.16, and 2.95 ± 0.18, respectively. Parity, birth type, Boer blood level, season and year of birth had a significant influence on the expression of efficiency-related traits (Kleiber ratios) in different growth phases. In terms of growth performance and efficiency-related traits, F2 and F3 crossbred goats did not show any benefit over F1 crossbred goats. Increasing Boer blood level above 50% would be worthless under the existing minimal input production system. Therefore, besides to improving the management of goats, producing the first filial generation would be suitable for medium to high input production systems.

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.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts

Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings, and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis. Adonis test on distance matrix from the animal correlation showed clustering with method, and higher correlations between methods than within (P < 1 × 10^-6). White blood cell count was predictive of sample representation when compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with DNA extraction and genotyping and improve representation of individuals in a pool.

Influence of host genetics in shaping the rumen bacterial community in beef cattle

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.

Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing

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.

Genetic Parameters of Birth Weight and Weaning Weight and Their Relationship with Gestation Length and Age at First Calving in Hanwoo (Bos taurus coreanae)

Simple Summary

Hanwoo cattle is considered one of the most economically important species and sources of nutrition for Koreans. Thus, both the reproductive performance and growth traits play an important role in the continuous development and productivity of Hanwoo farming. Therefore, to improve beef production and the profitability of Hanwoo farming, estimations of genetic parameters for birth weight (BW) and weaning weight (WW) and their relationship with age at first calving (AFC) and gestation length (GL) are necessary to understand and improve their responses to selection. Thus, this study estimated the variance components, heritability estimates of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to age at first calving (AFC), and gestation length (GL). Results revealed a moderate and high heritability estimate for BW and WW, which suggests a sluggish and rapid response of these traits to selection, respectively. The moderate and high genetic correlation between BW and reproductive traits (AFC and GL) revealed that the selection of a heavier BW might result in a longer AFC and GL. Although the genetic correlation for BW and AFC was moderate and positive, the phenotypic correlation of close to zero may indicate that the phenotypic expression for these traits is likely to be influenced by the genotype-environment interaction (GxE). Moreover, the genetic and phenotypic correlation between WW and reproductive traits (AFC and GL) indicates that the selection of a heavier WW may not influence the AFC and GL of Hanwoo cow. These estimated genetic parameters and correlations for the studied traits can be utilized for genetic breeding programs of Hanwoo cattle.

Abstract

Hanwoo is one of the most economically important animal species in Korea due to its significant contribution to nutrition. However, the current selection index only focuses to improve carcass traits of Hanwoo. Thus, this study aimed to estimate the genetic parameters of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to the age at first calving (AFC) and gestation length (GL) of Hanwoo. The genetic parameters for birth weight (BW) and weaning weight (WW) were estimated using the data obtained from 52,173 and 35,800 Hanwoo calves born from February 1998 to March 2017, respectively. Further, these data were used to determine their genetic and phenotypic correlation to age at first calving (AFC) and gestation length (GL). The heritability estimates of BW and WW and correlation coefficients were obtained using the average information restricted maximum likelihood (AIREML) procedure, fit in single and two-trait linear animal models. The estimated direct heritability for BW and WW was moderate (0.22 ± 0.02) and high (0.51 ± 0.03), respectively, while the maternal heritability for both traits was 0.12 ± 0.01 and 0.17 ± 0.01, respectively. The genetic correlation of BW and reproductive traits (AFC and GL) showed a moderate and high positive correlation coefficient of 0.33 ± 0.06 and 0.53 ± 0.02, respectively, while close to zero and low positive phenotypic correlations of 0.06 ± 0.01 and 0.21 ± 0.06 were also observed between the correlated traits, respectively. For the correlation analysis between WW and AFC, both the genetic and phenotypic correlation showed close to zero values of 0.04 ± 0.06 and −0.01 ± 0.01, respectively. Meanwhile, the genetic and phenotypic correlation between WW and GL showed low and negative correlations of −0.09 ± 0.06 and −0.09 ± 0.01, respectively. These obtained estimated variances for BW and WW and their corresponding genetic and phenotypic correlation to AFC and GL can be used as information for genetic improvement and subsequent economic improvement of Hanwoo farming.

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers

Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake. RNA-Seq was used to evaluate the transcript abundance of genes in the mesenteric fat from a total of 78 steers collected over 5 different cohorts. A meta-analysis was used to identify genes involved with gain, feed intake or the interaction of both phenotypes. The interaction analysis identified 11 genes as differentially expressed. For the main effect of gain, a total of 87 differentially expressed genes (DEG) were identified (P_ADJ<0.05), and 24 were identified in the analysis for feed intake. Genes identified for gain were involved in functions and pathways including lipid metabolism, stress response/protein folding, cell proliferation/growth, axon guidance and inflammation. The genes for feed intake did not cluster into pathways, but some of the DEG for intake had functions related to inflammation, immunity, and/or signal transduction (JCHAIN, RIPK1, LY86, SPP1, LYZ, CD5, CD53, SRPX, and NF2). At P_ADJ<0.1, only 4 genes (OLFML3, LOC100300716, MRPL15, and PUS10) were identified as differentially expressed in two or more cohorts, highlighting the importance of evaluating the transcriptome of more than one group of animals and incorporating a meta-analysis. This meta-analysis has produced many mesenteric fat DEG that may be contributing to gain and feed intake in cattle.

Microbiome of the upper nasal cavity of beef calves prior to weaning12

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.

Crossbreeding effects on growth and efficiency in beef cow-calf systems: evaluation of Angus, Caracu, Hereford and Nelore breed direct, maternal and heterosis effects

The objective of this study was to determine breed additive and heterosis effects on growth curves, total milk yield (TMY), calf weaning weight (WW), predicted energy intake (EI), and cow efficiency (CE) of purebred and crossbred beef cows raised in Southern Brazil. The data were from 175 purebred and crossbred cows representing eight genetic groups: Angus (A), Hereford (H), Nelore (N), A × H (AH), H × A (HA), A × N (AN), N × A (NA), and Caracu (C) × A (CA). Growth of the cows was modeled using the nonlinear Brody function and machine milking was used to assess TMY. WW was linearly adjusted to 210 d. EI was predicted with an equation in which the independent variables were estimates of parameters of the Brody function and TMY. The ratio of WW to EI estimated CE. Taurine–indicine heterosis effects were significant for all traits, and greater than those for taurine breed crosses. In general, crossbred cows were heavier at maturity, matured earlier, produced more milk, weaned heavier calves, and were predicted to consume more energy. Thus, they were more efficient than purebred cows, despite their greater predicted feed intake. Among the purebreds, A cows matured most rapidly, weighed the least at maturity, produced the most milk, weaned the heaviest calves, were predicted to consume the least energy; and were therefore most efficient among the breeds that were evaluated. These results are useful as inputs to bioeconomic models that can be used to predict productive and economic outcomes from crossbreeding and to facilitate recommendations for beef producers of southern Brazil and other similar subtropical climatic regions.

Comparison of different functions to describe growth from weaning to maturity in crossbred beef cattle1

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 R2 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.

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

Background

Bovine coronavirus (BCV) is associated with respiratory infections in cattle of all ages; however, a temporal study to evaluate the effect of BCV immunity on virus shedding and bovine respiratory disease (BRD) incidence in pre-weaned beef calves has not been reported. Thus, we report here a prospective study in three herds of crossbred beef calves (n = 817) with endemic BCV.

Serial blood samples for measurement of serum anti-BCV antibody titers and nasal swabs for detection of BCV and other common viral and bacterial BRD pathogens were collected from all calves or subsets of calves at predetermined times from birth through weaning. The calves were monitored for BRD and those that developed signs of respiratory disease were sampled for diagnostic testing. To discover additional risk factors that could have influenced BRD development, sequence analysis of the BCV strain(s) circulating in each herd, and the prevalence of common opportunistic bacterial pathogens in the upper respiratory tract of sick and apparently healthy cattle were also evaluated.

Results

Two hundred forty-eight of the 817 study calves (30.4%) were treated for BRD prior to weaning; 246 of those were from a single herd involved in two outbreaks of BRD leading to mass treatment of all calves in that group. Molecular diagnostic testing found BCV and Histophilus somni in nasal swabs taken at the time of BRD treatment. Between herd analyses revealed anti-BCV serum antibody abundance did not associate with the incidence of BRD or BCV shedding, though these measurements may have been hindered by the long periods between sample collections. Analysis of the BCV spike gene hypervariable region revealed four polymorphisms in 15 isolates from the three herds, making strain variation unlikely to account for differences in treatment rates between herds. Persistent or recurrent shedding episodes of BCV occurred in some animals treated for BRD.

Conclusion

Co-detection of BCV and H. somni at the time of the disease outbreak suggests that these pathogens contributed to disease pathogenesis. Developing appropriate control measures for respiratory BCV infections may help decrease the incidence of pre-weaning BRD. The role of antibodies in protection must still be further defined.

Electronic supplementary material

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

Heterosis in cattle crossbreeding schemes in tropical regions: meta-analysis of effects of breed combination, trait type, and climate on level of heterosis

The aim of this study was to investigate the effects of animal trait, breed combination, and climate on the expressed levels of heterosis in crossbreeding schemes using tropical cattle. A meta-analysis of 42 studies was carried out with 518 heterosis estimates. In total, 62.5% of estimates were found to be significantly different from zero, the majority of which (89.8%) were beneficial for the studied trait. Trait and breed combination were shown to have a significant effect on the size of heterosis (P < 0.001 and P = 0.044, respectively). However, climate did not have a significant effect. Health, longevity, and milk production traits showed the highest heterosis (31.84 ± 10.73%, 35.13 ± 14.35%, and 35.15 ± 3.29%, respectively), whereas fertility, growth, and maternal traits showed moderate heterosis (12.02 ± 4.10%, 12.25 ± 2.69%, and 15.69 ± 3.26%, respectively). Crosses between breeds from different types showed moderate to high heterosis ranging from 9.95 ± 4.53% to 19.53 ± 3.62%, whereas crosses between breeds from the same type did not express heterosis that was significantly different from zero. These results show that heterosis has significant and favorable impact on productivity of cattle farming in tropical production systems, particularly in terms of fitness but also milk production traits.

Genomic retained heterosis effects on fertility and lifetime productivity in beef heifers

This study evaluated the effects of three genomic indicators of heterosis on female fertility and lifetime productivity, and quantified changes over 11 production cycles in a crossbred cow herd. Pedigree-based breed composition (pBC) was determined and used to calculate retained heterozygosity for 412 replacement heifers born from 2004 to 2014 at the Lacombe Research and Development Centre (AB, Canada). Heifers were followed as cows over 1050 mating opportunities, 11 production cycles, and five parities. Heifers and their sires (51) were genotyped and these genotypes were used to predict each animal’s genomic breed composition (gBC) and three genomic indicators of heterosis: (1) retained heterozygosity (RHETg), (2) heterozygous proportion (H), and (3) retained heterosis (RHg). Correlations between pedigree and genomic breed fractions for Angus, Hereford, and Charolais were high (rp = 0.74–0.94; P < 0.001). Genomic indicators of heterosis were highly related (rp = 0.61 for RHETg vs. H; 0.71 for RHg vs. H; 0.96 for RHETg vs. RHg; P < 0.001). Each 10% change in RHETg resulted in 51 ± 20 d longer survival (P = 0.011) in the herd and 35.7 ± 15.2 kg more (P = 0.019) calf wean weight per cow exposed to breeding when summed over five parities. These differences resulted in an extra $161 per heifer in a year. Optimizing heterosis using genomic tools can be very beneficial for the cow herd if applied correctly.

Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves

OBJECTIVE

The purpose of this study was to evaluate potential relationships between cytokine gene expression, complete blood counts (CBC) and animals that were sick or would become sick. The CBC and the transcript abundance of cytokines and their receptors expressed in leukocytes were measured from calves at two early timepoints, and again after diagnosis with bovine respiratory disease (BRD).

RESULTS

Blood was collected from calves at pre-conditioning (n = 796) and weaning (n = 791) for CBC. Blood counts were also measured for the calves with BRD (n = 13), and asymptomatic calves (n = 75) after weaning. The CBC were compared for these animals at 3 time points. At diagnosis, neutrophils were higher and basophils lower in sick animals (P < 0.05). To further characterize BRD responses, transcript abundance of 84 cytokine genes were evaluated in 5 calves with BRD and 9 asymptomatic animals at all time points. There was more data for CBC than transcript abundance; hence, animal and temporary environmental correlations between CBC and transcript abundance were exploited to improve the power of the transcript abundance data. Expression of CCL16, CXCR1, CCR1 was increased in BRD positive animals compared to controls (P-corrected < 0.1). Cytokine expression data may help to provide insight into an animal's health.

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

BACKGROUND

Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations.

METHODS

Illumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb.

RESULTS

Seven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals.

CONCLUSIONS

Our results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis.

Rumen bacterial community structure impacts feed efficiency in beef cattle

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses.

Modeling heterotic effects in beef cattle using genome-wide SNP-marker genotypes

An objective of commercial beef cattle crossbreeding programs is to simultaneously optimize use of additive (breed differences) and non-additive (heterosis) effects. A total of 6,794 multibreed and crossbred beef cattle with phenotype and Illumina BovineSNP50 genotype data were used to predict genomic heterosis for growth and carcass traits by applying two methods assumed to be linearly proportional to heterosis. The methods were as follows: 1) retained heterozygosity predicted from genomic breed fractions (HET1) and 2) deviation of adjusted crossbred phenotype from midparent value (HET2). Comparison of methods was based on prediction accuracy from cross-validation. Here, a mutually exclusive random sampling of all crossbred animals (n = 5,327) was performed to form five groups replicated five times with approximately 1,065 animals per group. In each run within a replicate, one group was assigned as a validation set, while the remaining four groups were combined to form the reference set. The phenotype of the animals in the validation set was assumed to be unknown; thus, it resulted in every animal having heterosis values that were predicted without using its own phenotype, allowing their adjusted phenotype to be used for validation. The same approach was used to test the impact of predicted heterosis on accuracy of genomic breeding values (GBV). The results showed positive heterotic effects for growth traits but not for carcass traits that reflect the importance of heterosis for growth traits in beef cattle. Heterosis predicted by HET1 method resulted in less variable estimates that were mostly within the range of estimates generated by HET2. Prediction accuracy was greater for HET2 (0.37-0.98) than HET1 (0.34-0.43). Proper consideration of heterosis in genomic evaluation models has debatable effects on accuracy of EBV predictions. However, opportunity exists for predicting heterosis, improving accuracy of genomic selection, and consequently optimizing crossbreeding programs in beef cattle.

Association of preweaning and weaning serum cortisol and metabolites with ADG and incidence of respiratory disease in beef cattle

The objectives of this experiment were to determine the association of circulating cortisol, lactate, and glucose at, and prior to, weaning with ADG and incidences of bovine respiratory disease (BRD) in beef cattle. A blood sample was collected approximately 3 wk prior to weaning and at weaning from genetically diverse steers and heifers ( = 451). Cattle were weighed periodically throughout the study and ADG was calculated for the preweaning period (152 ± 15 d), the receiving period (45 d postweaning), the finishing period (200 d), and total postweaning ADG. Incidences of BRD were recorded and analyzed as a binary trait. Lung lesions were recorded at slaughter. Preweaning serum cortisol concentrations were positively associated ( = 0.040) with receiving ADG and explained 0.74% of the variance of receiving ADG. Preweaning glucose concentrations were positively associated ( < 0.001) with preweaning ADG and negatively associated with receiving ( = 0.003), finishing ( = 0.008), and total postweaning ADG ( = 0.002) and explained 2.0% of the variance in total postweaning ADG. Variation in preweaning serum glucose concentrations could be indicative of variation in milk consumption, and therefore indicate calves receiving less milk grow slower prior to weaning, but experience compensatory gain postweaning. Cattle that were diagnosed with BRD ( = 130) grew slower during the receiving phase ( = 0.004), but total postweaning ADG was not different from cattle not diagnosed with BRD ( = 0.683). Additionally, cattle that were diagnosed with BRD in the feedlot tended ( = 0.062) to have slightly lower preweaning serum glucose concentrations. Using a logistic regression analysis, none of the serum variables measured at or before weaning were predictive of developing BRD ( > 0.180). Weaning serum glucose concentrations tended to be predictive of the presence of lung lesions at weaning ( = 0.060). These data indicate that glucose measured early in life is associated with growth rate, and could indicate that carbohydrate metabolism could contribute to variation in ADG.

RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers

Background

Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency. In each cohort, 16 steers were selected from one of four gain and feed intake phenotypes (n = 4 per phenotype) in a 2 × 2 factorial arrangement with gain and feed intake as main effect variables. Each cohort was analyzed as a single experiment using a generalized linear model and results from the 5 cohort analyses were combined in a meta-analysis to identify differentially expressed genes (DEG) across the cohorts.

Results

A total of 51 genes were differentially expressed for the main effect of gain, 109 genes for the intake main effect, and 11 genes for the gain x intake interaction (P_corrected < 0.05). A jackknife sensitivity analysis showed that, in general, the meta-analysis produced robust DEGs for the two main effects and their interaction. Pathways identified from over-represented genes included mitochondrial energy production and oxidative stress pathways for the main effect of gain due to DEG including GPD1, NDUFA6, UQCRQ, ACTC1, and MGST3. For intake, metabolic pathways including amino acid biosynthesis and degradation were identified, and for the interaction analysis the pathways identified included GADD45, pyridoxal 5’phosphate salvage, and caveolar mediated endocytosis signaling.

Conclusions

Variation among DEG identified by cohort suggests that environment and breed may play large roles in the expression of genes associated with feed efficiency in the muscle of beef cattle. Meta-analyses of transcriptome data from groups of animals over multiple cohorts may be necessary to elucidate the genetics contributing these types of biological phenotypes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4769-8) contains supplementary material, which is available to authorized users.

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC)

Bovine respiratory disease complex (BRDC) is a multifactor disease, and disease incidence may be associated with an animal's commensal bacterial populations (microbiome) in the upper nasal cavity. Identifying these commensal bacterial populations in the upper nasal cavity may help us to understand the impact of the microbiome on incidence of BRDC in cattle. Various sampling techniques have previously been utilized to evaluate the microbiome of different locations of the upper nasal cavity in cattle. Therefore, our objective was to determine whether bacterial populations of the nasal cavity vary based on these sampling locations. Two common sampling techniques were evaluated, including 6-inch nasal swabs and deep nasopharyngeal swabs. Nasal swabs from calves were collected when the animal was diagnosed with BRDC after weaning in the feedlot in addition to collection of samples from asymptomatic cohorts. Samples were pooled in groups based on year the animal was in the feedlot (2015 or 2016), when the animal was diagnosed with BRDC (1 to 5 weeks after weaning), type of sample (6-inch nasal swab or deep nasopharyngeal swab), and health status (diagnosis with BRDC or control). Variable regions 1 through 3 along the 16S rRNA gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Overall, sampling site did not consistently influence diversity of the bacterial populations of the upper nasal cavity. However, the effect of disease incidence on the microbiome was depended on sampling time after weaning (P = 0.0462) for 2015, while the main effects of sampling time after weaning (P = 0.00992) and disease phenotype (P = 0.012) were significant for 2016. These data for 2016 demonstrate that in addition to bacterial profiles changing throughout weaning, calves diagnosed with BRDC have different bacterial profiles compared to their control cohorts. In addition, evaluation of the microbiome identified predominant bacteria genera in the upper nasal cavity included those previously reported to be associated with cattle diagnosed with BRDC including Mycoplasma sp., Psychrobacter sp., and Mannheimia sp. In summary, these results demonstrate that shorter, less invasive 6-inch nasal swabs produce similar results to deep nasopharyngeal swabs.

Economic selection index development for Beefmaster cattle II: General-purpose breeding objective

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.

Relationships between the genes expressed in the mesenteric adipose tissue of beef cattle and feed intake and gain

Mesenteric fat, a depot within the visceral fat, accumulates in cattle during maturation and finishing and may be a potential source of production inefficiency. The aim of this study was to determine whether the genes expressed in the mesenteric fat of steers were associated with body weight gain and feed intake. Sixteen steers chosen by their rank of distance from the bivariate mean for gain and feed intake were used for this study. Mesenteric fat was obtained and evaluated for differences in gene expression. A total of 1831 genes were identified as differentially expressed among steers with variation in feed intake and gain. Many of these genes were involved with metabolic processes such as proteolysis, transcription and translation. In addition, the Gene Ontology annotations including transport and localization were both over-represented among the differentially expressed genes. Pathway analysis was also performed on the differentially expressed genes. The superoxide radical degradation pathway was identified as over-represented based on the differential expression of the genes GPX7, SOD2 and TYRP1, suggesting a potential role for oxidative stress or inflammatory pathways among low gain-high intake animals. GPX7 and SOD2 were in lower transcript abundance, and TYRP1 was higher in transcript abundance among the low gain-high feed intake animals. The retinoate biosynthesis pathway was also enriched due to the differential expression of the genes AKR1C3, ALDH8A1, RDH8, RDH13 and SDR9C7. These genes were all more highly expressed in the low gain-high intake animals. The glycerol degradation and granzyme A signaling pathways were both associated with gain. Three glycerol kinase genes and the GZMA gene were differentially expressed among high vs. low gain animals. Mesenteric fat is a metabolically active tissue, and in this study, genes involved in proteolysis, transcription, translation, transport immune function, glycerol degradation and oxidative stress were differentially expressed among beef steers with variation in body weight gain and feed intake.

Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake

We have previously identified components of the immune system contributing to feed intake and gain in both the rumen and small intestine of beef steers. In this study, we examined the spleen, a major lymphatic organ near the digestive tract, to determine whether it was also influencing individual feed efficiency status through immune responses. Animals (n = 16) that were divergent for gain and intake were selected for tissue sampling. The spleen transcriptomes were evaluated by microarray. A total of 1216 genes were identified as differentially expressed. Genes were over-represented in Kyoto encyclopedia of genes and genomes (KEGG) pathways including biological regulation, protein folding, cell communication, immune systems process, response to stress, and RNA metabolic process. Several stress response or heat shock genes including HSPH1, HSPA1A, HSPA4, DNAJB4, DNAJA4, etc., were identified as a stress response functional gene cluster in the low gain-low intake animals. These genes were up-regulated amongst the low gain-low intake animals compared to all other groups. Canonical pathways associated with the differentially expressed genes included the coagulation system, extrinsic prothrombin activation, protein ubiquitination, unfolded protein response, and aldosterone signaling in epithelial cells. An analysis of expressed copy number variable (CNV) genes in the spleen produced some of the same genes and gene families that were differentially expressed. Our data suggests the splenic contribution to some of the underlying variation among gain and intake within this group of animals may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to gene copy number.

Relationship of leptin concentrations with feed intake, growth, and efficiency in finishing beef steers

The objective of this experiment was to determine the association of serum leptin concentrations with production measures including DMI, ADG, and G:F as well as carcass characteristics in genetically diverse finishing beef steers. Three cohorts of steers ( = 473 total) were individually fed a finishing ration for 92, 64, and 84 d for cohort 1, 2, and 3, respectively. Serum was collected on d 42, 22, and 19 of the experiment for cohort 1, 2, and 3, respectively. Leptin concentrations were positively correlated to DMI ( = 0.21, < 0.01) but negatively correlated to grams DMI per kilogram initial BW ( = -0.21, < 0.01). Leptin concentrations were also negatively correlated to ADG and G:F ( < 0.01). Leptin concentrations were positively correlated to 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and negatively correlated to LM area ( < 0.01). Using a mixed model analysis (SAS 9.3; SAS Inst. Inc., Cary, NC) to account for breed effects, leptin concentrations were positively associated with DMI ( = 0.01) and accounted for 1.10% of the variance. However, if initial BW and yield grade were included as covariates to account for body size and fatness, leptin was negatively associated with DMI ( = 0.02) and accounted for 0.54% of the variance. Regardless of covariates included in the model, leptin was negatively associated with ADG ( < 0.01) and G:F ( < 0.01) and accounted for 2.62 and 7.87% of the variance for ADG and G:F, respectively. Leptin concentrations were also positively associated with 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and accounted for 14.74, 12.74, and 6.99% of the variance for 12th-rib fat, yield grade, and marbling score, respectively. Leptin concentrations could be a useful physiological marker for growth and feed efficiency of finishing beef cattle. Genetic influences on the biology of leptin also need to be considered when using leptin as physiological marker for production measures.

Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes

Small intestine mass and cellularity were previously associated with cattle feed efficiency. The small intestine is responsible for the digestion of nutrients and absorption of fatty acids, amino acids and carbohydrates, and it contributes to the overall feed efficiency of cattle. The objective of this study was to evaluate transcriptome differences among the small intestine from cattle with divergent gain and feed intake. Animals most divergent from the bivariate mean in each of the four phenotypic Cartesian quadrants for gain × intake were selected, and the transcriptomes of duodenum, jejunum and ileum were evaluated. Gene expression analyses were performed comparing high gain vs. low gain animals, high intake vs. low intake animals and each of the phenotypic quadrants to all other groups. Genes differentially expressed within the high gain-low intake and low gain-high intake groups of animals included those involved in immune function and inflammation in all small intestine sections. The high gain-high intake group differed from the high gain-low intake group by immune response genes in all sections of the small intestine. In all sections of small intestine, animals with low gain-low intake displayed greater abundance of heat-shock genes compared to other groups. Several over-represented pathways were identified. These include the antigen-processing/presentation pathway in high gain animals and PPAR signaling, starch/sucrose metabolism, retinol metabolism and melatonin degradation pathways in the high intake animals. Genes with functions in immune response, inflammation, stress response, influenza pathogenesis and melatonin degradation pathways may have a relationship with gain and intake in beef steers.

Transcriptome differences in the rumen of beef steers with variation in feed intake and gain

BACKGROUND

Feed intake and gain are economically important traits in beef production. The rumen wall interacts with feed, microbial populations, and fermentation products important to cattle nutrition. As such, it is likely to be a critical component in the beef steer's ability to utilize feedstuffs efficiently. To identify genes associated with steer feed intake and body weight gain traits, and to gain an understanding of molecules and pathways involved in feed intake and utilization, RNA sequencing (RNA-Seq) was performed on rumen papillae from 16 steers with variation in gain and feed intake. Four steers were chosen from each of the four Cartesian quadrants for gain×feed intake and used to generate individual RNA-Seq libraries.

RESULTS

Normalized read counts from all of the mapped reads from each of the four groups of animals were individually compared to the other three groups. In addition, differentially expressed genes (DEGs) between animals with high and low gain, as well as high and low intake were also evaluated. A total of 931 genes were differentially expressed in the analyses of the individual groups. Eighty-nine genes were differentially expressed between high and low gain animals; and sixty-nine were differentially expressed in high versus low intake animals. Several of the genes identified in this study have been previously associated with feed efficiency. Among those are KLK10, IRX3, COL1A1, CRELD2, HDAC10, IFITM3, and VIM.

CONCLUSIONS

Many of the genes identified in this study are involved with immune function, inflammation, apoptosis, cell growth/proliferation, nutrient transport, and metabolic pathways and may be important predictors of feed intake and gain in beef cattle.