Strategies to improve dairy cow productivity and welfare in Vietnam Ngoc Bang Nguyen MSc. / BSc. A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2021 School of Veterinary Science Abstract In Vietnam, smallholder dairy farms (SDFs) account for more than 97% of the total national dairy herd, and the number of SDFs has increased rapidly recently due to the high demand for fresh milk. While studies aiming to improve the productivity and welfare of cows in SDFs could help increase national milk production, such studies are currently extremely limited due to the lack of available data about dairy cow husbandry management, breed, pedigree, and performance. The aims of this project were to describe the productivity of Vietnamese SDF cows and their welfare in typical dairying regions and to determine and prioritise potential nutrition, breeding, and management strategies to improve the productivity and welfare of those SDF cows. A total of 32 SDFs from four key contrasting dairy regions (8 farms per region) of Vietnam were chosen. The regions were those with highland/cooler climate: a southern highland region and a northern highland region; and those with lowland/hotter climate: a southern lowland region and a northern lowland region. Each farm was visited over an afternoon and during the following morning in autumn 2017 to collect necessary farming data and single-day data of all lactating cows. The farming data, including altitude, number of cattle, cow diets, feeding regimes, shed dimensions, heat stress abatement methods, and shed microclimate conditions, were obtained directly on the farms. Feed ingredients used for cow diets were sampled for chemical composition analysis. Single-day data of all lactating cows (n = 345), including milk yield, milk compositions, energy corrected milk yield (ECM), milk electrical resistance, body weight (BW), body condition score (BCS), number of inseminations per conception, panting score (PS, 4.5-point scale, 0 = normal, 4.5 = extremely heat- stressed) were measured directly on farms to be used as indicators of cow productivity and welfare. Genomic data of lactating cows were obtained by taking tail hair samples, extracting DNA, and genotyping with GGP bovine 50K chips. Infrared temperatures (IRTs) of lactating cows were measured at the inner vulval lip using an infrared thermometer, and measured at another ten different external areas, including: the outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof, and hind hoof, using an infrared camera. Data from all 32 farms were used for seven studies. The first study described herd structure and evaluated the productivity and welfare status of the cows. The second used genomic data to identify genetic diversity and breed composition. The third and fourth studies described and compared feeding regimes, diets, shed designs, heat stress abatement methods, and shed microclimate of the 32 farms in the four visited regions to evaluate the strengths and limitations of the cows’ nutrition and the heat stress management of each farm. The fifth study built multivariate models to identify nutrition, management and animal factors that were most associated with the productivity and welfare of the I cows. The sixth study tested the capability of IRTs relative to PS to assess the level of heat stress and the reduction in the cows’ milk yield under heat stress conditions. The seventh and last study tested the application of genomic selection and genome-wide association studies on milk production, body conformation (BW and BCS), and heat tolerance straits (PS and IRTs) of the SDF herds. The average herd size across regions was 29 animals comprising 11 lactating cows, four dry cows, six heifers, seven female calves, one male calf, one beef cattle, and no reproductively active bulls. All the cows were genetically very close to pure Holstein and retained a similar level of genetic diversity as the reference Holstein populations used in the USA, New Zealand, and France. The genetic proportionality of Holstein, Jersey, Brown Swiss, and Zebu, averaged across all herds, were 85.0%, 6.0%, 5.3%, and 4.5%, respectively. The most critical production and welfare issues were the high level of heat stress (96% of cows were moderate to highly heat-stressed in the afternoon), relatively low ECM (15.7 kg/cow/d), low BCS (2.8, 5-point scales), a high number of inseminations per conception in the lowland SDFs (1.9 to 3.2 times per conception), insufficient supply of water, insufficient floor allowance per cow (8 m2/cow), and excessive use of “tie” rather than “loose” stalls or pens for cows in sheds. From among the four regions, the cows in the southern lowland were least productive and had the poorest welfare conditions. The lactating cow diets in all regions were deficient in net energy and excessive in crude protein and fibre concentrations, which were associated with low milk yield and low feed efficiency in all regions. Increases in farm altitude, shed roof height, floor allowance for cows, percentages of cowshed sides open, and the use of roof soakers and fans were all associated with improved cowshed microclimate, reduced PS, decreases in the number of inseminations per conception, and improved milk production. All infrared temperatures showed potential to assess the level of heat stress in the cows. The infrared temperatures of the inner vulval lip, outer vulval surface, and inner tail base surface showed the best potential to predict ECM reduction during heat stress. Under SDF conditions, Holstein_BrownSwiss and Holstein_Jersey first crosses tended to be more productive and less heat-stressed than backcrosses of Holstein and Zebu with 15/16 Holstein purer. The moderate to high heritabilities (0.26 to 0.58) and moderate accuracies (0.23 to 0.50) of genomic estimated breeding values (GEBVs) for some milk production traits (ECM adjusted for BW and milk fat and protein concentrations), body conformation traits (BCS and BW), and heat tolerance traits (PS and IRTs at the rear udder, fore hoof and outer vulval surface) suggested the potential to apply genomic selection using single-test day phenotypic measurements for these traits. However, a larger sample size is required. Novel single nucleotide polymorphisms and genes for PS and infrared temperatures were located on chromosome (BTA) 5, BTA8, BTA11, BTA14, BTA19, and BTA20. II Overall, the most important short-term strategies to improve the productivity of SDF cows are heat stress amelioration and the measurement thereof using new technologies such as IRT. Next are nutritional strategies which include supplying ad libitum drinking water and the reformulation of cow diets by increasing available energy whilst decreasing fibre concentrations to meet the requirements of the cows in heat stress conditions. Long-term strategies could include the application of genomic selection to identify bulls and heifers with high genetic merit for milk production, heat tolerance and other key traits, from within the current Vietnamese SDF herd. III Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. IV Publications included in this thesis Since thesis submission, the following papers have been published: Bang NN, Chanh NV, Trach NX, Khang DN, Hayes BJ, Gaughan JB, Lyons RE, Hai NT and McNeill DM (2021). Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms. Animals, 11 (3), 674. https://doi.org/10.3390/ani11030674 (Chapter 3). Bang NN, Chanh NV, Trach NX, Khang DN, Hayes BJ, Gaughan JB, Lyons RE, Hai NT and McNeill DM (2021). Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms. Animals, 11 (3), 729. https://doi.org/10.3390/ani11030729 (Chapter 5). Bang NN, Gaughan JB, Hayes BJ, Lyons RE, Chanh NV, Trach NX, Khang DN and McNeill DM (2021). Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate - A preliminary study. Animals, 11 (2), 351. https://doi.org/10.3390/ani11020351 (Chapter 6). Submitted manuscripts included in this thesis Since thesis submission, the following manuscript has been submitted for publication: Bang NN, Hayes BJ, Lyons RE, Randhawa IAS, Gaughan JB and McNeill DM (2021).