Dairy Cows Offered Fresh Chicory Instead of Ensiled Pasture during an Acute Heat Challenge Produced More Milk and Had Lower Body Temperatures.

The frequency, duration, and intensity of heat waves in Australia are increasing. To reduce the impact of heat waves on milk production, novel management strategies are required. Altering the forage type and amount offered affect the heat load on dairy cows and offer potential strategies to ameliorate the effects of hot weather. Thirty-two multiparous, lactating Holstein-Friesian cows were assigned one of four dietary treatments: chicory high amount, chicory low amount, pasture silage high amount, or pasture silage low amount. These cows were exposed to a heat wave in controlled-environment chambers. Cows that were offered fresh chicory had similar feed intake to cows that were offered pasture silage (15.3 kg DM/d). However, cows that were offered chicory produced greater energy-corrected milk (21.9 vs. 17.2 kg/d) and had a lower maximum body temperature (39.4 vs. 39.6 °C) than cows that were offered pasture silage overall. Cows that were offered the high amount of forage had greater feed intake (16.5 vs. 14.1 kg DM/d) and energy corrected milk yield (20.0 vs. 17.9 kg/d) than cows that were offered the low amount, as intended, but with no difference in maximum body temperature (39.5 °C). We conclude that feeding chicory instead of pasture silage to dairy cows shows promise as a dietary strategy to ameliorate the effect of heat exposure, and there was no advantage in restricting feed amount.

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

BACKGROUND: Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. RESULTS: GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. CONCLUSIONS: The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended.

Effects of Heat Stress in Dairy Cows Offered Diets Containing Either Wheat or Corn Grain during Late Lactation.

Cereal grains that differ in the rate and extent of ruminal fermentation differ in heat increment and may be used to improve thermoregulation during heat stress. This experiment investigated the responses of dairy cows in late lactation to a heat challenge when offered wheat-grain or corn-grain. Eighteen lactating cows, 220 ± 94 (mean ± standard deviation) days in milk, 3.7 ± 0.17 years of age and 558 ± 37 kg bodyweight, were allocated treatments containing 6 kg dry matter (DM)/day of wheat grain or 6 kg DM/day corn grain (9 per treatment) plus 14 kg DM/day of alfalfa hay. Measurements were made during a 7-day pre-challenge period at ambient conditions in individual stalls, during a 4-day heat challenge (temperature humidity index of 74 to 84) in individual controlled-climate chambers, then during a 7-day recovery period at ambient conditions in individual stalls. During the heat challenge, cows offered corn had lower respiration rates (p = 0.017) and greater feed intake (p = 0.021) but energy-corrected milk (p = 0.097) was not different to that of cows offered wheat. Feeding corn grain to dairy cows during a heat challenge reduced some of the negative impacts of heat stress, enabling the cows to consume more forage compared with supplementing with wheat grain.

Dietary Fat and Betaine Supplements Offered to Lactating Cows Affect Dry Matter Intake, Milk Production and Body Temperature Responses to an Acute Heat Challenge.

Supplementing the diet of lactating cows with ingredients that increase energy density, or reduce internal heat production, may reduce some of the negative impacts of hot weather on milk yield. Thirty-two dairy cows were assigned either: (1) basal diet only, (2) basal diet plus canola oil, (3) basal diet plus betaine, or (4) basal diet plus canola oil and betaine. The basal diet was lucerne hay, pasture silage, and grain. Cows were exposed to a four-day heat challenge (temperature-humidity index 74 to 84) in controlled-environment chambers. Canola oil supplementation increased milk production (22.0 vs. 18.7 kg/d) across all periods of our experiment and increased body temperature (39.6 vs. 39.0 °C) during the heat challenge. Betaine supplementation reduced maximum body temperature during the pre-challenge period (39.2 vs. 39.6 °C) but not during the heat challenge (40.3 °C). Cows fed canola oil had greater declines in dry matter intake (5.4 vs 2.7 kg DM) and energy corrected milk (1.3 vs. 1.0 kg) from the pre-challenge to the heat challenge than other cows. Contrary to our expectations, the combination of fat and betaine supplements did not result in a clear benefit in terms of milk production or body temperature. Further work is warranted to understand the interactions between diet and hot weather.

Economic Analysis of Offering Different Herbage Allowances to Dairy Cows Fed a Partial Mixed Ration.

The economics of grazing dairy cows offered a range of herbage allowances and fed supplements as a partial mixed ration (PMR) were examined where profit was defined as the margin between total milk income and the cost of pasture plus PMR supplement. The analysis made use of milk production and feed intake data from two dairy cow nutrition experiments, one in early lactation and the other in late lactation. In early lactation and at a PMR intake of 6 kg DM/cow per day, the profit from the cows with access to a medium herbage allowance (25 kg DM/cow per day) was AUD 1.40/cow per day higher than that for cows on a low allowance (15 kg DM/cow per day). At a higher PMR intake of 14 kg DM/cow per day, the profit from the cows on a medium herbage allowance was AUD 0.45/cow per day higher than the cows on a low allowance; there was no additional profit from increasing the herbage allowance from medium to high (40 kg DM/cow per day). In late lactation, the profit from the cows fed a PMR with a medium herbage allowance (20 kg DM/cow per day) was only higher than the cows on a low allowance (12 kg DM/cow per day) when the PMR intake was between 6 and 12 kg DM/cow per day. There was also a difference of AUD +0.50/cow per day between the PMR with medium and high herbage allowance (32 kg DM/cow per day). It was concluded that farmers who feed a PMR to dairy cows should offer at least a medium herbage allowance to optimize profit. While feeding additional PMR increases milk production and profit, further gains would be available by offering a higher herbage allowance. These findings provide an estimate of the net benefits of different herbage allowances when feeding a PMR and will enable farmers to manage their feeding systems more profitably.

Measurement of Enteric Methane Emissions by the SF6 Technique Is Not Affected by Ambient Weather Conditions.

Despite the fact that the sulphur hexafluoride (SF6) tracer technique was developed over 25 years ago to measure methane production from grazing and non-housed animals, no studies have specifically investigated whether ambient wind speed, temperature, relative humidity and rainfall influence the accuracy of the method. The aim of this research was to investigate how these weather factors influence the measurement of enteric methane production by the SF6 technique. Six different cohorts of dairy cows (40 per cohort) were kept outdoors and fed a common diet during spring in 3 consecutive years. Methane production from individual cows was measured daily over the last 5 days of each 32-day period. An automated weather station measured air temperature, wind speed, relative humidity and rainfall every 10 min. Regression analyses were used to relate the average daily wind speed, average daily temperature, average daily relative humidity and total daily rainfall measurements to dry matter intake, average daily methane production and methane yield of each cohort of cows. It was concluded that the modified SF6 technique can be used outdoors during a range of wind speeds, ambient temperatures, relative humidities and rainfall conditions without causing a significant effect on the measurement of methane production or methane yield of dairy cows.

Economic Threshold Analysis of Supplementing Dairy Cow Diets with Betaine and Fat during a Heat Challenge: A Pre- and Post-Experimental Comparison.

Ex ante economic analysis can be used to establish the production threshold for a proposed experimental diet to be as profitable as the control treatment. This study reports (1) a pre-experimental economic analysis to estimate the milk production thresholds for an experiment where dietary supplements were fed to dairy cows experiencing a heat challenge, and (2) comparison of these thresholds to the milk production results of the subsequent animal experiment. The pre-experimental thresholds equated to a 1% increase in milk production for the betaine supplement, 9% increase for the fat supplement, and 11% increase for fat and betaine in combination, to achieve the same contribution to farm profit as the control diet. For the post-experimental comparison, previously modelled climate predictions were used to extrapolate the milk production results from the animal experiment over the annual hot-weather period for the dairying region in northern Victoria, Australia. Supplementing diets with fat or betaine had the potential to produce enough extra milk to exceed the production thresholds, making either supplement a profitable alternative to feeding the control diet during the hot-weather period. Feeding fat and betaine in combination failed to result in the extra milk required to justify the additional cost when compared to the control diet.

Mitochondrial protein gene expression and the oxidative phosphorylation pathway associated with feed efficiency and energy balance in dairy cattle.

Feed efficiency and energy balance are important traits underpinning profitability and environmental sustainability in animal production. They are complex traits, and our understanding of their underlying biology is currently limited. One measure of feed efficiency is residual feed intake (RFI), which is the difference between actual and predicted intake. Variation in RFI among individuals is attributable to the metabolic efficiency of energy utilization. High RFI (H_RFI) animals require more energy per unit of weight gain or milk produced compared with low RFI (L_RFI) animals. Energy balance (EB) is a closely related trait calculated very similarly to RFI. Cellular energy metabolism in mitochondria involves mitochondrial protein (MiP) encoded by both nuclear (NuMiP) and mitochondrial (MtMiP) genomes. We hypothesized that MiP genes are differentially expressed (DE) between H_RFI and L_RFI animal groups and similarly between negative and positive EB groups. Our study aimed to characterize MiP gene expression in white blood cells of H_RFI and L_RFI cows using RNA sequencing to identify genes and biological pathways associated with feed efficiency in dairy cattle. We used the top and bottom 14 cows ranked for RFI and EB out of 109 animals as H_RFI and L_RFI, and positive and negative EB groups, respectively. The gene expression counts across all nuclear and mitochondrial genes for animals in each group were used for differential gene expression analyses, weighted gene correlation network analysis, functional enrichment, and identification of hub genes. Out of 244 DE genes between RFI groups, 38 were MiP genes. The DE genes were enriched for the oxidative phosphorylation (OXPHOS) and ribosome pathways. The DE MiP genes were underexpressed in L_RFI (and negative EB) compared with the H_RFI (and positive EB) groups, suggestive of reduced mitochondrial activity in the L_RFI group. None of the MtMiP genes were among the DE MiP genes between the groups, which suggests a non-rate limiting role of MtMiP genes in feed efficiency and warrants further investigation. The role of MiP, particularly the NuMiP and OXPHOS pathways in RFI, was also supported by our gene correlation network analysis and the hub gene identification. We validated the findings in an independent data set. Overall, our study suggested that differences in feed efficiency in dairy cows may be linked to differences in cellular energy demand. This study broadens our knowledge of the biology of feed efficiency in dairy cattle.

Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle.

BACKGROUND: Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear (NuMP) and mitochondrial (MtMP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses. RESULTS: MP genes were differentially expressed (DE; over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE NuMP genes in varying proportions of over-expression and under-expression. On the other hand, DE of MtMP genes was observed in < 50% of tissues and notably MtMP genes within a tissue was either all over-expressed or all under-expressed. A high proportion of NuMP (up to 60%) and MtMP (up to 100%) genes were over-expressed in tissues with expected high metabolic demand; heart, skeletal muscles and tongue, and under-expressed (up to 45% of NuMP, 77% of MtMP genes) in tissues with expected low metabolic rates; leukocytes, thymus, and lymph nodes. These tissues also invariably had the expression of all MtMP genes in the direction of dominant NuMP genes expression. The NuMP and MtMP genes were highly co-expressed across tissues and co-expression of genes in a cluster were non-random and functionally enriched for energy generation pathway. The differential gene expression and co-expression patterns were validated in independent cow and sheep datasets. CONCLUSIONS: The results of this study support the concept that there are biological interaction of MP genes from the mitochondrial and nuclear genomes given their over-expression in tissues with high energy demand and co-expression in tissues. This highlights the importance of considering MP genes from both genomes in future studies related to mitochondrial functions and traits related to energy metabolism.

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues.

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues. RESULTS: Using whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1 Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits. CONCLUSIONS: Using novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.

Extensive variation between tissues in allele specific expression in an outbred mammal.

BACKGROUND: Allele specific gene expression (ASE), with the paternal allele more expressed than the maternal allele or vice versa, appears to be a common phenomenon in humans and mice. In other species the extent of ASE is unknown, and even in humans and mice there are several outstanding questions. These include; to what extent is ASE tissue specific? how often does the direction of allele expression imbalance reverse between tissues? how often is only one of the two alleles expressed? is there a genome wide bias towards expression of the paternal or maternal allele; and finally do genes that are nearby on a chromosome share the same direction of ASE? Here we use gene expression data (RNASeq) from 18 tissues from a single cow to investigate each of these questions in turn, and then validate some of these findings in two tissues from 20 cows. RESULTS: Between 40 and 100 million sequence reads were generated per tissue across three replicate samples for each of the eighteen tissues from the single cow (the discovery dataset). A bovine gene expression atlas was created (the first from RNASeq data), and differentially expressed genes in each tissue were identified. To analyse ASE, we had access to unambiguously phased genotypes for all heterozygous variants in the cow's whole genome sequence, where these variants were homozygous in the whole genome sequence of her sire, and as a result we were able to map reads to parental genomes, to determine SNP and genes showing ASE in each tissue. In total 25,251 heterozygous SNP within 7985 genes were tested for ASE in at least one tissue. ASE was pervasive, 89 % of genes tested had significant ASE in at least one tissue. This large proportion of genes displaying ASE was confirmed in the two tissues in a validation dataset. For individual tissues the proportion of genes showing significant ASE varied from as low as 8-16 % of those tested in thymus to as high as 71-82 % of those tested in lung. There were a number of cases where the direction of allele expression imbalance reversed between tissues. For example the gene SPTY2D1 showed almost complete paternal allele expression in kidney and thymus, and almost complete maternal allele expression in the brain caudal lobe and brain cerebellum. Mono allelic expression (MAE) was common, with 1349 of 4856 genes (28 %) tested with more than one heterozygous SNP showing MAE. Across all tissues, 54.17 % of all genes with ASE favoured the paternal allele. Genes that are closely linked on the chromosome were more likely to show higher expression of the same allele (paternal or maternal) than expected by chance. We identified several long runs of neighbouring genes that showed either paternal or maternal ASE, one example was five adjacent genes (GIMAP8, GIMAP7 copy1, GIMAP4, GIMAP7 copy 2 and GIMAP5) that showed almost exclusive paternal expression in brain caudal lobe. CONCLUSIONS: Investigating the extent of ASE across 18 bovine tissues in one cow and two tissues in 20 cows demonstrated 1) ASE is pervasive in cattle, 2) the ASE is often MAE but ranges from MAE to slight overexpression of the major allele, 3) the ASE is most often tissue specific and that more than half the time displays divergent allele specific expression patterns across tissues, 4) across all genes there is a slight bias towards expression of the paternal allele and 5) genes expressing the same parental allele are clustered together more than expected by chance, and there are several runs of large numbers of genes expressing the same parental allele.

Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle.

Mammals have a large cohort of endo- and ecto- symbiotic microorganisms (the microbiome) that potentially influence host phenotypes. There have been numerous exploratory studies of these symbiotic organisms in humans and other animals, often with the aim of relating the microbiome to a complex phenotype such as body mass index (BMI) or disease state. Here, we describe an efficient methodology for predicting complex traits from quantitative microbiome profiles. The method was demonstrated by predicting inflammatory bowel disease (IBD) status and BMI from human microbiome data, and enteric greenhouse gas production from dairy cattle rumen microbiome profiles. The method uses unassembled massively parallel sequencing (MPS) data to form metagenomic relationship matrices (analogous to genomic relationship matrices used in genomic predictions) to predict IBD, BMI and methane production phenotypes with useful accuracies (r = 0.423, 0.422 and 0.466 respectively). Our results show that microbiome profiles derived from MPS can be used to predict complex phenotypes of the host. Although the number of biological replicates used here limits the accuracy that can be achieved, preliminary results suggest this approach may surpass current prediction accuracies that are based on the host genome. This is especially likely for traits that are largely influenced by the gut microbiota, for example digestive tract disorders or metabolic functions such as enteric methane production in cattle.