Genomic Prediction and Genome-Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows.

Genomic selection (GS) and genome-wide association studies (GWAS) have not been investigated in Vietnamese dairy cattle, even for basic milk production traits, largely due to the scarcity of individual phenotype recording in smallholder dairy farms (SDFs). This study aimed to estimate heritability (h2) and test the applicability of GS and GWAS for milk production, body conformation and novel heat tolerance traits using single test day phenotypic data. Thirty-two SDFs located in either the north (a lowland vs. a highland) or the south (a lowland vs. a highland) of Vietnam were each visited for an afternoon and the next morning to collect phenotype data of all lactating cows (n = 345). Tail hair from each cow was sampled for subsequent genotyping with a 50K SNP chip at that same visit. Milk production traits (single-test day) were milk yield (MILK, kg/cow/day), energy corrected milk yield adjusted for body weight (ECMbw, kg/100 kg BW/day), fat (mFA, %), protein (mPR, %) and dry matter (mDM, %). Conformation traits were body weight (BW, kg) and body condition score (BCS, 1 = thin to 5 = obese). Heat tolerance traits were panting score (PS, 0 = normal to 4.5 = extremely heat-stressed) and infrared temperatures (IRTs, °C) at 11 areas on the external body surface of the cow (inner vulval lip, outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof and hind hoof), assessed by an Infrared Camera. Univariate linear mixed models and a 10-fold cross-validation approach were applied for GS. Univariate single SNP mixed linear models were applied for the GWAS. Estimated h2 (using the genotype information to build relationships among animals) were moderate (0.20-0.37) for ECMbw, mFA, mPR, mRE, BW, BCS and IRT at rear udder; low (0.08-0.19) for PS and other IRTs; and very low (≤ 0.07) for MILK, ECM and mDM. Accuracy of genomic estimated breeding values (GEBVs) was low (≤ 0.12) for MILK, ECM, mDM and IRT at hind hoof; and moderate to high (0.32-0.46) for all other traits. The most significant regions on chromosomes (BTA) associated with milk production traits were 0.47-1.18 Mb on BTA14. Moderate to high h2 and moderate accuracies of GEBVs for mFA, mPR, ECMbw, BCS, BW, PS and IRTs at rear udder and outer vulval surface suggested that GS using single test day phenotypic data could be applied for these traits. However, a greater sample size is required to decrease the bias of GEBVs by GS and increase the power of detecting significant quantitative trait loci (QTLs) by GWAS.

Infrared thermography as a tool for the measurement of negative emotions in dairy cows.

In commercial dairy cows, the conditions in which they are kept may lead to negative emotional states associated with the development of chronic physiological and behavioural abnormalities that may compromise their health, welfare and productivity. Such states include fear, stress or anxiety. Behavioural rather than physiological tests are more likely to be used to indicate these states but can be limited by their subjectivity, need for specialised infrastructure and training (of the operator and sometimes the animal) and the time-consuming nature of data collection. Popularly used physiological measures such as blood cortisol may be more appropriate for acute rather than chronic assessments but are easily confounded, for example by a response to the act of measurement per se. More sophisticated physiological measures such as functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) may be impractical due to cost and time and, like blood cortisol, have the confounding associated with the act of measurement. By contrast, infrared thermography of external body surfaces is remote, non-invasive, easily repeated and follows an objective methodology, allowing longitudinal data acquisition for the inference of changes in chronic emotional state over time. The objective of this review was to investigate the potential of infrared thermography to measure cow emotions. In lactating dairy cows, maximum IRT of the eyes and coronary band of the limbs seem to be most representative of thermoregulatory changes, which are repeatable and correlate with behavioural and physiological indicators of emotional state. IRT methodologies have the potential to become a fundamental tool for the objective assessment of welfare state in dairy cows.

Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms.

Panting score (PS) is a common research tool used to assess the physiological state of cows exposed to heat stress, but it is subjective. Infrared temperature (IRT), measured by either infrared thermometers or cameras, may be a more objective and reliable alternative. Very few studies thus far have evaluated the associations between PS, IRT, and milk production. We investigated the applicability of IRT compared with PS as a means of assessing heat stress and milk yield reduction in dairy cows in tropical smallholder dairy farms (SDF). In autumn 2017, SDF located across 4 typical dairy regions of Vietnam were each visited once to collect farm (n = 32) and individual cow data (n = 344). For each SDF, heat load index (HLI) inside the cowsheds, an indicator of environmental heat load calculated from ambient temperature, humidity, and wind speed, was measured. For each cow, PS (0 indicates a cow breathing normally, not panting; 4.5 indicates an extremely heat-stressed cow with excessive panting, tongue fully extended, and excessive drooling), IRT of the cow's body, single-day energy-corrected milk yield (ECM), body weight, and body condition score were measured. Cow genotype, age, lactation number, and days in milk were recorded. The IRT of the cows' inner vulval lip (IVuT) were measured with an infrared thermometer; and the IRT of the cows' vulval surface (OVuT), inner tail base surface (ITBT), ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, fore hoof, and hind hoof were also measured with an infrared camera. Multivariate mixed-effects models were used to assess the associations between HLI with PS and IRT, and associations between PS and IRT with ECM while accounting for the effects of other cow variables. All IRT correlated positively with PS (Pearson correlation, r = 0.23-0.50). Each unit increase in HLI was associated with increases of 0.07 units in PS and 0.09 to 0.23°C in IRT. Each degree (°C) increase in IVuT, OVuT, and ITBT was associated with decreases of 0.75, 0.87, and 0.70 kg/cow per day in ECM, respectively, whereas PS and other IRT were not significantly associated with ECM. Thus, all IRT showed potential to assess the heat stress level of cows; and IVuT, OVuT, and ITBT, but not PS and other IRT, showed potential to predict ECM reduction in cows during heat stress. First cross (F1) Holstein Brown Swiss and F1 Holstein Jersey showed lower PS and yielded higher ECM than the third backcross (B3) Holstein Zebu (7/8 Holstein + 1/8 Zebu) and pure Holstein. Thus, F1 Holstein Brown Swiss and F1 Holstein Jersey could be more suitable for tropical SDF than B3 Holstein Zebu and pure Holstein.

Genomic diversity and breed composition of Vietnamese smallholder dairy cows.

Vietnamese smallholder dairy cows (VDC) are the result of crossbreeding between different zebu (ZEB) and taurine dairy breeds through many undefined generations. Thus, the predominant breed composition of VDC is currently unknown. This study aimed to evaluate the level of genetic diversity and breed composition of VDC. The SNP data of 344 animals from 32 farms located across four dairy regions of Vietnam were collected and merged with genomic reference data, which included three ZEB breeds: Red Sindhi, Sahiwal and Brahman, three taurine breeds: Holstein (HOL), Jersey (JER) and Brown Swiss (BSW), and a composite breed: Chinese Yellow cattle. Diversity and admixture analyses were applied to the merged data set. The VDC were not excessively inbred, as indicated by very low inbreeding coefficients (Wright's FIS ranged from -0.017 to 0.003). The genetic fractions in the test herds suggested that the VDC are primarily composed of HOL (85.0%); however, JER (6.0%), BSW 5.3%) and ZEB (4.5%) had also contributed. Furthermore, major genotype groupings in the test herds were pure HOL (48%), B3:15/16HOL_1/16ZEB (22%) and B2:7/8HOL_1/8ZEB (12%). The genetic makeup of the VDC is mainly components of various dairy breeds but also has a small percentage of ZEB; thus, the VDC could be a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.

Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam.

This study aimed to rank potential drivers of cow productivity and welfare in tropical smallholder dairy farms (SDFs) in Vietnam. Forty-one variables were collected from 32 SDFs located in four geographically diverse dairy regions, with eight SDFs per region. Twelve variables, including milk yield (MILK), percentages of milk fat (mFA), protein (mPR), dry matter (mDM), energy-corrected milk yield (ECM), heart girth (HG), body weight (BW), ECM per 100 kg BW (ECMbw), body condition score (BCS), panting score (PS), inseminations per conception (tAI), and milk electrical resistance (mRE) of cows, were fitted as outcome variables in the models. Twenty-one other variables describing farm altitude, housing condition, and diet for the cows, cow genotypes, and cow physiological stage were fitted as explanatory variables. Increased farm altitude was associated with increases in ECM and mRE and with decreases in PS and tAI (P < 0.05). Increases in roof heights and percentage of shed side open were associated with increases in ECM, mFA, and mDM (P < 0.05). Increased dry matter intake and dietary densities of dry matter and fat were associated with increased MILK, ECM, and ECMbw and decreased tAI (P < 0.05). Increased dietary lignin density was associated with increased PS. Increased genetic proportion of Brown Swiss in the herd was associated with increased MILK, ECM, and ECMbw (P < 0.05). Thus, to improve cow productivity and welfare in Vietnamese SDFs, the following interventions were identified for testing in future cause-effect experiments: increasing floor area per cow, roof heights, shed sides open, dry matter intake, dietary fat density, and the genetic proportion of Brown Swiss and decreasing dietary lignin density.

A sampling strategy for the determination of infrared temperature of relevant external body surfaces of dairy cows.

Infrared thermography is a tool to investigate the welfare of cattle. This study aimed to identify a sampling strategy for recording infrared thermograms in dairy cows, in order to most efficiently determine biologically relevant changes in the maximum infrared temperature (IRT) of the eyes and coronary band of forelimbs. Thirty-one dairy cows were used for the study. They were assessed with four replicates of thermograms for each of the head and lower forelimb per cow for 6 mostly consecutive days (sessions). The data obtained were subjected to random effects Analysis of Variance which was used to estimate the variance components for this sampling model, using maximum IRT of both eyes; (left + right eye)/2 and both limbs; (left + right coronary band of forelimb)/2 as dependant variables. The variance components were used to calculate least significant differences (LSD) between two theoretical treatment groups under different sampling scenarios. Analysis showed that there was minimal improvement in precision beyond 2 thermograms within a session but there was improvement with increasing the number of sessions from 2 to 3. The LSD of both eyes and both limbs reached a biologically relevant difference (0.4 and 0.9 °C, respectively) at a minimum number of 14 - 16 cows monitored for 2 consecutive thermography sessions, or 10 - 12 cows for 3 sessions. We conclude that no more than 2 replicate IRT measures are required per session but that measuring on 3 consecutive days should be considered, depending on whether time or number of cows used is the primary limitation.

Assessing response to dry-off in dairy cows kept outdoors using spontaneous behaviours and infrared thermography-a pilot study.

We used spontaneous behaviours to assess response to dry-off involving abrupt dietary and milking frequency changes, followed by regrouping, after the last milking in 15 clinically healthy Holstein-Frisian cows kept outdoors. Moreover, we explored the potential of infrared thermography to detect eye temperature variations possibly induced by dry-off. On days - 1, 0, 1 and 2 relative to dry-off, we recorded whether cows vocalised during feed delivery; ate fresh feed within 5 min; and mean maximum eye temperature at approximately 1 h after feed delivery. On days 1 and 2, cows were more likely to eat fresh feed compared to days - 1 and 0. No difference in likelihood of vocalising was found. Compared to day - 1, eye temperature was substantially higher on days 0 and 2. Collectively, the results suggest that cows responded, both behaviourally and physiologically, to the abrupt dry-off management. The interpretation of the current findings deserves further investigation using larger sample sizes, more controlled environments and further behavioural, physiological, cognitive and clinical measures.

Non-Invasive Physiological Indicators of Heat Stress in Cattle.

Cattle are susceptible to heat stress, especially those kept on high levels of nutrition for the purpose of maximising growth rates, which leads to a significant heat increment in their bodies. Consequences include compromised health and productivity and mortalities during extreme events, as well as serious economic loss. Some measures of heat stress, such as plasma cortisol and temperature in the rectum, vagina, or rumen, are invasive and therefore unlikely to be used on farms. These may cause additional stress to the animal due to handling, and that stress in itself can confound the measure. Consequently, it is desirable to find non-invasive alternatives. Panting score (PS), cortisol metabolites in faeces, milk, or hair, and the infrared temperature of external body surfaces are all potentially useful. Respiratory indicators are difficult and time consuming to record accurately, and cortisol metabolites are expensive and technically difficult to analyse. Infrared temperature appears to offer the best solution but requires further research to determine the thresholds that define when corrective actions are required to ensure optimal health and productivity. Research in this area has the potential to ultimately improve the welfare and profitability of cattle farming.

Lung biopsy in the diagnosis of pediatric ANCA-associated vasculitis.

OBJECTIVE: To investigate pulmonary histopathologic features in a cohort of pediatric patients with anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) who underwent a lung biopsy as part of their evaluation. We report the safety and the findings of lung biopsies in this population. METHODS: After IRB approval, we performed a retrospective chart review of all patients <18 years of age presenting to our institution with a diagnosis of pediatric AAV (pAAV) who underwent lung biopsy. We reviewed histopathologic features, serologies, the timing of biopsy, and complications. RESULTS: Fourteen patients met inclusion criteria, nine patients with microscopic polyangiitis (MPA), and five patients with granulomatosis with polyangiitis (GPA). All patients had positive ANCA serology. 13/14 patients required admission on initial presentation for respiratory symptoms; 11/13 required respiratory support. The indication for biopsy was confirmation of diagnosis before initiating therapy in 11 patients (78%), part of the infectious evaluation in two (14%), and part of interstitial lung disease evaluation in one (7%). 11/14 (78%) biopsies had findings consistent with AAV diagnosis: 6/9 (67%) of the MPA patients compared with 5/5 (100%) of the GPA patients. The most common findings on histopathology were vascular inflammation and signs of alveolar hemorrhage. The only reported complication after lung biopsy was pneumothorax in four patients (28%). CONCLUSION: Lung biopsy had a higher diagnostic yield in GPA compared with MPA patients. In our cohort, a diagnosis of AAV could be made with clinical features and positive serology but was confirmed by lung histopathology in the majority of cases. Obtaining a lung biopsy for diagnostic purposes in pAAV should be reserved for uncertain cases where the diagnosis cannot be confirmed clinically and with serology.

Assessment of Performance and Some Welfare Indicators of Cows in Vietnamese Smallholder Dairy Farms.

Smallholder dairy farms (SDFs) are distributed widely across lowland and highland regions in Vietnam, but data on the productivity and welfare status of these cows remains limited. This cross-sectional study was conducted to describe and compare the productivity and welfare status of SDF cows across contrasting regions. It was conducted in autumn 2017 on 32 SDFs randomly selected from four typical but contrasting dairy regions (eight SDFs per region); a south lowland, a south highland, a north lowland, and a north highland region. Each farm was visited over a 24-h period (an afternoon followed by a morning milking and adjacent husbandry activities) to collect data of individual lactating cows (n = 345) and dry cows (n = 123), which included: milk yield and concentrations, body weight (BW), body condition score (BCS, 5-point scale, 5 = very fat), inseminations per conception, and level of heat stress experienced (panting score, 4.5-point scale, 0 = no stress). The high level of heat stress (96% of lactating cows were moderate to highly heat-stressed in the afternoon), low energy corrected milk yield (15.7 kg/cow/d), low percentage of lactating cows (37.3% herd), low BW (498 and 521 kg in lactating and dry cows, respectively), and low BCS of lactating cows (2.8) were the most important productivity and welfare concerns determined and these were most serious in the south lowland. By contrast, cows in the north lowland, a relatively hot but new dairying region, performed similarly to those in the south highland; a region historically considered to be one of the most suitable for dairy cows in Vietnam due to its cool environment. This indicates the potential to mitigate heat stress through new husbandry strategies. Cows in the north highland had the highest BW (535 and 569 kg in lactating and dry cows, respectively) and the highest energy corrected milk yield (19.2 kg/cow/d). Cows in all regions were heat-stressed during the daytime, although less so in the highlands compared to the lowlands. Opportunities for research into improving the productivity and welfare of Vietnamese SDF cows are discussed.

Issues of Feeding Strategy for Lactating Cows in Vietnamese Smallholder Dairy Farms.

A limited literature suggests relatively simple feeding regimes and diet formulation strategies for dairy cows in Vietnamese smallholder dairy farms (SDFs). This study aimed to classify and compare feeding regimes and nutrient balance for lactating cows between four typical dairy regions (south lowland, south highland, north lowland, and north highland) in Vietnam and evaluate the possibility of systematic dietary imbalance. Eight SDFs from each of the four regions were visited for two adjacent milking periods per farm. For each visit, frequency and methods of feed and water supply to the lactating cows were recorded, and individual fat corrected milk yield (ECM) of lactating cows were calculated from milk yield and fat concentration. The amount of each diet ingredient offered and refused by each lactating group was weighed and sampled for calculation of dry matter intake per cow (DMI) and analysis of nutrient composition in the component offered. PCDairy, a diet formulation computer model, was used to calculate actual and recommended dietary nutrient concentrations and predict potential milk production. Factor analysis, cluster analysis, and ANOVA were applied to determine grouping effects across as well as between regions. Feeding regimes and diets were grouped into three and nine clusters, respectively. Farmers in the same region tended to apply similar diets and feeding regimes. Across regions, only 47% of all SDFs supplied water ad libitum to the cows. The most used roughages including Napier grass, corn silage, fresh corn with cob, and rice straw were all relatively high in neutral detergent fibre (NDF), acid detergent fibre (ADF), and acid detergent lignin (ADL). The diets in all regions were excessive in crude protein, NDF, ADF, ADL, and most minerals (Ca, P, Mg, K, Na, S, Fe, Zn, Cu, and Mn) but insufficient in net energy and non-fibre carbohydrate. Feed efficiency (1.06 kg FCM/kg DMI) of the diets were sub-optimal. Feeding regimes and dietary nutrient balance of the south lowland SDFs were most problematic. Increasing dietary net energy concentration by increasing the use of starch and fat and decreasing dietary fibre concentration by decreasing the use of Napier grass or rice straw to balance the diets might help improve the milk production and thereby increase feed efficiency.

Characteristics of Cowsheds in Vietnamese Smallholder Dairy Farms and Their Associations with Microclimate-A Preliminary Study.

In smallholder dairy farms (SDFs), farmers often build cowsheds using local materials and based on self-accumulated experience without due consideration to reducing the risk of heat stress. This study aimed to characterise the heat stress abatement strategies and microclimate within SDF cowsheds from four typical dairy regions of Vietnam (south lowland, south highland, north lowland and north highland) and identify the housing parameters most associated with the microclimate. The study was conducted on 32 SDFs (eight SDFs per region) in autumn 2017. Twelve housing management variables, illustrating cowshed design and heat stress abatement methods of each SDF, were collected. Six microclimate parameters, collected within the cowshed, were temperature (AT), humidity, air speed (AS), heat load index (HLI), Temperature-humidity index (THI) and accumulated heat load units (AHLU) during a day (06:00 h to 18:00 h). Factor analysis and cluster analysis was applied to group cowsheds of SDFs into clusters where SDFs in the cluster had the same cowshed characteristics. Multivariable linear models were applied to define the parameters most likely to inform future research into heat stress mitigation on SDF. Averaged from 08:00 h to 18:00 h, microclimate inside the cowsheds was considered hot (HLI > 79) in the highland and very hot (HLI > 86) in the lowland regions. Cows in the lowland regions accumulated high heat load (AHLU > 50) by 18:00 h. Cowsheds of SDFs varied widely and grouped into seven cowshed types, but no type was more effective than others in reducing heat stress conditions within cowsheds. Using roof soakers together with fans decreased AT and HLI by 1.3 °C and 3.2 units, respectively, at 14:00 h compared to 11:00 h. Each 100 m increase in altitude was associated with decreases of 0.4 °C in AT, 1.3 units in HLI and 0.8 units in THI (p < 0.001). Each meter increase in the eave height of the cowshed roof was associated with decreases of 0.87 °C in AT, 3.31 units in HLI and 1.42 units in THI, and an increase of 0.14 m/s in AS (p < 0.05). The cowshed parameters that should be prioritised for future research into the amelioration of heat stress in SDF cows include using the roof soakers together with fans, increasing altitude, eave roof height and floor area per cow.