Dry matter intake in US Holstein cows: exploring the genomic and phenotypic impact of milk components and body weight composite.

Large data sets allow estimating feed required for individual milk components or body maintenance. Phenotypic regressions are useful for nutrition management, but genetic regressions are more useful in breeding programs. Dry matter intake (DMI) records from 8,513 lactations of 6,621 Holstein cows were predicted from phenotypes or genomic evaluations for milk components and body size traits. The mixed models also included days in milk, age-parity subclass, trial date, management group, and body weight change during 28- and 42-d feeding trials in mid-lactation. Phenotypic regressions of DMI on milk (0.014 ± 0.006), fat (3.06 ± 0.01), and protein (4.79 ± 0.25) were much less than corresponding genomic regressions (0.08 ± 0.03, 11.30 ± 0.47, and 9.35 ± 0.87) or sire genomic regressions multiplied by 2 (0.048 ± 0.04, 6.73 ± 0.94, and 4.98 ± 1.75). Thus, marginal feed costs as fractions of marginal milk revenue were higher from genetic than phenotypic regressions. According to the energy-corrected milk formula, fat production requires 69% more DMI than protein production. In the phenotypic regression, it was estimated that protein production requires 56% more DMI than fat. However, the genomic regression for the animal showed a difference of only 21% more DMI for protein compared with fat, while the sire genomic regressions indicated approximately 35% more DMI for fat than protein. Estimates of annual maintenance in kg DMI / kg body weight/lactation were similar from phenotypic regression (5.9 ± 0.14), genomic regression (5.8 ± 0.31), and sire genomic regression multiplied by 2 (5.3 ± 0.55) and are larger than those estimated by NASEM (2021) based on NEL equations. Multiple regressions on genomic evaluations for the 5 type traits in body weight composite (BWC) showed that strength was the type trait most associated with body weight and DMI, agreeing with the current BWC formula, whereas other traits were less useful predictors, especially for DMI. The Net Merit formula used to weight different genetic traits to achieve an economically optimal overall selection response was revised in 2021 to better account for these estimated regressions. To improve profitability, breeding programs should select smaller cows with negative residual feed intake that produce more milk, fat, and protein.

The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions.

The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH4]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries (i.e., Australia, Canada, Denmark, Germany, Spain, Switzerland, and United States) contribute with genotypes and phenotypes including DMI and CH4. However, combining data are challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH4 records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH4 phenotypes in genomic analysis.

Consistency of dry matter intake in Holstein cows: Heritability estimates and associations with feed efficiency.

Resilience can be defined as the capacity to maintain performance or bounce back to normal functioning after a perturbation, and studying fluctuations in daily feed intake may be an effective way to identify resilient dairy cows. Our goal was to develop new phenotypes based on daily dry matter intake (DMI) consistency in Holstein cows, estimate genetic parameters and genetic correlations with feed efficiency and milk yield consistency, and evaluate their relationships with production, longevity, health, and reproduction traits. Data consisted of 397,334 daily DMI records of 6,238 lactating Holstein cows collected from 2007 to 2022 at 6 research stations across the United States. Consistency phenotypes were calculated based on the deviations from expected daily DMI for individual cows during their respective feeding trials, which ranged from 27 to 151 d in duration. Expected values were derived from different models, including simple average, quadratic and cubic quantile regression with a 0.5 quantile, and locally estimated scatterplot smoothing (LOESS) regression with span parameters 0.5 and 0.7. We then calculated the log of variance (log-Var-DMI) of daily deviations for each model as the consistency phenotype. Consistency of milk yield was also calculated, as a reference, using the same methods (log-Var-Milk). Genetic parameters were estimated using an animal model, including lactation, days in milk and cohort as fixed effects, and animal as random effect. Relationships between log-Var-DMI and traits currently considered in the US national genetic evaluation were evaluated using Spearman's rank correlations between sires' breeding values. Heritability estimates for log-Var-DMI ranged from 0.11 ± 0.02 to 0.14 ± 0.02 across models. Different methods (simple average, quantile regressions, and LOESS regressions) used to calculate log-Var-DMI yielded very similar results, with genetic correlations ranging from 0.94 to 0.99. Estimated genetic correlations between log-Var-DMI and log-Var-Milk ranged from 0.51 to 0.62. Estimated genetic correlations between log-Var-DMI and feed efficiency ranged from 0.55 to 0.60 with secreted milk energy, from 0.59 to 0.63 with metabolic body weight, and from 0.26 to 0.31 with residual feed intake (RFI). Relationships between log-Var-DMI and the traits in the national genetic evaluation were moderate and positive correlations with milk yield (0.20 to 0.21), moderate and negative correlations with female fertility (-0.07 to -0.20), no significant correlations with health and longevity, and favorable correlations with feed efficiency (-0.23 to -0.25 with feed saved and 0.21 to 0.26 with RFI). We concluded that DMI consistency is heritable and may be an indicator of resilience. Cows with lower variation in the difference between actual and expected daily DMI (more consistency) may be more effective in maintaining performance in the face of challenges or perturbations, whereas cows with greater variation in observed versus expected daily DMI (less consistency) are less feed efficient and may be less resilient.

Impact of parity differences on residual feed intake estimation in Holstein cows.

Residual feed intake (RFI) has been used as a measure of feed efficiency in farm animals. In lactating dairy cattle, RFI is typically obtained as the difference between dry matter intake observations and predictions from regression on known energy sinks, and effects of parity, days in milk, and cohort. The impact of parity (lactation number) on the estimation of RFI is not well understood, so the objectives of this study were to (1) evaluate alternative RFI models in which the energy sinks (metabolic body weight, body weight change, and secreted milk energy) were nested or not nested within parity, and (2) estimate variance components and genetic correlations for RFI across parities. Data consisted of 72,474 weekly RFI records of 5,813 lactating Holstein cows collected from 2007 to 2022 in 5 research stations across the United States. Estimates of heritability, repeatability, and genetic correlations between weekly RFI for parities 1, 2, and 3 were obtained using bivariate repeatability animal models. The nested RFI model showed better goodness of fit than the nonnested model, and some partial regression coefficients of dry matter intake on energy sinks were heterogeneous between parities. However, the Spearman's rank correlation between RFI values calculated from nested and nonnested models was equal to 0.99. Similarly, Spearman's rank correlation between the RFI breeding values from these 2 models was equal to 0.98. Heritability estimates for RFI were equal to 0.16 for parity 1, 0.19 for parity 2, and 0.22 for parity 3. Repeatability estimates for RFI across weeks within parities were high, ranging from 0.51 to 0.57. Spearman's rank correlations of sires' breeding values were 0.99 between parities 1 and 2, 0.91 between parities 1 and 3, and 0.92 between parities 2 and 3. We conclude that nesting energy sinks within parity when computing RFI improves model goodness of fit, but the impact on the estimated breading values appears to be minimal.

The effect of supplementing native rumen microbes on milk production of dairy cows.

We evaluated the effects of 2 direct-fed microbial (DFM) supplements containing 4 native rumen microorganisms on the production of dairy cows. Ninety Holstein cows (43% primiparous) were fed a common diet. Mean days in milk, milk yield, and body weight at the beginning of the study (mean ± standard deviation) were 92 ± 23 d, 45 ± 10 kg/d, and 659 ± 86 kg, respectively. After 14 d, they were blocked by parity, days in milk, and energy-corrected milk (ECM) per unit of metabolic body weight. Within block, cows were randomly assigned to treatments, which were top-dressed daily for the next 112 d. Treatments were 150 g of ground corn mixed with (1) no live DFM (CON), (2) 5 g of a live DFM (Galaxis 2.0; G2), and (3) 5 g of a live DFM (Galaxis 2.0 Plus; G2P). G2 and G2P were products of Native Microbials Inc. (San Diego, CA) and contained the same organisms but in different concentrations. Supplementation with DFM did not alter yield of total milk, protein, or fat, but slightly decreased body weight gain and body condition score gain with no difference between G2 and G2P. The DFM tended to decrease dry matter intake (DMI) and tended to improve ECM/DMI. The DFM did not alter digestibility of fiber, starch, or protein and did not alter concentrations of glucose or nonesterified fatty acids, but tended to decrease concentration of insulin in plasma. Direct-fed microbials decreased somatic cell counts in milk with no difference between G2 and G2P. In conclusion, supplementation with native DFM had little impact on animal production and efficiency.

Impact of epistasis effects on the accuracy of predicting phenotypic values of residual feed intake in U. S Holstein cows.

The impact of genomic epistasis effects on the accuracy of predicting the phenotypic values of residual feed intake (RFI) in U.S. Holstein cows was evaluated using 6215 Holstein cows and 78,964 SNPs. Two SNP models and seven epistasis models were initially evaluated. Heritability estimates and the accuracy of predicting the RFI phenotypic values from 10-fold cross-validation studies identified the model with SNP additive effects and additive × additive (A×A) epistasis effects (A + A×A model) to be the best prediction model. Under the A + A×A model, additive heritability was 0.141, and A×A heritability was 0.263 that consisted of 0.260 inter-chromosome A×A heritability and 0.003 intra-chromosome A×A heritability, showing that inter-chromosome A×A effects were responsible for the accuracy increases due to A×A. Under the SNP additive model (A-only model), the additive heritability was 0.171. In the 10 validation populations, the average accuracy for predicting the RFI phenotypic values was 0.246 (with range 0.197-0.333) under A + A×A model and was 0.231 (with range of 0.188-0.319) under the A-only model. The average increase in the accuracy of predicting the RFI phenotypic values by the A + A×A model over the A-only model was 6.49% (with range of 3.02-14.29%). Results in this study showed A×A epistasis effects had a positive impact on the accuracy of predicting the RFI phenotypic values when combined with additive effects in the prediction model.

Estimates of genetic parameters for feeding behavior traits and their associations with feed efficiency in Holstein cows.

Residual feed intake (RFI) is commonly used to measure feed efficiency but individual intake recording systems are needed. Feeding behavior may be used as an indicator trait for feed efficiency using less expensive precision livestock farming technologies. Our goal was to estimate genetic parameters for feeding behavior and the genetic correlations with feed efficiency in Holstein cows. Data consisted of 75,877 daily feeding behavior records of 1,328 mid-lactation Holstein cows in 31 experiments conducted from 2009 to 2020 with an automated intake recording system. Feeding behavior traits included number of feeder visits per day, number of meals per day, duration of each feeder visit, duration of each meal, total duration of feeder visits, intake per visit, intake per meal [kg of dry matter (DM)], feeding rate per visit, and feeding rate per meal (kg of DM per min). The meal criterion was estimated as 26.4 min, which means that any pair of feeder visits separated by less than 26.4 min were considered part of the same meal. The statistical model included lactation and days in milk as fixed effects, and experiment-treatment, animal, and permanent environment as random effects. Genetic parameters for feeding behavior traits were estimated using daily records and weekly averages. Estimates of heritability for daily feeding behavior traits ranged from 0.09 ± 0.02 (number of meals; mean ± standard error) to 0.23 ± 0.03 (feeding rate per meal), with repeatability estimates ranging from 0.23 ± 0.01 (number of meals) to 0.52 ± 0.02 (number of feeder visits). Estimates of heritability for weekly averages of feeding behavior traits ranged from 0.19 ± 0.04 (number of meals) to 0.32 ± 0.04 (feeding rate per visit), with repeatability estimates ranging from 0.46 ± 0.02 (duration of each meal) to 0.62 ± 0.02 (feeding rate per visit and per meal). Most of the feeding behavior measures were strongly genetically correlated, showing that with more visits or meals per day, cows spend less time in each feeder visit or meal with lower intake per visit or meal. Weekly averages for feeding behavior traits were analyzed jointly with RFI and its components. Number of meals was genetically correlated with milk energy (0.48), metabolic body weight (-0.27), and RFI (0.19). Duration of each feeder visit and meal were genetically correlated with milk energy (0.43 and 0.44, respectively). Total duration of feeder visits per day was genetically correlated with DM intake (0.29), milk energy (0.62), metabolic body weight (-0.37), and RFI (0.20). Intake per visit and meal were genetically correlated with DM intake (0.63 and 0.87), milk energy (0.47 and 0.69), metabolic body weight (0.47 and 0.68), and RFI (0.31 and 0.65). Feeding rate was genetically correlated with DM intake (0.69), metabolic body weight (0.67), RFI (0.47), and milk energy (0.21). We conclude that measures of feeding behavior could be useful indicators of dairy cow feed efficiency, and individual cows that eat at a slower rate may be more feed efficient.

Circulating Metabolites Indicate Differences in High and Low Residual Feed Intake Holstein Dairy Cows.

Selection for more feed efficient dairy cows is key to improving sustainability and profitability of dairy production; however, underlying mechanisms contributing to individual animal feed efficiency are not fully understood. The objective of this study was to identify circulating metabolites, and pathways associated with those metabolites, that differ between efficient and inefficient Holstein dairy cows using targeted metabolite quantification and untargeted metabolomics. The top and bottom fifteen percent of cows (n = 28/group) with the lowest and highest residual feed intake in mid-lactation feed efficiency trials were grouped retrospectively as high-efficient (HE) and low-efficient (LE). Blood samples were collected for quantification of energy metabolites, markers of hepatic function, and acylcarnitines, in addition to a broader investigation using untargeted metabolomics. Short-chain acylcarnitines, C3-acylcarnitine, and C4-acylcarntine were lower in HE cows (n = 18/group). Untargeted metabolomics and multivariate analysis identified thirty-nine differential metabolites between HE and LE (n = 8/group), of which twenty-five were lower and fourteen were higher in HE. Pathway enrichment analysis indicated differences in tryptophan metabolism. Combined results from targeted metabolite quantification and untargeted metabolomics indicate differences in fatty acid and amino acid metabolism between HE and LE cows. These differences may indicate post-absorptive nutrient use efficiency as a contributor to individual animal variation in feed efficiency.

Colostrum supplementation with n-3 fatty acids alters plasma polyunsaturated fatty acids and inflammatory mediators in newborn calves.

Calves may experience increased oxidative stress at birth through activation of metabolic and respiratory processes. Reducing oxidative stress may enhance calf viability in early life. Our objective was to determine the dose response to fish and flaxseed oil when supplemented in colostrum on concentrations of plasma fatty acid (FA), FA metabolites, and index of oxidative stress during the critical first week of life in calves to understand how supplementing n-3 FA may decrease oxidative stress. We hypothesized that n-3 FA supplemented in colostrum in a linear dose-dependent fashion would associate with increased plasma n-3 FA concentrations and decreased oxidative stress. Twenty-four male and female Holstein calves were randomly assigned to receive 0, 30, 60, or 120 mL of a 1:1 fish to flaxseed oil supplement in colostrum. All calves received 2.8 L of previously frozen colostrum (≥22% Brix) with their respective treatment within 6 h after birth. Blood was sampled before first feeding after birth and on d 1, 2, 4, 7, and 14 d of age to assess oxidant status and plasma free PUFA, phospholipid FA, and oxylipid concentrations. Health indicators were observed daily. Indicators of general health and growth were unaffected by treatment. Supplemented calves exhibited greater concentrations of n-3 FA in plasma as free and phospholipid FA and some n-3 and n-6 FA-derived oxylipids in the first week of life in a linear fashion with increasing supplemental dose. Fish and flaxseed oil treatments did not alter oxidant status but overall decreased isoprostane concentrations in plasma, indicating oxidative stress was decreased. Together, these responses indicate that the fish and flaxseed oil supplement was antiinflammatory. In conclusion, supplementing colostrum with 30, 60, and 120 mL of a 1:1 mixture of fish and flaxseed oil linearly increased plasma concentrations of n-3 FA and metabolites and decreased biomarkers of oxidative stress, but did not alter oxidant status or affect health or growth. Our findings suggest neonatal calves may benefit from n-3 FA supplementation in colostrum to encourage a greater antiinflammatory state.

Colostrum supplementation with n-3 fatty acids does not alter calf outcome on a healthy commercial farm.

Our objective was to supplement colostrum with n-3 fatty acids (FA) to provide anti-inflammatory mediators that may improve the immune response of neonatal calves. Elevated markers of inflammation have been associated with increased occurrence of calf disease in early life, thus decreasing animal productivity. We hypothesized that a colostrum supplement containing 60-mL of a 1:1 ratio fish:flaxseed oil blend with or without 200 mg of α-tocopherol might provide an advantageous start to early life by decreasing oxidative stress and regulating the inflammatory response. Calves were blocked by birth order and randomly assigned to 1 of 3 treatments: no supplement added to colostrum (control), 60 mL of 1:1 fish:flaxseed oil blend, and 60 mL of 1:1 fish:flaxseed oil blend with 200 mg of α-tocopherol. In total, 180 heifer calves (n = 60 per treatment) were enrolled on a commercial farm. After colostrum feeding, all calves were housed in individual hutches and fed milk replacer 3 times per day. Health was scored 3 times per week until weaning at 8 wk of age. Weight, wither height, and heart girth were measured after birth, 3 wk, and 8 wk of age to assess preweaning growth. A subgroup of 54 calves (18 blocks or 18 calves per treatment) were sampled 2 d (± 8 h) after birth to evaluate oxidant status, serum total protein, and inflammatory gene and cytokine protein expression in blood after an in vitro lipopolysaccharide (LPS) challenge as indicators of health and immunity. At 9 wk, calves were transported 18 h to another farm, and medical records were kept as an indicator of disease incidence up to 13 wk of age. Calf mortality was 1.8%, which is below industry average, and exceptional health scores were observed throughout the study. Health scores and growth were similar throughout the preweaning period regardless of treatment. Serum total protein indicated successful passive transfer in all calves, and oxidant status index was not affected by treatments on d 2 of age. Concentrations of tumor necrosis factor α increased with LPS stimulation, but the increase was not altered by treatment. Likewise, leukocyte gene expression of tumor necrosis factor α, IL-8 and IL-10, and cyclooxygenase-2 increased upon LPS stimulation, but the fold change did not differ with treatment. In conclusion, 60 mL of 1:1 ratio fish:flaxseed oil colostrum supplement did not enhance preweaning calf performance. Supplementing n-3 FA in a one-time meal may not provide the anti-inflammatory benefits observed with continuous feeding.

Colostrum supplementation with n-3 fatty acids and α-tocopherol alters plasma polyunsaturated fatty acid profile and decreases an indicator of oxidative stress in newborn calves.

Our objective was to characterize the effects of supplementing newborn calves with n-3 fatty acids (FA) and α-tocopherol on blood lipid profiles and oxidant status in early life. Sixteen calves received 0 or 60 mL of 1:1 fish and flaxseed oil with 200 mg of α-tocopherol in 2.8 L of colostrum within 6 h after birth. Colostrum was >22% on the Brix scale. Blood was sampled on d 1, 2, 4, 7, 14, and 21 after birth for assessment of plasma polyunsaturated FA, α-tocopherol, total serum protein, and oxidant status index, an indirect indicator of oxidative stress that examines the balance between the concentration of reactive oxygen and nitrogen species and antioxidant capacity in serum. Health was observed daily. Weight and hip height were recorded at birth, 3 wk, and 8 wk. Data were analyzed with a Mixed procedure of SAS 9.4 (SAS Institute Inc., Cary, NC). Treatment did not alter concentration of total protein in blood serum, prevalence of diarrhea or other signs of disease, or rate of growth. Feeding n-3 FA and α-tocopherol increased plasma concentrations of the n-3 FA, including α-linolenic, eicosapentaenoic, and docosahexaenoic acids, with a concomitant decrease in oxidant status index during the first week of life. Concentrations of α-tocopherol decreased with supplementation, but all calves maintained adequate concentrations. Oxidant status index of treated calves returned to the level of control calves by d 14. We conclude that a colostrum supplement of n-3 FA and α-tocopherol is safe to administer to newborn calves, reduces oxidant status in the first week of life, and may improve health and performance.

Presence of Acetamide in Milk and Beef from Cattle Consuming AFEX-Treated Crop Residues.

AFEX treatment of crop residues can greatly increase their nutrient availability for ruminants. This study investigated the concentration of acetamide, an ammoniation byproduct, in AFEX-treated crop residues and in milk and meat from ruminants fed these residues. Acetamide concentrations in four AFEX-treated cereal crop residues were comparable and reproducible (4-7 mg/g dry matter). A transient acetamide peak in milk was detected following introduction of AFEX-treated residues to the diet, but an alternative regimen showed the peak can be effectively mitigated. Milk acetamide concentration following this transition was 6 and 10 ppm for cattle and buffalo, respectively, but also decreased over time for cattle while tending to decrease (p = 0.08) for buffalo. There was no difference in acetamide concentration in the meat of cattle consuming AFEX-treated residues for 160 days compared to controls. Further investigation is necessary to determine the metabolism of acetamide in ruminants and a maximum acceptable daily intake for humans.

Effect of ammonia fiber expansion on the available energy content of wheat straw fed to lactating cattle and buffalo in India.

The seasonal lack of availability of lush green forages can force dairy farmers in developing nations to rely on crop residues such as wheat and rice straw as the major feed source. We tested whether ammonia fiber expansion (AFEX) treatment of wheat straw would increase the energy available to Murrah buffalo and Karan-Fries cattle consuming 70% of their diet as wheat straw in India. Forty lactating animals of each species were blocked by parity and days in milk and randomly assigned to 1 of 4 treatment diets (n = 10). Treatments were a nutrient-rich diet with 0 to 20% straw (positive control; PC) and 3 high-straw diets with various levels of AFEX-treatment: (1) 70% untreated straw (no AFEX), (2) 40 to 45% untreated straw with 25 to 30% AFEX-treated straw (low AFEX), and (3) 20% untreated straw with 50% AFEX-treated straw (high AFEX). The AFEX-treated straw was pelleted. Urea was added to the no and low AFEX diets so they were isonitrogenous with the high AFEX diet. Animals were individually fed the PC diet for 14 d followed by 7 d of adaptation to treatments, full treatments for 28 to 35 d, and finally PC diets for 21 d. Compared with buffalo fed the PC diet, those fed high-straw diets consumed 29% less feed dry matter, put out 16% less milk energy, and lost 0.8 kg/d more body weight; the AFEX treatment of straw did not alter intake or milk production but greatly ameliorated the body weight loss (-1.0 kg/d for no AFEX and -0.07 kg/d for high AFEX). In Karan-Fries cattle, high-straw diets decreased dry matter intake by 39% and milk energy by 24%, and the high AFEX diet increased intake by 42% and milk energy by 18%. The AFEX treatment increased digestibilities of organic matter, dry matter, neutral detergent fiber, acid detergent fiber, and crude protein by 6 to 13 percentage points in buffalo and 5 to 10 points in cattle. In conclusion, AFEX treatment increased the digestibility and energy availability of wheat straw for lactating buffalo and cattle and has commercial potential to improve milk production and feed efficiency when high-quality forages or grains are not available.

Transcriptome analysis of epithelial and stromal contributions to mammogenesis in three week prepartum cows.

Transcriptome analysis of bovine mammary development has provided insight into regulation of mammogenesis. However, previous studies primarily examined expression of epithelial and stromal tissues combined, and consequently did not account for tissue specific contribution to mammary development. Our objective was to identify differences in gene expression in epithelial and intralobular stromal compartments. Tissue was biopsied from non-lactating dairy cows 3 weeks prepartum, cut into explants and incubated for 2 hr with insulin and hydrocortisone. Epithelial and intralobular stromal tissues were isolated with laser capture microdissection. Global gene expression was measured with Bovine Affymetrix GeneChips, and data were preprocessed using RMA method. Moderated t-tests from gene-specific linear model analysis with cell type as a fixed effect showed more than 3,000 genes were differentially expressed between tissues (P<0.05; FDR<0.17). Analysis of epithelial and stromal transcriptomes using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathways Analysis (IPA) showed that epithelial and stromal cells contributed distinct molecular signatures. Epithelial signatures were enriched with gene sets for protein synthesis, metabolism and secretion. Stromal signatures were enriched with genes that encoded molecules important to signaling, extracellular matrix composition and remodeling. Transcriptome differences also showed evidence for paracrine interactions between tissues in stimulation of IGF1 signaling pathway, stromal reaction, angiogenesis, neurogenesis, and immune response. Molecular signatures point to the dynamic role the stroma plays in prepartum mammogenesis and highlight the importance of examining the roles of cell types within the mammary gland when targeting therapies and studying mechanisms that affect milk production.

Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts.

A cDNA microarray resource enhanced for transcripts specific to the bovine mammary gland (BMAM) has been developed and used in pilot studies to examine gene expression profiles in the mammary gland. One goal driving development of this resource was to shed some light on the pathways and mechanisms specifically related to bovine mammary gland growth and development. To accomplish this, gene expression patterns from bovine adipose, liver, adrenal, lymph, spleen, thymus, gut, and developing mammary tissue were compared using the BMAM microarray. We have thus identified a putative set of 16 genes being preferentially expressed in developing mammary gland. Another of our long-term goals is to elucidate the genes and pathways associated with bovine lactation and involution and to use these as a model for human mammary gland development as it relates to human breast cancer risks. To begin this process, we conducted a pilot study, comparing gene expression profiles of lactating bovine mammary tissue against nonlactating tissue on the BMAM microarray. Our results have yielded many novel and interesting genes exhibiting differential expression in lactating mammary tissue, including oncogenes (VAV3, C-myc), mediators of apoptosis (Caspase 8), and cell cycle regulators (LASP1).