Search

Context: Feed is the largest expense on a dairy farm, therefore improving feed efficiency is important. Recording dry-matter intake (DMI) is a prerequisite for calculating feed efficiency. Genetic variation of feed intake and feed efficiency varies across lactation stages and parities. DMI is an expensive and difficult-to-measure trait. This raises the question of which time periods during lactation would be most appropriate to measure DMI.Aims: The aim was to evaluate whether sequence variants selected from genome-wide association studies (GWAS) for DMI recorded at multiple lactation time periods and parities would increase the accuracy of genomic estimated breeding values (GEBVs) for DMI and residual feed intake (RFI).Methods: Data of 2274 overseas lactating cows were used for the GWAS to select sequence variants. GWAS was performed using the average of the DMI phenotypes in a 30-day window of six different time periods across the lactation. The most significant sequence variants were selected from the GWAS at each time period for either first or later parities. GEBVs for DMI and RFI in Australian lactating cows were estimated using BayesRC with 50 k single nucleotide polymorphisms (SNPs) and selected GWAS sequence variants.Key results: There were differences in DMI genomic correlations and heritabilities between first and later parities and within parity across lactation time periods. Compared with using 50 k single-nucleotide polymorphisms (SNPs) only, the accuracy of DMI GEBVs increased by up to 11% by using the 50 k SNPs plus the selected sequence variants. Compared with DMI, the increase in accuracy for RFI was lower (by 6%) likely because the sequence variants were selected from GWAS for DMI not RFI. The accuracies for DMI and RFI GEBVs were highest by using selected sequence variants from the DMI GWAS in the mid- to late-lactation periods in later parity.Conclusions: Our results showed that DMI phenotypes in late lactation time periods could capture more genetic variation and increase genomic prediction accuracy through the use of custom genotype panels in genomic selection.Implications: Collecting DMI at the optimal time period(s) of lactation may help develop more accurate and cost-effective breeding values for feed efficiency in dairy cattle.

There has been an increasing interest in residual feed intake (RFI) as a measure of net feed efficiency in dairy cattle. RFI phenotypes are obtained as residuals from linear regression encompassing relevant factors (i.e., energy sinks) to account for body tissue mobilization. However, fitting energy sink phenotypes as regression variables in standard linear regression was criticized because phenotypes are subject to measurement errors. Multiple-trait models have been proposed which derive RFI by follow-up partial regression. By re-arranging the single-trait linear regression, we showed a causal RFI interpretation underlying the linear regression for RFI. It postulates recursive effects in energy allocation from energy sinks on dry matter intake, but the feedback or simultaneous effects are assumed to be nonexistent. A Bayesian recursive structural equation model was proposed for directly predicting RFI and energy sinks and estimating relevant genetic parameters simultaneously. A simplified Markov chain Monte Carlo algorithm that implemented the Bayesian recursive model was described. The recursive model is asymptotically equivalent to one-step linear regression for RFI, yet extends the analytical capacity to multiple-trait analysis. It is equivalent to Bayesian-implemented, multiple-trait model reparameterized based on Cholesky decomposition of phenotypic (co)variance matrix for evaluating RFI, but varied in assumptions about relationships between energy sinks., Comment: 12 pages, 2 Tables, and 1 Figure

Using the 10× Genomics Chromium Controller, we obtained scRNA-seq data of 5064 and 1372 individual cells from two Holstein calf ruminal epithelial tissues before and after weaning, respectively. We detected six distinct cell clusters, designated their cell types, and reported their marker genes. We then examined these clusters' underlining cell types and relationships by performing cell cycle, pseudotime trajectory, regulatory network, weighted gene co-expression network and gene ontology analyses. By integrating these cell marker genes with Holstein GWAS signals, we found they were enriched for animal production and body conformation traits. Finally, we confirmed their cell identities by comparing them with human and mouse stomach epithelial cells. This study presents an initial effort to implement single-cell transcriptomic analysis in cattle, and demonstrates ruminal tissue epithelial cell types and their developments during weaning, opening the door for new discoveries about tissue/cell type roles in complex traits at single-cell resolution.

Intestinal organoids grown in extracellular matrix exhibit epithelial cell polarity with the apical surface internal to the organoid, limiting its access for functional studies. Apical-out organoids can be formed in matrix-free media (in suspension), which introduces different challenges for organoid manipulation (e.g., loss during media changes or washing) due to their “free-floating” nature. Both techniques result in multiple depths of view during visualization. We aimed to determine whether uniformly sized apical-out organoids from chicken could be grown, visualized, and recovered from microcavity culture plates designed for uniform growth of spheroids. Apical-out organoids were developed from crypts/villi isolated from duodenum/jejunum of embryonic-day 18 chicks (ROSS 308) placed in culture media in 12 wells of a 24-well, round-bottom Elplasia culture plate (Corning) at 37°C, 5% CO2 (Day 0). Each well has ~554 microcavities and was seeded with an estimated 300 crypts/villi. Organoid number and area (μm2) were determined daily using an ECHO Revolve Microscope (4x magnification) on Days 1 to 6 from 7 fields of view per well (~33 microcavities per field of view). On Day 1, mean ± SE organoid area was 3,106 ± 60 μm2 (n = 3,590); mean of 43 ± 1 organoids per field. Some organoids exhibited budding by Day 6 where mean area was 5,208 ± 125 μm2 (n = 2,599); 31 ± 1 organoids per field. Organoids were easily recovered from the microcavities of each well for seeding into a 96-well plate and maintenance for an additional 32 h. Analysis at 16.5, 20, 24, 28, and 32 h using PrestoBlue HS (Invitrogen) and a fluorometric microplate reader indicated organoids remained viable for downstream analysis. In conclusion, microcavity culture plates greatly increased ease of visualization, counting, and manipulation of organoids grown in suspension, but organoid size was highly variable.

Improving feed efficiency (FE) of dairy cattle may boost farm profitability and reduce the environmental footprint of the dairy industry. Residual feed intake (RFI), a candidate FE trait in dairy cattle, can be defined to be genetically uncorrelated with major energy sink traits (e.g., milk production, body weight) by including genomic predicted transmitting ability of such traits in genetic analyses for RFI. We examined the genetic basis of RFI through genome-wide association (GWA) analyses and post-GWA enrichment analyses and identified candidate genes and biological pathways associated with RFI in dairy cattle. Data were collected from 4,823 lactations of 3,947 Holstein cows in 9 research herds in the United States. Of these cows, 3,555 were genotyped and were imputed to a high-density list of 312,614 SNP. We used a single-step GWA method to combine information from genotyped and nongenotyped animals with phenotypes as well as their ancestors' information. The estimated genomic breeding values from a single-step genomic BLUP were back-solved to obtain the individual SNP effects for RFI. The proportion of genetic variance explained by each 5-SNP sliding window was also calculated for RFI. Our GWA analyses suggested that RFI is a highly polygenic trait regulated by many genes with small effects. The closest genes to the top SNP and sliding windows were associated with dry matter intake (DMI), RFI, energy homeostasis and energy balance regulation, digestion and metabolism of carbohydrates and proteins, immune regulation, leptin signaling, mitochondrial ATP activities, rumen development, skeletal muscle development, and spermatogenesis. The region of 40.7 to 41.5 Mb on BTA25 (UMD3.1 reference genome) was the top associated region for RFI. The closest genes to this region, CARD11 and EIF3B, were previously shown to be related to RFI of dairy cattle and FE of broilers, respectively. Another candidate region, 57.7 to 58.2 Mb on BTA18, which is associated with DMI and leptin signaling, was also associated with RFI in this study. Post-GWA enrichment analyses used a sum-based marker-set test based on 4 public annotation databases: Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Reactome pathways, and medical subject heading (MeSH) terms. Results of these analyses were consistent with those from the top GWA signals. Across the 4 databases, GWA signals for RFI were highly enriched in the biosynthesis and metabolism of amino acids and proteins, digestion and metabolism of carbohydrates, skeletal development, mitochondrial electron transport, immunity, rumen bacteria activities, and sperm motility. Our findings offer novel insight into the genetic basis of RFI and identify candidate regions and biological pathways associated with RFI in dairy cattle.

The rumen is a critical organ mediating nutrient uptake and use in cattle. Healthy rumen development is essential to ensure animal feed efficiency. In this work, we present an analysis of transcriptomic dynamics in rumen epithelium during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning (eighteen Holstein bull calves, 3 X 6 groups). These two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on key pathways. Our analysis identifies putative signaling events and effectors. Gene activity shifts indicated the transcriptomic reprogramming required to induce developmental changes in ruminal epithelium and functional transitions. A principal component analysis distinguished the temporal expression patterns that clustered separately between pre- and post-weaning groups. A GO-term enrichment analysis reflected functional (physical and metabolic) development of ruminal epithelium and revealed the greatest number of DEGs were enriched in biological processes related to energy metabolism. Canonical pathway and upstream regulator analyses revealed transcription reprogramming with clusters of critical pathways and upstream regulators controlling functional and developmental transitions with no significant differences between hay- and concentrate-fed groups at weaning. The most highly activated transcription factors expressed during the weaning transition were PPARGC1A, INSR, NFE2L2, MYC, MYCN, and PPARA. Overall, the dietary shift from liquid to solid feeds prompted transcriptional reprogramming in rumen epithelial tissue reflecting critical nutrient-gene interactions occurring during the developmental progression of ruminant digestion.

Residual feed intake (RFI) is an estimate of animal feed efficiency, calculated as the difference between observed and expected feed intake. Expected intake typically is derived from a multiple regression model of dry matter intake on energy sinks, including maintenance and growth in growing animals, or maintenance, gain in body reserves, and milk production in lactating animals. The best period during the production cycle of a dairy cow to estimate RFI is not clear. Here, we characterized RFI in growing Holstein heifers (RFIGrowth; ∼10 to 14 mo of age; n = 226) and cows throughout a 305-d lactation (RFILac-Full; n = 118). The goals were to characterize relationships between RFI estimated at different production stages of the dairy cow; determine effects of selection for efficiency during growth on subsequent lactation and feed efficiency; and identify the most desirable testing scheme for RFILac-Full. For RFIGrowth, intake was predicted from multiple linear regression of metabolizable energy (ME) intake on mid-test body weight (BW)0.75 and average daily gain (ADG). For RFILac-Full, predicted intake was based on regression of BW0.75, ADG, and energy-corrected milk yield. Mean energy intake of the least and most efficient growing heifers (±0.5 standard deviations from mean RFIGrowth of 0) differed by 3.01 Mcal of ME/d, but the groups showed no difference in mid-test BW or ADG. Phenotypic correlation between RFIGrowth and RFI of heifers estimated in the first 100 d in milk (RFILac100DIM; n = 130) was 0.37. Ranking of these heifers as least (mean + 0.5 standard deviations), middle, or most efficient (mean - 0.5 standard deviations) based on RFIGrowth resulted in 43% maintaining the same ranking by RFILac100DIM. On average, the most efficient heifers ate 3.27 Mcal of ME/d less during the first 100 DIM than the least efficient heifers, but exhibited no differences in average energy-corrected milk yield, ADG, or BW. The correlation between RFILac100DIM and RFILac-Full was 0.72. Thus, RFIGrowth may serve as an indicator trait for RFI during lactation, and selection for heifers exhibiting low RFIGrowth should improve overall herd feed efficiency during lactation. Correlation analysis between RFILac-Full (10 to 305 DIM) and subperiod estimates of RFI during lactation indicated a test period of 64 to 70 d in duration occurring between 150 to 220 DIM provided a reliable approximation (r ≥ 0.90) of RFILac-Full among the test periods evaluated.

Simple Summary With the increasing cost of production, increasing global population, and a greater focus on sustainability, methods to improve cow efficiency are becoming critical for the dairy industry. An efficient cow is the one that produces the same amount of milk and milk solids while consuming less feed and remaining healthy and fertile; thus, allowing for a reduction of costs without reduced production. This simulation showed that directly selecting on feed conversion efficiency allowed for an economically advantageous and more balanced response to selection than indirect selection on feed intake. If too much selection pressure is placed on feed efficiency, there are negative implications for other traits within the selection index. Further work is required to optimize the methods for including feed efficiency in a selection index. Abstract The inclusion of feed efficiency in the breeding goal for dairy cattle has been discussed for many years. The effects of incorporating feed efficiency into a selection index were assessed by indirect selection (dry matter intake) and direct selection (residual feed intake) using deterministic modeling. Both traits were investigated in three ways: (1) restricting the trait genetic gain to zero, (2) applying negative selection pressure, and (3) applying positive selection pressure. Changes in response to selection from economic and genetic gain perspectives were used to evaluate the impact of including feed efficiency with direct or indirect selection in an index. Improving feed efficiency through direct selection on residual feed intake was the best scenario analyzed, with the highest overall economic response including favorable responses to selection for production and feed efficiency. Over time, the response to selection is cumulative, with the potential for animals to reduce consumption by 0.16 kg to 2.7 kg of dry matter per day while maintaining production. As the selection pressure increased on residual feed intake, the response to selection for production, health, and fertility traits and body condition score became increasingly less favorable. This work provides insight into the potential long-term effects of selecting for feed efficiency as residual feed intake.

We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.

Background Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. Results Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. Conclusions This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.

Olfactory receptors are G-protein-coupled chemoreceptors expressed on millions of olfactory sensory neurons within the nasal cavity. These receptors detect environmental odorants and signal the brain regarding the location of feed, potential mates, and the presence of possible threats (e.g., predators or chemical toxins). Olfactory receptors also are present in organs outside of the nasal cavity where they bind to molecules such as nutrients and metabolites from the animal's internal environment to elicit physiological responses, including changes in gut motility, ventilation rate, and cellular migration. Recent evidence supports an additional role of olfactory receptors in the regulation of appetite in humans and rodents. In particular, genetic variation among individuals in specific odorant receptor genes has been linked to differences in their feeding behaviors, food choices, and the regulation of energy balance. This review provides a general overview of the olfactory receptors of vertebrates and their genetic variability and provides supporting evidence for a physiological role of olfactory receptors in appetite regulation of livestock. Basic research on olfactory receptors of livestock and their ligands should facilitate the development of novel odorant receptor agonists and identification of specific olfactory receptor variants that may be developed to enhance animal production efficiency.

The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain β-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output.

Simple Summary The rumen is the critical organ mediating nutrient uptake and use in cattle. Health development is essential to ensure animal feed efficiency. In this report, we present an analysis of gene expression dynamic in rumen epithelium during the transition from pre-ruminant to ruminant in cattle fed with hay or concentrated diets at weaning. The global shifts in gene expression and correlated transcription factors activities indicate transcriptional reprogramming during weaning. Transcriptional reprogramming in rumen epithelial tissue reflects critical nutrient-gene interactions occurring during the developmental progression. The results unveiled that nutrient-gene interactions compel transcriptional reprogramming. Our findings also suggest that this transcriptional reprogramming is the molecular basis of the transitional development of pre-ruminant to the ruminant in cattle. Abstract We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways. The dietary shift from liquid to solid feeds prompted the shifting of gene activity. The number of differentially expressed genes increased significantly after weaning. Bioinformatic analysis revealed gene activity shifts underline the functional transitions in the ruminal epithelium and signify the transcriptomic reprogramming. Gene ontogeny (GO) term enrichment shows extensively activated biological functions of differentially expressed genes in the ruminal epithelium after weaning were predominant metabolic functions. The transcriptomic reprogramming signifies a correlation between gene activity and changes in metabolism and energy production in the rumen epithelium, which occur at weaning when transitioning from glucose use to VFA use by epithelium during the weaning.

Feed efficiency (FE), characterized as the fraction of feed nutrients converted into salable milk or meat, is of increasing economic importance in the dairy industry. We conjecture that FE is a complex trait whose variation and relationships or partial efficiencies (PE) involving the conversion of dry matter intake to milk energy and metabolic body weight may be highly heterogeneous across environments or management scenarios. In this study, a hierarchical Bayesian multivariate mixed model was proposed to jointly infer upon such heterogeneity at both genetic and nongenetic levels on PE and variance components (VC). The heterogeneity was modeled by embedding mixed effects specifications on PE and VC in addition to those directly specified on the component traits. We validated the model by simulation and applied it to a joint analysis of a dairy FE consortium data set with 5,088 Holstein cows from 13 research stations in Canada, the Netherlands, the United Kingdom, and the United States. Although no differences were detected among research stations for PE at the genetic level, some evidence was found of heterogeneity in residual PE. Furthermore, substantial heterogeneity in VC across stations, parities, and ration was observed with heritability estimates of FE ranging from 0.16 to 0.46 across stations.

Background The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively utilizing the increased amount of genome sequences reported. However, while such annotation has been well explored in a diverse set of tissues and cell types in human and model organisms, relatively little data are available for livestock genomes, hindering our understanding of complex trait variation, domestication, and adaptive evolution. Here, we present the first complete global landscape of regulatory elements in cattle and explore the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator—butyrate. Results We established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle, through genome-wide profiling for six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial primary cells (REPC), rumen tissues, and Madin-Darby bovine kidney epithelial cells (MDBK). We demonstrated that each chromatin state exhibited specific enrichment for sequence ontology, transcription, methylation, trait-associated variants, gene expression-associated variants, selection signatures, and evolutionarily conserved elements, implying distinct biological functions. After butyrate treatments, we observed that the weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states, occurred concomitantly with significant alterations in gene expression and DNA methylation, which was significantly associated with heifer conception rate and stature economic traits. Conclusion Our results demonstrate the crucial role of functional genome annotation for understanding genome regulation, complex trait variation, and adaptive evolution in livestock. Using butyrate to induce the dynamics of the epigenomic landscape, we were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Electronic supplementary material The online version of this article (10.1186/s12915-019-0687-8) contains supplementary material, which is available to authorized users.

Numerous endocrine cell subtypes exist within the intestinal mucosa and produce peptides contributing to the regulation of critical physiological processes including appetite, energy metabolism, gut function, and gut health. The mechanisms of action and the extent of the physiological effects of these enteric peptides are only beginning to be uncovered. One peptide in particular, glucagon-like peptide 2 (GLP-2) produced by enteroendocrine L cells, has been fairly well characterized in rodent and swine models in terms of its ability to improve nutrient absorption and healing of the gut after injury. In fact, a long-acting form of GLP-2 recently has been approved for the management and treatment of human conditions like inflammatory bowel disease and short bowel syndrome. However, novel functions of GLP-2 within the gut continue to be demonstrated, including its beneficial effects on intestinal barrier function and reducing intestinal inflammation. As knowledge continues to grow about GLP-2's effects on the gut and its mechanisms of release, the potential to use GLP-2 to improve gut function and health of food animals becomes increasingly more apparent. Thus, the purpose of this review is to summarize: (1) the current understanding of GLP-2's functions and mechanisms of action within the gut; (2) novel applications of GLP-2 (or stimulators of its release) to improve general health and production performance of food animals; and (3) recent findings, using dairy calves as a model, that suggest the therapeutic potential of GLP-2 to reduce the pathogenesis of intestinal protozoan infections.

As a critical and high-value tool to study the development of rumen, we established a stable rumen epithelial primary cell (REPC) culture from a two-week-old Holstein bull calf rumen epithelial tissue. The transcriptomic profiling of the REPC and the direct effects of butyrate on gene expression were assessed. Correlated gene networks elucidated the putative roles and mechanisms of butyrate action in rumen epithelial development. The top networks perturbed by butyrate were associated with epithelial tissue development. Additionally, two critical upstream regulators, E2F1 and TGFB1, were identified to play critical roles in the differentiation, development, and growth of epithelial cells. Significant expression changes of upstream regulators and transcription factors provided further evidence in support that butyrate plays a specific and central role in regulating genomic and epigenomic activities influencing rumen development. This work is the essential component to obtain a complete global landscape of regulatory elements in cattle and to explore the dynamics of chromatin states in rumen epithelial cells induced by butyrate at early developmental stages., Agriculture; Bioinformatics; Cell biology; Developmental biology; Butyrate, epigenetic regulation; epithelium; rumen; transcriptome

Background Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been applied in livestock, although few studies have focused on Holstein cattle. Results We describe 191 CNV detected using intensity data from over 700,000 SNP genotypes generated with the BovineHD Genotyping BeadChip (Illumina, San Diego, CA) in 528 Holstein cows. The CNV were used for GWAS analysis of 10 important production traits of 473 cattle related to feed intake, milk quality, and female fertility, as well as 2 composite traits of net merit and productive life. In total, we detected 57 CNV associated (P

Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.

Genome-wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 cows from 16 stations in 4 counties. Of these cows, 4,916 had genotypes on 57,347 single nucleotide polymorphism (SNP) markers. We compared a GWA analysis based on the more classical residual feed intake (RFI) model with one based on a previously proposed multiple trait (MT) approach for modeling FE using an alternative measure (DMI|MILKE,MBW). Both models were based on a single-step genomic BLUP procedure that allowed the use of phenotypes from both genotyped and nongenotyped cows. Estimated effects for single SNP markers were small and not statistically important but virtually identical for either FE measure (RFI vs. DMI|MILKE,MBW). However, upon further refining this analysis to develop joint tests within nonoverlapping 1-Mb windows, significant associations were detected between either measure of FE with a window on each of Bos taurus autosomes BTA12 and BTA26. There was, as expected, no overlap between detected genomic regions for DMI|MILKE,MBW and genomic regions influencing the energy sink traits (i.e., MILKE and MBW) because of orthogonal relationships clearly defined between the various traits. Conversely, GWA inferences on DMI can be demonstrated to be partly driven by genetic associations between DMI with these same energy sink traits, thereby having clear implications when comparing GWA studies on DMI to GWA studies on FE-like measures such as RFI.

Glucagon-like peptide-2 (GLP-2) is a 33-amino acid peptide derived from proteolytic cleavage of proglucagon by prohormone convertase 1/3 in enteroendocrine L cells. Studies conducted in humans, in rodent models, and in vitro indicate that GLP-2 is secreted in response to the presence of molecules in the intestinal lumen, including fatty acids, carbohydrates, amino acids, and bile acids, which are detected by luminal chemosensors. The physiological actions of GLP-2 are mediated by its G protein-coupled receptor expressed primarily in the intestinal tract on enteric neurons, enteroendocrine cells, and myofibroblasts. The biological activity of GLP-2 is further regulated by dipeptidyl peptidase IV, which rapidly cleaves the N-terminus of GLP-2 that is responsible for GLP-2 receptor activation. Within the gut, GLP-2 increases nutrient absorption, crypt cell proliferation, and mesenteric blood flow and decreases gut permeability and motility, epithelial cell apoptosis, and inflammation. Outside the gut, GLP-2 reduces bone resorption, can suppress appetite, and is cytoprotective in the lung. Thus, GLP-2 has been studied intensively as a therapeutic to improve intestinal function of humans during parenteral nutrition and following small bowel resection and, more recently, as a treatment for osteoporosis and obesity-related disorders and to reduce cellular damage associated with inflammation of the gut and lungs. Recent studies demonstrate that many biological actions and properties of GLP-2 in ruminants are similar to those in nonruminants, including the potential to reduce intestinal nitro-oxidative stress in calves caused by parasitic diseases such as coccidiosis. Because of its beneficial impacts on nutrient absorption, gut healing, and normal gut development, GLP-2 therapy offers significant opportunities to improve calf health and production efficiency. However, GLP-2 therapies require an extended time course to achieve desired physiological responses, as well as daily administration because of the hormone's short half-life. Thus, practical means of administration and alternative strategies to enhance basal GLP-2 secretion (e.g., through specific feed additives), which are more likely to achieve consumer acceptance, are needed. Opportunities to address these challenges are discussed.

The 4 major tocopherol isoforms differ in their biochemical reactivity and cellular effects due to basic chemical structural differences. Alpha-tocopherol has been well studied regarding effects on bovine polymorphonuclear leukocyte (PMN) function and its involvement in respiratory burst. However, no studies to date have identified the effects of supplementing a mixed tocopherol oil (Tmix) particularly enriched in non-α tocopherol isoforms (i.e., γ- and δ-isoforms) on fundamental immunometabolic changes in dairy cows. Therefore, the objectives of this study were to determine whether short-term feeding of vegetable oil-derived Tmix alters specific biomarkers of metabolism, whole-blood leukocyte populations, respiratory burst, immunometabolic-related gene expression of PMN, or gene expression of isolated PMN when challenged with lipopolysaccharides (LPS). Clinically healthy multiparous lactating Holstein cows (n = 12; 179 ± 17 d in milk, 40.65 ± 3.68 kg of milk yield) were fed Tmix (620 g/d) for 7 consecutive days. Jugular blood (EDTA anticoagulant) was collected from all cows on d 0 before treatment initiation and again on d 7 after Tmix feeding. Total stimulated respiratory burst activity (RBA) and leukocyte populations were assessed in whole blood, and tocopherol isoform concentrations, metabolites, and hormones were measured in plasma. For gene expression analysis, isolated PMN from cows before and after Tmix feeding were incubated with LPS at a final concentration of either 0.0 or 1.5 µg/mL. Feeding of Tmix for 7 d increased the concentrations of α- and γ-tocopherol. The Tmix did not alter plasma insulin but decreased cholesterol. The Tmix did not alter whole-blood RBA or the leukocyte populations. The LPS challenge increased the expression of proinflammatory genes TNFA and IL6. However, Tmix treatment did not alter the patterns of LPS-affected expression of genes (e.g., TNFA, ITGB2, PPARA, and RXRA) associated with the immune or metabolic response. In conclusion, short-term feeding of Tmix may have no negative effect on animal health as Tmix increased α- and γ-tocopherol concentrations in blood and did not impair whole-blood RBA or alter leukocyte populations. The data provide further support that the α- and γ-tocopherol isoforms do not interfere with normal immune or metabolic function.

The ruminal epithelium is a complex tissue that serves as an important protective barrier as well as a metabolically important tissue for whole-animal energy metabolism. Up to 70% of the energetic needs of mature animals are absorbed as short-chain fatty acids through the stratified squamous epithelium, and it serves as the primary producer of ketones in fed animals. Both physical and metabolic development are incomplete at birth and are triggered by short-chain fatty acids. Regulatory control of the proliferation and differentiation necessary for normal development is a useful model for the scientific investigation of nutrient-gene interactions.

13 páginas, 5 figuras, 1 tabla., The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following introduction of solid feed to the weaning neonate as well as affecting the metabolism of other nutrients and absorption of nutrients in in vitro experiments. The objective of the present study was to validate expression stability of eight putative reference genes bovine rumen, considering the intrinsic heterogeneity of bovine rumen with regard to different luminal characteristics due to direct infusion of butyrate to double the intra-ruminal content of the rumen liquor. Our focus was on identifying stable reference genes which are suitable to normalize real-time RT-qPCR experiments from rumen samples collected from clinical assays, irrespective of localization within the organ and the across physiological state. The most stably expressed genes included: ACTB, UXT, DBNDD2, RPS9, DDX54 and HMBS. Their high stability values suggest these reference genes will facilitate better evaluation of variation of across an array of conditions including: localization within the rumen, differences among cattle fed an array of rations, as well as response to development in the weaning animal. Moreover, we anticipate these reference genes may be useful for expression studies in other ruminants., This work was supported by the Fulbright/Ministry of Education of Spain Visiting Scholarship PRX14/00601 to Dr. Marı´a Jose´ Ranilla. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Brown marmorated stink bug (BMSB; Halyomorpha halys) is an emerging invasive species of grave concern to agriculture as a polyphagous plant pest with potential negative effects on the dairy industry. The purpose of this study was to determine the risk of including BMSB-contaminated silage in lactating dairy cow rations. First, 6 dairies, either highly infested (n=3; 30 to 100 bugs per stalk) or not infested (n=3), were sampled to assess the prevalence of bug secretion compounds tridecane (major component) and E-2-decenal (stink odor component) in silage and milk. Second, using wild BMSB, a mini-silo dose-response experiment (adding 100, 50, 25, 10, and 1 freshly crushed bugs/0.5kg of chopped corn) was conducted to assess the effect of ensiling on BMSB stink odor compounds. Finally, synthetic BMSB stink odor compounds (10g of tridecane and 5g of E-2-decenal) were ruminally infused twice daily over 3 d, and samples of milk, urine, and rumen fluid were collected to evaluate disposition. Bug stink odor compounds were sampled by solid-phase microextraction (SPME) and analyzed by gas chromatography-mass spectrometry (GC-MS). Milk production and feed composition were unaffected when BMSB-contaminated silage was fed. Moreover, no E-2-decenal was detected in silage or milk (detection threshold = 0.00125μg/mL). The dose-response of tridecane in mini-silo samples exhibited a linear relationship (R(2)=0.78) with the amount of BMSB added; however, E-2-decenal was completely decomposed and undetectable in spiked mini-silos after ensiling. Both synthetic secretion compounds infused into rumen were undetectable in all milk and urine samples. E-2-Decenal was not detectable in rumen fluid, whereas tridecane was detected only at 15 min postinfusion but not present thereafter. Feed intake was unaffected by infusion treatment and BMSB secretion compounds (E-2-decenal and tridecane) were not observed in milk. E-2-Decenal and tridecane from the metathoracic gland of BMSB are not able to contaminate milk either due to the ensiling process or because of metabolism within the rumen. Concern over BMSB stink odor compounds contaminating the fluid milk supply, even on highly infested farms, is not warranted.

The Efficient Dairy Genome Project is an international research initiative led by Canada that brings together research and industry experts and is focused on developing genomic selection tools for improving feed efficiency (FE) and decreasing methane emissions (ME) in dairy cattle. Genotypes and phenotypic data for FE, ME, and milk MIR spectral data from research herds in six countries are being collated in a secure project database for the continuous data exchange among country members. Consolidated data will be used to implement genomic evaluations for the novel traits using a combined reference population. As the 4-year project enters its final year, results in various areas are accumulating: structural variants, economic weights and selection index, consumer and producer level social studies. The project generated whole-genome sequences for 32 Holstein bulls which was combined with existing sequence data on another 451 Holstein animals from previous projects. This information has been used to find structural variants in the genome that may be contributing to or affecting these traits. Such variants will help us understand the underlying biology of these traits and/or serve as genetic markers to select desired animals.

Improved feed efficiency is a primary goal in dairy production to reduce feed costs and negative impacts of production on the environment. Estimates for efficiency of feed conversion to milk production based on residual feed intake (RFI) in dairy cattle are limited, primarily due to a lack of individual feed intake measurements for lactating cows. Feed intake was measured in Holstein cows during the first 90 d of lactation to estimate the heritability and repeatability of RFI, minimum test duration for evaluating RFI in early lactation, and its association with other production traits. Data were obtained from 453 lactations (214 heifers and 239 multiparous cows) from 292 individual cows from September 2007 to December 2011. Cows were housed in a free-stall barn and monitored for individual daily feed consumption using the GrowSafe 4000 System (GrowSafe Systems, Ltd., Airdrie, AB, Canada). Animals were fed a total mixed ration 3 times daily, milked twice daily, and weighed every 10 to 14 d. Milk yield was measured at each milking. Feed DM percentage was measured daily, and nutrient composition was analyzed from a weekly composite. Milk composition was analyzed weekly, alternating between morning and evening milking periods. Estimates of RFI were determined as the difference between actual energy intake and predicted intake based on a linear model with fixed effects of parity (1, 2, ≥ 3) and regressions on metabolic BW, ADG, and energy-corrected milk yield. Heritability was estimated to be moderate (0.36 ± 0.06), and repeatability was estimated at 0.56 across lactations. A test period through 53 d in milk (DIM) explained 81% of the variation provided by a test through 90 DIM. Multiple regression analysis indicated that high efficiency was associated with less time feeding per day and slower feeding rate, which may contribute to differences in RFI among cows. The heritability and repeatability of RFI suggest an opportunity to improve feed efficiency through genetic selection, which could reduce feed costs, manure output, and greenhouse gas emissions associated with dairy production.

Damage to the intestinal epithelium reduces nutrient absorption and animal growth, and can have negative long-term health effects on livestock. Because the intestinotropic hormone glucagon-like peptide 2 (GLP-2) has been shown to contribute to gut integrity, reduce inflammation, and improve nutrient absorption, the present study was designed to determine whether administration of GLP-2 to calves with coccidiosis in the first month of life affects intestinal growth and mediates negative effects of the proinflammatory response. Holstein bull calves (n=19) were assigned to 4 treatment groups of 4 to 5 calves each: (1) infected with Eimeria bovis, GLP-2 treated; (2) noninfected, GLP-2 treated; (3) infected with E. bovis, buffer treated; and (4) noninfected, buffer treated. Infected calves received 100,000 to 200,000 sporulated E. bovis oocysts suspended in milk replacer on d 0 of the study. On d 18, calves in the GLP-2 groups received a subcutaneous injection of 50 μg of bovine GLP-2/kg of body weight twice daily for 10 d, and calves in the buffer-treated groups received an equivalent volume of sodium bicarbonate buffer only. On d 28, calves were slaughtered 2h after injection of 5-bromo-2'-deoxyuridine (BrdU). Intestinal tissues were measured and villus height, crypt depth, and BrdU immunostaining were evaluated in segments of the small intestine. Nitrotyrosine immunostaining, a measure of nitro-oxidative damage, was evaluated in the ileum and cecum. No GLP-2 treatment by E. bovis infection interaction was observed for any parameter measured, with the exception of nitrotyrosine immunostaining in the cecum. Large intestinal weight was greater in infected than noninfected calves and with GLP-2 treatment relative to buffer treatment. Calves that received GLP-2 also had greater small intestinal weight but no difference in cell proliferation, as assessed by BrdU labeling, relative to buffer-treated calves. No treatment effects were detected for villus height, crypt depth, or villus height:crypt depth ratio in segments of the small intestine. Protein tyrosine nitration was over 3-fold greater in the ileum and cecum of infected calves relative to noninfected calves, and GLP-2 therapy reduced tyrosine nitration in infected calves by 47% in the ileum and 69% in the cecum relative to buffer-treated calves. Treatment with GLP-2 promotes intestinal growth in neonatal calves and reduces the detrimental effects of nitro-oxidative stress in the ileocecum of calves with coccidiosis.

Heat stress (HT) during the dry period compromises mammary gland development, decreases future milk production, and impairs the immune status of dairy cows. Our objective was to evaluate the effect of cooling HT cows during the dry period on gene expression of the mammary gland and peripheral blood mononuclear cells (PBMC). Cows were dried off 46 d before their expected calving and assigned to 2 treatments, HT or cooling (CL). Cows in the CL group were cooled with sprinklers and fans whereas HT cows were not. After parturition, all cows were housed in a freestall barn with cooling. The PBMC were isolated at dry-off and at -20, 2, and 20 d relative to calving from a subset of cows (HT, n=9; CL, n=10), and mammary biopsies were taken at the same intervals (HT, n=7; CL, n=6) for RNA extraction. Gene expression was assessed using a custom multiplex gene expression assay based on traditional reverse transcription-PCR. Genes involved in prolactin (PRL) signaling [PRL receptor long form, PRL receptor short form, suppressor of cytokine signaling (SOCS)2, SOCS3, IGF2, IGF binding protein 5, and cyclin D1], fatty acid metabolism (acetyl-CoA carboxylase α (ACACA) and lipoprotein lipase (LPL)], and IGF1 were evaluated in mammary tissue, and genes related to fatty acid metabolism [ACACA, fatty acid synthase (FASN), and LPL], cytokine production [IL6, IL8, and tumor necrosis factor (TNF)], and IGF1 were evaluated in PBMC. No differences were observed in PRL signaling or fatty acid metabolism gene expression in the mammary gland. In PBMC, HT cows had greater mRNA expression of IGF1 and TNF during the transition period relative to CL and upregulated IL8 and downregulated FASN mRNA expression at 2 d relative to calving. We conclude that cooling HT cows during the dry period alters expression of genes involved in cytokine production and lipid metabolism in PBMC.

Genomic evaluations for 161,341 Holsteins were computed by using 311,725 of 777,962 markers on the Illumina BovineHD Genotyping BeadChip (HD). Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Holstein genotypes were from 1,510 animals with HD markers, 82,358 animals with 45,187 (50 K) markers, 1,797 animals with 8,031 (8 K) markers, 20,177 animals with 6,836 (6 K) markers, 52,270 animals with 2,683 (3 K) markers, and 3,229 nongenotyped dams (0 K) with >90% of haplotypes imputable because they had 4 or more genotyped progeny. The Holstein HD genotypes were from 1,142 US, Canadian, British, and Italian sires, 196 other sires, 138 cows in a US Department of Agriculture research herd (Beltsville, MD), and 34 other females. Percentages of correctly imputed genotypes were tested by applying the programs findhap and FImpute to a simulated chromosome for an earlier population that had only 1,112 animals with HD genotypes and none with 8 K genotypes. For each chip, 1% of the genotypes were missing and 0.02% were incorrect initially. After imputation of missing markers with findhap, percentages of genotypes correct were 99.9% from HD, 99.0% from 50 K, 94.6% from 6 K, 90.5% from 3 K, and 93.5% from 0 K. With FImpute, 99.96% were correct from HD, 99.3% from 50 K, 94.7% from 6 K, 91.1% from 3 K, and 95.1% from 0 K genotypes. Accuracy for the 3 K and 6 K genotypes further improved by approximately 2 percentage points if imputed first to 50 K and then to HD instead of imputing all genotypes directly to HD. Evaluations were tested by using imputed actual genotypes and August 2008 phenotypes to predict deregressed evaluations of US bulls proven after August 2008. For 28 traits tested, the estimated genomic reliability averaged 61.1% when using 311,725 markers vs. 60.7% when using 45,187 markers vs. 29.6% from the traditional parent average. Squared correlations with future data were slightly greater for 16 traits and slightly less for 12 with HD than with 50 K evaluations. The observed 0.4 percentage point average increase in reliability was less favorable than the 0.9 expected from simulation but was similar to actual gains from other HD studies. The largest HD and 50 K marker effects were often located at very similar positions. The single-breed evaluation tested here and previous single-breed or multibreed evaluations have not produced large gains. Increasing the number of HD genotypes used for imputation above 1,074 did not improve the reliability of Holstein genomic evaluations.

Glucagon-like peptide 2 (GLP-2) therapy was shown previously to reduce inflammation-related gut damage from coccidiosis in dairy calves, and feeding of artificial sweetener stimulates GLP-2 secretion from intestinal L cells. The purpose of this study was to determine whether GLP-2 treatment or artificial sweetener feeding beginning 1 wk before an experimental inoculation with the coccidian parasite Cryptosporidium parvum can reduce infection-related intestinal damage in Holstein bull calves. Newborn calves were assigned to 1 of 4 treatment groups of 6 calves each, including noninfected control calves injected s.c. every 12 h with control buffer (CON), infected control calves injected s.c. every 12 h with control buffer (INF), infected calves injected s.c. every 12 h with 50 µg/kg of body weight of GLP-2 (GLP2), and infected calves injected s.c. every 12 h with control buffer and supplemented in the diet with Sucram (Pancosma, Geneva, Switzerland) at 400 mg/kg of dry matter of milk replacer (SUC). Treatments were initiated on d 1, and calves in INF, GLP2, and SUC were orally dosed on d 8 with 12,500 C. parvum oocysts. Fecal scores were recorded daily, plasma was collected on d 1, 8, 12, 15, and 18 to evaluate markers of inflammation, and fecal samples were collected on d 1, 8, and every other day thereafter to determine the presence of oocysts. Calves were euthanized on d 18 for collection of intestinal tissues and histological and gene expression analyses. Relative to CON, calves in INF exhibited an increase in diarrhea severity, increased plasma serum amyloid A concentration on d 15 and 18, reduced intestinal villus height, increased villus apoptosis and crypt cell proliferation, and increased intestinal mRNA expression of MARVELD2 and GPX2. However, calves in SUC and GLP2 had reduced diarrhea severity and fecal C. parvum oocyst shedding, reduced plasma serum amyloid A concentration on d 15 and 18, and, depending on the intestinal segment, increased villus height, reduced crypt cell proliferation, and reduced mRNA expression of MARVELD2, GPX2, and other tight junction proteins relative to INF. Lastly, GLP2 and SUC exhibited increased intestinal mass-to-length ratio and decreased length-to-empty body weight ratio relative to INF. Our findings suggest that GLP-2 and Sucram treatments administered before a low-level C. parvum exposure may contribute to fewer effects on intestinal integrity, morphology, and inflammation in response to infection, and shorter, denser intestines.

Feed efficiency in dairy cattle has gained much attention recently. Due to the cost-prohibitive measurement of individual feed intakes, combining data from multiple countries is often necessary to ensure an adequate reference population. It may then be essential to model genetic heterogeneity when making inferences about feed efficiency or selecting efficient cattle using genomic information. In this study, we constructed a marker x environment interaction model that decomposed marker effects into main effects and interaction components that were specific to each environment. We compared environment-specific variance component estimates and prediction accuracies from the interaction model analyses, an across-environment analyses ignoring population stratification, and a within-environment analyses using an international feed efficiency data set. Phenotypes included residual feed intake, dry matter intake, net energy in milk, and metabolic body weight from 3,656 cows measured in 3 broadly defined environments: North America (NAM), the Netherlands (NLD), and Scotland (SAC). Genotypic data included 57,574 single nucleotide polymorphisms per animal. The interaction model gave the highest prediction accuracy for metabolic body weight, which had the largest estimated heritabilities ranging from 0.37 to 0.55. The within environment model performed the best when predicting residual feed intake, which had the lowest estimated heritabilities ranging from 0.13 to 0.41. For traits (dry matter intake and net energy in milk) with intermediate estimated heritabilities (0.21 to 0.50 and 0.17 to 0.53, respectively), performance of the 3 models was comparable. Genomic correlations between environments also were computed using variance component estimates from the interaction model. Averaged across all traits, genomic correlations were highest between NAM and NLD, and lowest between NAM and SAC. In conclusion, the interaction model provided a novel way to evaluate traits measured in multiple environments in which genetic heterogeneity may exist. This model allowed estimation of environment-specific parameters and provided genomic predictions that approached or exceeded the accuracy of competing within- or across environment models. Agriculture and Food Research Initiative Competitive Grants from the USDA National Institute of Food and Agriculture (Washington, DC) [2008-35205-18711, 2011-68004-30340]; Hatch grant from the Wisconsin Agricultural Experiment Station (Madison, WI) [MSN139239]; National Association of Animal Breeders (Columbia, MO) This project was supported by Agriculture and Food Research Initiative Competitive Grants no. 2008-35205-18711 and 2011-68004-30340 from the USDA National Institute of Food and Agriculture (Washington, DC). Support from Hatch grant no. MSN139239 from the Wisconsin Agricultural Experiment Station (Madison, WI) is acknowledged, and K. A. Weigel acknowledges partial financial support from the National Association of Animal Breeders (Columbia, MO). Public domain – authored by a U.S. government employee

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of copy number variations (CNVs) using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intake (RFI). We detected 443 candidate CNV regions (CNVRs) that represent 18.4 Mb (0.6 %) of the genome. To investigate the functional impacts of CNVs, we created two groups of 30 individual animals with extremely low or high estimated breeding values (EBVs) for RFI, and referred to these groups as low intake (LI; more efficient) or high intake (HI; less efficient), respectively. We identified 240 (~9.0 Mb) and 274 (~10.2 Mb) CNVRs from LI and HI groups, respectively. Approximately 30-40 % of the CNVRs were specific to the LI group or HI group of animals. The 240 LI CNVRs overlapped with 137 Ensembl genes. Network analyses indicated that the LI-specific genes were predominantly enriched for those functioning in the inflammatory response and immunity. By contrast, the 274 HI CNVRs contained 177 Ensembl genes. Network analyses indicated that the HI-specific genes were particularly involved in the cell cycle, and organ and bone development. These results relate CNVs to two key variables, namely immune response and organ and bone development. The data indicate that greater feed efficiency relates more closely to immune response, whereas cattle with reduced feed efficiency may have a greater capacity for organ and bone development.

Increasing feed costs and the desire to improve environmental stewardship have stimulated renewed interest in improving feed efficiency of livestock, including that of US dairy herds. For instance, USDA cost projections for corn and soybean meal suggest a 20% increase over 2010 pricing for a 16% protein mixed dairy cow ration in 2011, which may lead to a reduction in cow numbers to maintain profitability of dairy production. Furthermore, an October 2010 study by The Innovation Center for US Dairy to assess the carbon footprint of fluid milk found that the efficiency of feed conversion is the single greatest factor contributing to variation in the carbon footprint because of its effects on methane release during enteric fermentation and from manure. Thus, we are conducting research in contemporary US Holsteins to identify cows most efficient at converting feed to milk in temperate climates using residual feed intake (RFI), a measure used successfully to identify the beef cattle most efficient at converting feed to gain. Residual feed intake is calculated as the difference between predicted and actual feed intake to support maintenance and production (e.g., growth in beef cattle, or milk in dairy cattle). Heritability estimates for RFI in dairy cattle reported in the literature range from 0.01 to 0.38. Selection for a decreased RFI phenotype can reduce feed intake, methane production, nutrient losses in manure, and visceral organ weights substantially in beef cattle. We have estimated RFI during early lactation (i.e., to 90 d in milk) in the Beltsville Agricultural Research Center Holstein herd and observed a mean difference of 3.7 kg/d (P 0.20) in mean BW, ADG, or energy-corrected milk exhibited between the 2 groups. These results indicate promise for using RFI in dairy cattle to improve feed conversion to milk. Previous and current research on the use of RFI in lactating dairy cattle are discussed, as well as opportunities to improve production efficiency of dairy cattle using RFI for milk production.

The rumen bacterial composition of both pre- ruminant dairy calves and cows and beef steers was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent and -independent clustering methods. The core rumen microbiome, regardless of the rumen developmental status or breeds, consisted of 8 phyla, 11 classes, 15 families, and 17 genera. Principal component analysis and clustering demonstrated that the bacterial communities in the rumen of pre-ruminant dairy calves, dairy cows, and beef steers were clearly distinguishable. Approximately 66% of phyla and 41% of Operational Taxonomic Units (OTUs) in a typical rumen bacterial community differed in relative abundance between the developing and mature rumen. Greater abundance of Fibrobacteraceae and Ruminococaceae in the rumen of beef steers likely reflected the need for enhanced fiber-digesting capacity in beef cattle. Our results should facilitate understanding of the structural and functional relationships in the rumen microbial ecosystem.

Improving feed efficiency in dairy production is an important endeavor, as it can reduce feed costs and negative impacts of production on the environment. Feed efficiency is a multivariate phenotype that is characterized by a variety of phenotypic variables, such as dry matter intake, body weight gain, and milk yield. Currently, there is no consensus method for quantifying the feed efficiency of lactating dairy cattle for the purpose of breeding selection. Residual feed intake, which is the difference between actual feed intake and predicted intake, has been one of the commonly used measures for feed efficiency. However, such a measure is heterogeneous showing substantial variation in the cow population and has relatively low heritability (0.01∼0.38). Hence, its utility in breeding selection is limited. In particular, no prior study has utilized genetic data directly in the development of feed efficiency measures. In this paper, we aim to identify cattle clusters with homogeneous feed efficiency features that are ready to link to genetic variants, and thus can have greater utility in breading selection. In order to achieve this goal, we explore a new multi-view clustering method that jointly analyzes two views of data: phenotypic measures and genotypes, and identifies cattle clusters that are characterized by specific phenotypic features and also associated with genetic markers. Using a set of feed efficiency data collected by USDA, three cattle subgroups have been identified by our analysis, and they offer instructive insights into future feed efficiency studies.

The temporal sequence of microbial establishment in the rumen of the neonatal ruminant has important ecological and pathophysiological implications. In this study, we characterized the rumen microbiota of pre-ruminant calves fed milk replacer using two approaches, pyrosequencing of hypervariable V3-V5 regions of the 16S rRNA gene and whole-genome shotgun approach. Fifteen bacterial phyla were identified in the microbiota of pre-ruminant calves. Bacteroidetes was the predominant phylum in the rumen microbiota of 42-day-old calves, representing 74.8% of the 16S sequences, followed by Firmicutes (12.0%), Proteobacteria (10.4%), Verrucomicrobia (1.2%) and Synergistetes (1.1%). However, the phylum-level composition of 14-day-old calves was distinctly different. A total of 170 bacterial genera were identified while the core microbiome of pre-ruminant calves included 45 genera. Rumen development seemingly had a significant impact on microbial diversity. The dazzling functional diversity of the rumen microbiota was reflected by identification of 8298 Pfam and 3670 COG protein families. The rumen microbiota of pre-ruminant calves displayed a considerable compositional heterogeneity during early development. This is evidenced by a profound difference in rumen microbial composition between the two age groups. However, all functional classes between the two age groups had a remarkably similar assignment, suggesting that rumen microbial communities of pre-ruminant calves maintained a stable function and metabolic potentials while their phylogenetic composition fluctuated greatly. The presence of all major types of rumen microorganisms suggests that the rumen of pre-ruminant calves may not be rudimentary. Our results provide insight into rumen microbiota dynamics and will facilitate efforts in formulating optimal early-weaning strategies.

Heat stress (HT) and photoperiod affect milk production and immune status of dairy cows. The objective was to evaluate the effects of HT abatement prepartum under controlled photoperiod on hepatic metabolic gene expression and cellular immune function of periparturient Holstein cows (n=21). Cows were dried off 46 d before expected calving date and assigned to treatments by mature equivalent milk production. The treatments were 1) HT and 2) cooling (CL), both imposed during a photoperiod of 14L:10D. Rectal temperature was measured twice daily, whereas respiration rate was measured 3 times/wk at 1500 h during the entire dry period. After calving, cows were housed in a freestall barn with cooling, and milk yield was recorded daily up to 140 d in milk. Liver samples were taken at dry off, -20, 2, and 20 d relative to calving by biopsy. Under a similar schedule, neutrophil function was determined in blood of cows on HT (n=12) and CL (n=9). Blood samples were taken on -46, -32, -18, 0, 14, 28, and 42 d relative to calving for measurement of metabolites and were collected twice daily from -7 to 2 d relative to calving for prolactin (PRL) analysis. The HT cows had greater concentrations of PRL at 0 d relative to calving (150 vs. 93; SEM=11 ng/mL) and had higher afternoon rectal temperatures (39.4 vs. 39.0; SEM=0.04°C) and elevated respiration rates (78 vs. 56; SEM=2 breaths/min) during the prepartum period compared with CL cows. Relative to HT cows, CL cows had greater hepatic expression of PRL-R, SOCS-3, and CAV-1 mRNA. Neutrophil oxidative burst was greater in CL cows relative to HT cows at 2 d (61 vs. 42; SEM=6%) and at 20 d (62 vs. 49; SEM=5%) relative to calving, and phagocytosis was greater in CL cows at 20 d (47 vs. 33; SEM=4%) relative to calving compared with HT cows. Humoral response, as measured by IgG secretion against ovalbumin challenge, was greater for CL cows at -32 d (0.44 vs. 0.33; SEM=0.05 OD) and -21 d (0.60 vs. 0.50±0.04 OD) relative to calving compared with HT cows. These results suggest that HT abatement during the dry period improved innate and acquired immune status as measured by neutrophil function and immunoglobulin secretion against ovalbumin challenge, and altered hepatic gene expression related to PRL signaling in the periparturient period or subsequent lactation.

Glucagon-like peptide 2 (GLP-2), secreted by enteroendocrine cells, has several physiological effects on the intestine of monogastric species, including promotion of growth of intestinal epithelium, reduction of epithelial cell apoptosis, and enhancement of intestinal blood flow, nutrient absorption, and epithelial barrier function. The regulatory functions of GLP-2 in the ruminant gastrointestinal tract (GIT) have not been well studied. The objectives of this investigation were to characterize the mRNA expression of 4 members of the GLP-2 pathway throughout the bovine GIT, including (1) proglucagon (GCG), the parent peptide from which GLP-2 is derived through cleavage by prohormone convertase; (2) prohormone convertase (PCSK1); (3) GLP-2 receptor (GLP2R); and (4) dipeptidyl peptidase IV (DPP4), the enzyme that inactivates GLP-2. Gene expression was evaluated in rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, and rectum collected at slaughter from prepubertal heifers, mature cows in early, mid, and late lactation, and nonlactating cows (n = 3 per stage) by a gene expression profiling assay. In addition, mRNA expression of 14 genes involved in nutrient transport, enzyme activity, blood flow, apoptosis, and proliferation were evaluated in the 9 GIT tissues for their association with GCG and GLP2R mRNA expression. Immunohistochemistry was used to localize GLP2R protein in tissues of the lower GIT. Results indicated that mRNA expression of GCG, PCSK1, GLP2R, and DPP4 varies across the 9 GIT tissues, with greatest expression in small and large intestines, and generally nondetectable levels in forestomachs. Expression of DPP4 and GLP2R mRNA varied by developmental stage or lactational state in intestinal tissues. Expression of GCG or GLP2R mRNA was correlated with molecular markers of proliferation, apoptosis, blood flow, enzyme activity, and urea transport, depending on the tissue examined, which suggests a potential for involvement of GLP-2 in these physiological processes in the ruminant GIT. The GLP2R protein was expressed in intestinal crypts of the bovine GIT, which is consistent with the distribution in monogastric species. Our findings support a functional role of the GLP-2 pathway in bovine GIT and the potential for use of GLP-2 as a therapy to improve intestinal function and nutrient absorption in ruminants.

The biological activities and mechanisms of action of individual transoctadecenoic acids (trans-18:1 FA) have not been completely elucidated. We examined the effects of several individual trans-18:1 FA isomers and trans-10, cis-12 conjugated linoleic acid (CLA) on fat synthesis, and expression of lipogenic genes in mammary and liver tissue in lactating mice. From d 6 to 10 postpartum, 30 lactating C57BL/6J mice were randomly assigned to either a control (CTR) diet containing 20 g/kg oleic acid or diets in which the oleic acid was either completely replaced by partially hydrogenated vegetable oil (PHVO), trans-7 18:1 (T7), trans-9 18:1 (T9), or trans-11 18:1 (T11) or partially replaced with 6.66 g/kg trans-10, cis-12 CLA. Milk fat percentage was decreased by CLA (44%), T7 (27%), and PHVO (23%), compared with CTR. In the mammary gland, CLA decreased the expression of genes related to de novo FA synthesis, desaturation, triacylglycerol formation, and transcriptional regulation. PHVO and T7 diets decreased the expression of 1-acylglycerol-3-phosphate O-acyltransferase and thyroid hormone responsive SPOT14 homolog (THRSP) mRNA. In contrast, dietary trans FA (tFA) did not affect hepatic lipogenic gene expression. However, mice fed CLA, T7, and PHVO diets had increased liver weights due to hepatic steatosis. Trans-7 18:1 was extensively desaturated to trans-7, cis-9 CLA in mammary and liver tissues. Dietary trans-7 18:1 could lead to milk fat depression in lactating mice, possibly through its desaturation product trans-7, cis-9 CLA. Also, the differences between the effects of trans-10, cis-12 CLA and other tFA could be attributed to its effects on carbohydrate response element binding protein and PPARg, in addition to sterol regulatory element binding transcription factor 1c and THRSP. J. Nutr. 140: 919–924, 2010.

A putative causative mutation underlying a QTL was identified as a lysine to alanine non-conservative substitution at amino acid 232 of the gene encoding the acylCoA:diacylglycerol acyltransferase (DGAT1) protein. Our goal was to characterize the allelic substitution effects of this DGAT1 mutation in a large sample of Holstein bulls from North America. Statistically significant effects were identified for all of the milk production traits and somatic cell scores. Estimated average effects of substituting the lysine allele for the alanine variant on Holstein bull daughter yield deviations were -81 kg, 3.7 kg, -1.1 kg, 0.063%, 0.012%, and -0.023 units for milk yield, fat yield, protein yield, fat component, protein component, and SCS, respectively. These estimates were largely in agreement with previous studies; however, the magnitudes of the estimates were much smaller in this study. Impacts on economic indices for net merit, cheese merit, and fluid merit were modest. Because of the strong antagonism between fat and protein yield and how those traits influence economic indices, selection for DGAT1 genotypes will likely not find widespread application in the U.S.

The gastrointestinal tract (GIT) has multiple functions including digestion, nutrient absorption, secretion of hormones and excretion of wastes. In the ruminant animal, development of this organ system is more complex than that of the monogastric animal due to the necessity to establish a fully functional and differentiated rumen, in which a diverse microbial population of bacteria, fungi and protozoa support fermentation and digestion of dietary fiber. Central to the goal of animal scientists to enhance nutrient uptake and production efficiency of ruminants is the need for a comprehensive understanding of GIT development, as well as conditions that alter the digestion process. The relatively recent availability of genome sequence information has permitted physiological investigations related to the process of digestion for many agriculturally important species at the gene transcript level. For instance, numerous studies have evaluated the expression of ruminant GIT genes to gain insight into mechanisms involved in normal function, physiology and development, such as nutrient uptake and transport across the epithelial cell barrier throughout the alimentary canal, maintenance of rumen pH, and regulation of GIT motility and cell proliferation. Further, multiple studies have examined the effects of dietary modification, including feeding of supplemental fat, starch and protein, or a forage- v. concentrate-based diet on expression of critical gene pathways in the gut. In addition, the expression of genes in the GIT in response to disease, such as infection with gastrointestinal parasites, has been investigated. This review will summarize some of the recent scientific literature related to the gene expression in the GIT of ruminants, primarily cattle, sheep and goats, as it pertains to normal physiology, and dietary, developmental, and disease effects to provide an overview of critical proteins participating in the overall digestive processes, and their physiological functions. Recent findings from our laboratory will be highlighted also related to expression of the glucagon-like peptide two-hormone pathway in the GIT of dairy cattle during in various stages of the development and lactation, alterations in gene pathways associated with the rumen development and differentiation in the weaning calf, and genes of the GIT responding to Ostertagia, a common nematode infection of the cattle. Finally, prospective areas of investigation will be highlighted.

Environmental factors, especially temperature and light exposure, influence the health and productivity of dairy cows during lactation, possibly via similar physiological mechanisms. For example, heat stress is a critical component of decreased milk yield during summer. However, less is known about the effect of heat stress during the dry period. The objective of this study was to evaluate the effects of heat stress prepartum under a controlled photoperiod on lactation performance and hepatic metabolic gene expression of periparturient multiparous Holstein cows (n = 16). Cows were dried off approximately 46 d before expected calving date and assigned to treatment randomly after blocking by mature equivalent milk production and parity. Treatments consisted of either heat stress (HT) or cooling (CL) with fans and sprinklers, both under a photoperiod of 14L:10D. Rectal temperature was measured twice daily during the dry period. After calving, cows were housed in a freestall barn with cooling devices, and milk yield was recorded daily up to 210 d in milk. Blood samples were taken from dry off until +42 d relative to calving for metabolites and from -2 until +2 d relative to calving for hormone analysis. Daily dry matter intake was measured from -35 to +42 d relative to calving. Liver biopsies were collected at dry off, -20, +2, and +20 d relative to calving for cows on HT (n = 5) and CL (n = 4) to measure mRNA expression of suppressors of cytokine signaling-2 (SOCS-2), insulin-like growth factor binding protein-5 (IGFBP-5), a key transcription factor in lipid biosynthesis (SREBP-1c), and enzymes of lipid metabolism (FASN, ACACA, and ACADVL) by real-time quantitative PCR. Heat stress increased rectal temperatures (39.2 vs. 38.8 degrees C), plasma prolactin concentrations at -1 (171 vs. 79 ng/mL) and 0 d (210 vs. 115 ng/mL) relative to calving, and decreased dry matter intake at 0 and +14 d relative to calving and 3.5% fat-corrected milk postpartum (26.1 vs. 35.4 kg/d) compared with CL cows. Relative to CL cows, hepatic mRNA expression of SOCS-2 and IGFBP-5 was downregulated in HT cows. Expression of ACADVL was upregulated in CL cows at d +2 but downregulated at d +20 relative to HT cows. Concentrations of C16:0 and cis C18:1 were greater in the milk and liver of CL cows compared with HT cows, which reflects greater lipid mobilization. These results suggest that heat-stress abatement in the dry period improves subsequent lactation, possibly via suppression of plasma prolactin surge around calving, SOCS-2 expression, and regulation of hepatic lipid metabolism.

Growing ruminants under extended dietary restriction exhibit compensatory growth upon ad libitum feeding, which is associated with increased feed efficiency, lower basal energy requirements, and changes in circulating concentrations of metabolic hormones. To identify mechanisms contributing to these physiological changes, 8-month-old steers were fed either ad libitum (control; n = 6) or 60-70% of intake of control animals (feed-restricted; n = 6) for a period of 12 weeks. All steers were fed ad libitum for the remaining 8 weeks of experimentation (realimentation). Liver was biopsied at days -14, +1, and +14 relative to realimentation for gene expression analysis by microarray hybridization. During early realimentation, feed-restricted steers exhibited greater rates of gain and feed efficiency than controls and an increase in expression of genes functioning in cellular metabolism, cholesterol biosynthesis, oxidative phosphorylation, glycolysis, and gluconeogenesis. Gene expression changes during feed restriction were similar to those reported in mice, indicating similar effects of caloric restriction across species. Based on expression of genes involved in cell division and growth and upregulation of genes encoding mitochondrial complex proteins in early realimentation, it was concluded that reduced hepatic size and increased mitochondrial function may contribute to improved feed efficiency observed during compensatory growth.

Thyroid hormones are galactopoietic and help to establish the mammary gland’s metabolic priority during lactation. Expression patterns for genes that can alter tissue sensitivity to thyroid hormones and thyroid hormone activity were evaluated in the mammary gland and liver of cows at 53, 35, 20, and 7 days before expected parturition, and 14 and 90 days into the subsequent lactation. Transcript abundance for the three isoforms of iodothyronine deiodinase, type I ( DIO1), type II ( DIO2) and type III ( DIO3), thyroid hormone receptors alpha1 ( TRα 1), alpha2 ( TRα 2) and beta1 ( TRβ 1), and retinoic acid receptors alpha ( RXRα) and gamma ( RXRγ), which act as coregulators of thyroid hormone receptor action, were evaluated by quantitative RT-PCR. The DIO3 is a 5-deiodinase that produces inactive iodothyronine metabolites, whereas DIO1 and DIO2 generate the active thyroid hormone, triiodothyronine, from the relatively inactive precursor, thyroxine. Low copy numbers of DIO3 transcripts were present in mammary gland and liver. DIO2 was the predominant isoform expressed in mammary gland and DIO1 was the predominant isoform expressed in liver. Quantity of DIO1 mRNA in liver tissues did not differ with physiological state, but tended to be lowest during lactation. Quantity of DIO2 mRNA in mammary gland increased during lactation ( P < 0.05), with copy numbers at 90 days of lactation 6-fold greater than at 35 and 20 days prepartum. When ratios of DIO2/DIO3 mRNA were evaluated, the increase was more pronounced (>100-fold). Quantity of TRβ 1 mRNA in mammary gland increased with onset of lactation, whereas TRα 1 and TRα 2 transcripts did not vary with physiological state. Conversely, quantity of RXRα mRNA decreased during late gestation to low levels during early lactation. Data suggest that increased expression of mammary TRβ 1 and DIO2, and decreased RXRα, provide a mechanism to increase thyroid hormone activity within the mammary gland during lactation.

It is well established that estrogen is required for mammary epithelial cell proliferation and ductal development in the growing animal, and that lobuloalveolar development during gestation is dependent on progesterone. The effects of these steroid hormones on gene expression in the mammary gland are mediated primarily by their respective nuclear hormone receptors, which function as hormone-bound transcription factors. To gain insight into how estrogen and progesterone regulate mammary gland growth and function in cattle, we and others have characterized the expression patterns of their cognate nuclear hormone receptors in the bovine mammary gland throughout development, pregnancy, and lactation. This work has identified a lack of expression of estrogen receptor beta and a greater abundance of progesterone receptor during lactation in the bovine mammary gland, compared with the rodent gland. We speculate that interactions among the estrogen receptor isoforms that regulate progesterone receptor expression may contribute to these species differences. Further, demonstrated expression of substantial quantities of estrogen receptor within the prepubertal bovine mammary fat pad, along with coordinated insulin-like growth factor-I expression, suggests that this tissue may stimulate parenchymal growth via an estrogen-responsive paracrine mechanism. In addition, the recent availability of bovine genomic sequence information and microarray technologies has permitted the study of global gene expression in the mammary gland in response to the steroid environment. We have identified more than 100 estrogen-responsive genes, of which the majority are novel estrogen gene targets. Estrogen-induced changes in gene expression were consistent with increased mammary epithelial cell proliferation, increased extracellular matrix turnover in parenchyma, and increased extracellular matrix deposition in the fat pad. A comparison of estrogen-responsive genes in the mammary glands of humans, mice, and cattle suggests considerable variation among species, as well as potential differences in regulatory elements in common estrogen receptor gene targets. Continuing studies using advanced molecular techniques should assist in elucidating the complex regulation of mammary function at the transcript level.

Genetic improvement of feed efficiency (FE) in dairy cattle requires greater attention given increasingly important resource constraint issues. A widely accepted yet occasionally contested measure of FE in dairy cattle is residual feed intake (RFI). The use of RFI is limiting for several reasons, including interpretation, differences in recording frequencies between the various component traits that define RFI, and potential differences in genetic versus nongenetic relationships between dry matter intake (DMI) and FE component traits. Hence, analyses focusing on DMI as the response are often preferred. We propose an alternative multiple-trait (MT) modeling strategy that exploits the Cholesky decomposition to provide a potentially more robust measure of FE. We demonstrate that our proposed FE measure is identical to RFI provided that genetic and nongenetic relationships between DMI and component traits of FE are identical. We assessed both approaches (MT and RFI) by simulation as well as by application to 26,383 weekly records from 50 to 200 d in milk on 2,470 cows from a dairy FE consortium study involving 7 institutions. Although the proposed MT model fared better than the RFI model when simulated genetic and nongenetic associations between DMI and FE component traits were substantially different from each other, no meaningful differences were found in predictive performance between the 2 models when applied to the consortium data.

Identification of estrogen-responsive genes is an essential step toward understanding mechanisms of estrogen action during mammary gland development. To identify these genes, 16 prepubertal heifers were used in a 2 × 2 factorial experiment, with ovarian status (intact or ovariectomized) as the first factor and estrogen treatment as the second (control or estradiol). Heifers were ovariectomized at ∼4.5 mo of age, and estrogen treatments were initiated 1 mo later. After 3 days of treatment, gene expression was analyzed in the parenchyma and fat pad of the bovine mammary gland using a high-density oligonucleotide microarray. Oligonucelotide probes represented 40,808 tentative consensus sequences from TIGR Bos taurus Gene Index and 4,575 singleton expressed sequence tags derived from libraries of pooled mammary gland and gut tissues. Microarray data were analyzed by use of the SAS mixed procedure, with an experiment-wide permutation-based significance level of P < 0.1. Considerable differences in basal gene expression were noted between mammary parenchyma and fat pad. A total of 124 estrogen-responsive genes were identified, with most responding only in the parenchyma or the fat pad. The majority of genes identified were not previously reported to be estrogen responsive. These undoubtedly include genes that are regulated indirectly but also include known estrogen-targeted genes and novel genes with potential estrogen-responsive elements in their promoter regions. The distinctive expression patterns regulated by estrogen in parenchyma and fat pad shed light on the need for both tissues to obtain normal mammary development.