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Item A study of factors affecting test day records of dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in Animal Science at Massey University(Massey University, 1972) Wickham, Brian WalterDairyfarming in New Zealand is fundamentally concerned with obtaining an income from the sale of milk and milk fat produced by ones cows. A dairy farmer's income can be increased by either reducing the costs of production and/or increasing the value of milk and milk fat sold. One method by which income can be increased is the culling of low producers and selection of high producing replacements. In New Zealand Herd Improvement Associations provide three systems whereby the production of individual cows is measured monthly, bimonthly or twice yearly. In using these records for culling and selective breeding there are two main groups of influences that have to be taken into account - environmental influences and genetic influences. In selective breeding the major objective is in fact to separate the environmental and genetic influences so that the genetically "best" animals can be used to produce the next generation. Any attempt to evaluate either the genetic or environmental influences on test records must take into account the other. For example in bull selection the daughters of the bulls being compared may be of different ages and milked in different herds. The relative genetic value of the bulls can only be evaluated after the influence of age and herd, on daughter production, has been taken into account. Likewise in evaluating the influence of age on production the cows in each age class may be the daughters of different sires. Only by taking account of these genetic differences can the affect of the environmental factor be evaluated.Item Use of genetic information about the herd in the design and management of dairy farm systems : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science majoring in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2003) Bryant, Jeremy RalphThe aim of this thesis was to find ways of using the genetic information available about the cows to assist in improving the management of the herd and replacements. In particular models were developed which used Estimated Breeding Values to determine the feed demand of the cow and target liveweights for replacement heifers. The relationships between estimated breeding values (EBV) and cow performance at a range of feeding levels, and the effect of genetic merit on the partitioning of feed to milk or liveweight gain throughout the lactation, were also investigated. At low levels of feeding, the absolute differences in milk yield between cows corresponded to the absolute differences in breeding values between cows. However, at high levels of feeding the difference in milk yields between genetic groups are greater than the difference in breeding values. This constitutes a form of genotype x environment interaction, which has important practical and economic implications for daily farms, and for the expected value of genetic improvements. High genetic merit (HGM) cows partitioned a significantly higher proportion of metabolisable energy intake into milk than low genetic merit (LGM) cows in early (0.68 vs 0.62), peak (0.59 vs 0.57), mid (0.58 vs 0.56) and late lactation (0.53 vs 0.51) (HGM vs LGM respectively). In early lactation, HGM cows utilised more body reserves for milk production (-0.06 vs -0.004, for HGM and LGM, respectively). In addition, HGM and LGM cows appeared to compensate for low intakes in early lactation by reducing the level of MEI partitioned to milk, which probably prevented excessive weight losses. These results with grazing cows confirm published data with cows fed on other rations. Results from a grazing experiment, with 5 separate farmlets at 5 different stocking rates, were used to provide genetic information and performance per cow of a "calibration" herd corresponding to maximum profitability per farm (max EFS). The genetic and performance information for the calibration herd was then used to predict the performance of other cows or herds based on the difference in EBV for liveweight and milksolids. From these predicted values for liveweight and milksolids the "Genetic Feed Demand" (GFD) of the herd was calculated at max EFS. The GFD can then be used to adapt and improve the Comparative Stocking Rate (CSR) equation by replacing kg liveweight/ha with total GFD. Optimum values for the new CSR of 0.7 to 0.8 are proposed. This simple adjustment using genetic values provides a better estimate of the feed demand of the herd. From this an appropriate number of cows for the specified feed supply can be determined Another model was developed to use the liveweight EBV to formulate a set of liveweight targets for individual heifers of any breeds at different ages throughout the first two years of their life. Feeding regimes for the heifers were also proposed. A heifer herd management report was outlined that could be used by farmers and graziers to focus special attention on those individual heifers which were significantly lighter or heavier than their target weights for age. In conclusion, greater use should be made of genetic information of individual cows and herds when designing and managing dairy farm systems. Genetic values can be used in a number of ways to ensure cows or heifers are fed more appropriately so they achieve levels of performance, which are closer to their pre-determined genetic potential. Genetic information should also be included in tools that are used to model the management of dairy farm systems, as this will improve the accuracy of prediction.Item Genome-wide association study for stature in New Zealand dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2013) Tan, Mun EeThe objective of this thesis was to perform a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) associated with stature in New Zealand dairy cattle. The phenotype data set used for this study contained the animal key, sire code of the bull, birth date, breed code, proportion of Holstein-Friesian genes, proportion of Jersey genes, percentage of North American Holstein genes, estimated breeding values (EBV) for live weight and stature and their reliabilities of 3140 bulls. The genotype data set contained the genotype of 692,598 SNPs for every bull and another file contained the name and position of the SNPs. The GWAS was performed on Holstein-Friesian, Jersey and Holstein-Friesian × Jersey crossbred bulls using PLINK software version 1.07. Stature EBV was used as the phenotype. The phenotypes were adjusted for percentage of Holstein-Friesian, Jersey, North American Holstein genes and year of birth using multiple regression. Manhattan plots and multi Manhattan plots of P-values adjusted to genomic control against the chromosomes were plotted to identify top SNPs with the most significant P-values above the significant threshold line. Based on the top 50 SNPs according to the P-value, this study identified nine chromosomes or BTA in the HF population with SNPs significantly associated with stature, BTA2, 3, 4, 5, 6, 11, 12, 14 and 24. SNPs with significant effect on stature were detected in six chromosomes, BTA9, 10, 12, 18, 19 and 25 in the JE population while the SNPs determined to be significantly associated with stature were located on eleven chromosomes, BTA1, 3, 4, 5, 7, 9, 10, 14, 18, 22 and 24 in the XB population. Several SNPs located above the suggestive threshold in the Manhattan plots were also inspected and kept in view for future studies. The results from this study suggest that the highlighted SNPs with significant associations to stature can serve as candidate SNPs for further investigation to determine the regions of QTLs and ultimately the exact genes that affect stature with other correlated traits in dairy cattle.Item A study of physiological differences between low and high breeding index friesian heifers : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University(Massey University, 1989) Xing, Guo-QiangFriesian heifers from two genetic lines divergently selected for milk production were compared in their metabolic physiology and endocrinology in three experiments. Studies were conducted on the heifers, which were matched for age and bodyweight, in order to identify metabolic differences which might be used as genetic markers for lactational performance. In the first experiment diurnal variation in plasma metabolite and hormone concentrations and responses to metabolic challenges of glucose, insulin, glucagon, and adrenaline, were measured in 6 high breeding index (HBI) and 6 low breeding index (LBI) heifers aged 6 to 8 months and fed 75% or 125% maintenance energy requirement (MER). Basal plasma concentrations of creatinine, GH and NEFA were not influenced by selection line. Plasma insulin concentrations after feeding were greater in the LBI than in the HBT heifers. Relative to the concentrations which existed at the time of feeding, the elevation in plasma glucose concentration was greater in the HBI than in the LBI heifers from 7 to 9 hours after feeding. Elevation in plasma urea concentration on feeding was greater in HBI than in LBI heifers. Urea concentrations then declined more rapidly in the selected animals during the postprandial period such that concentrations were lower in HBI than in LBI heifers from 11 till 23 hours after feeding. Responses to metabolic challenge were generally not different between the lines and there were no line x allowance interactions except in the NEFA response to adrenaline where HBI heifers responded more than LBI heifers at 75% MER but not at 125% MER. When compared with heifers fed 125% MER, those fed 75% MER exhibited: increased plasma creatinine concentrations; a smaller increment in plasma urea concentration after feeding; greater plasma NEFA levels in the post-prandial period; lower insulin concentrations during a 24 hour sampling period; decreased insulin release and glucose removal after glucose administration; greater plasma NEFA concentrations and reduced glucose clearance after insulin injection; enhanced glycogenolytic responses to glucagon and adrenaline; and increased lipolytic responses to glucagon and adrenaline. In the second experiment, 8 HBI and 8 LBI Friesian heifers aged 6 months were treated with progesterone by Controlled Internal Drug Release (CIDR) devices and fed 70% MER. Initially, basal plasma metabolite and hormone concentrations were measured in samples collected during a 6 hour intensive sampling period. In the following period, the line x dose interactions of intravenous glucose (0, 75, 150 and 300 mg/kg lwt) and insulin (0, 0.1, 1, and 10 ug/kg lwt) on metabolic responses were evaluated in a split-plot design carried out over a period of 8 days. Basal plasma urea and creatinine concentrations were marginally greater (P<0.10) in the LBI heifers than in the HBI heifers but no differences were found between the two lines in plasma concentrations of GH, insulin, glucagon, glucose or NEFA. No significant line differences were found in the number of secretion spikes or the magnitude of the spikes for basal GH or insulin. Glucagon concentrations were measured using a specific double antibody radioimmunoassay developed as part of this programme. There were marked dose effects of both glucose and insulin challenges on concentrations of insulin, glucose and NEFA. In addition, the HBI heifers released more insulin than the LBI heifers after the glucose challenge in a manner independent of glucose dose. Moreover, volume of plasma glucose distribution (Vd), or the distribution coefficient (∆) was smaller, and glucose disappearance rate greater (in terms of elimination rate constant (k) or the half-life (t1/2> of the injected glucose), in the HBI than in the LBI heifers. Insulin challenge resulted in slightly higher plasma insulin concentrations in the HBI heifers than in the LBI heifers. No significant interactions of line x dose in plasma metabolites and hormone concentrations were observed after either glucose or insulin challenges. The third experiment compared 8 HBI and 8 LBI yearling heifers, fed 140% MER and receiving progesterone treatment, with respect to: diurnal patterns of plasma concentrations of metabolites and hormones; volume of body fluid distribution; ingestive behaviour in terms of rate of eating; responses of lipolysis and glycogenolysis to adrenaline challenge at various times after feeding and fasting; metabolic responses to fasting and refeeding; and pancreatic insulin release and glucose disappearance after glucose challenges administered before and after the withdrawal of progesterone-impregnated CIDRs. Diurnal plasma concentrations of glucose, were greater, but plasma urea and creatinine levels were lower, in HBI than in LBI heifers. Plasma glucagon levels at the onset of feeding/refeeding were only briefly greater in HBI heifers than in LBI heifers. The volumes of urea distribution, plasma distribution (as measured by Evans blue (T1824) distribution), and the extracellular fluid distribution (as measured by thiocyanate (NaSCN) distribution) were similar between the HBI and LBI heifers. In general, rate of eating was similar between the lines over the experiments except it was greater in the LBI than in the HBI heifers on the first day of measurement. In addition, the eating rate fell substantially in the LBI but not in HBI heifers 28 hours after the withdrawal of progesterone-CIDRs. Lipolytic response to adrenaline was minimal 7 hours after feeding, and maximal after 72 hours of fasting, whereas the reverse was true for glycogenolytic responses. There were significant line x time of challenge interactions in pre-challenge plasma NEFA concentrations, HBI heifers fasted for 72 hours exhibiting greater elevation in plasma NEFA concentration. Time of challenge relative to feeding/fasting did not, however, influence the magnitude of selection line effects on lipolytic or glycogenolytic responses. Basal plasma insulin concentration and pancreatic insulin release after glucose challenges were greater in HBI than the LBI heifers, irrespective of the presence or absence of progesterone-impregnated CIDRs. Although basal plasma glucose concentration was greater in the HBI than in the LBI heifers, glucose disappearance was similar between the two lines following glucose challenge in this experiment. There was a significant line x progesterone presence/withdrawal interaction in the pre-challenge plasma glucose concentrations. Plasma glucose concentrations were greater in the HBI than in the LBI heifers 46 hours after the removal of progesterone CIDRs but not prior to removal of the CIDRs. These results demonstrated that genetic variation exists in nitrogen, lipid, glucose and insulin metabolism between the HBI and the LBI heifers. Appropriate experimental conditions such as different feeding regimens, use of metabolic challenges and control of oestrous activity, alone or in combination, were useful means of maximising these genetic differences. While these metabolic characteristics have the potential to become markers for dairy merit, their genetic relationships with milk production should be confirmed in further studies and these traits should also be evaluated in progeny tested bulls before their wide use in dairy cattle breeding.Item A search for quantitative trait loci involved in physiological processes related to milk production in dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2008) Hutchinson, Kathryn Joy; Hutchinson, Kathryn JoyMetabolic challenges have previously been used to identify physiological markers to assist with the selection of both sexes dairy cattle at an early age to increase rate of genetic gain. Physiological markers have not been implemented in selection programmes due to low accuracy. An experiment was undertaken to investigate the use of metabolic quantitative trait loci (QTL) for improving the rate of genetic gain in dairy cattle. Three metabolic challenges (adrenaline, glucose, and thyrotropin-releasing hormone) were conducted on 882 18-month-old Friesian-Jersey F2 crossbred heifers. An initial whole genome scan was conducted by genotyping 1679 animals within the trial pedigree for 283 microsatellite markers, obtained primarily from published marker maps. QTL analyses were performed on the Friesian-Jersey crossbred trial data using metabolic and milk production phenotypes. 581 QTL were significant at the 1% level and 275 of them were QTL of metabolic phenotypes. An objective of this study was to identify chromosomal regions in which endocrine and milk production QTL were co-located, in the hope that these regions would contain genes with a significant impact on the control of milk production. The region selected for a candidate gene study was 47-51 cM of BTA14 due to the close proximity of metabolic and milk production QTL co-located in this region. Comparative mapping was used to generate a list of 105 genes in the region of interest. The genes considered the most suitable candidates for the QTL in the region were tripartite motif-containing 55, ubiquitin-conjugating enzyme E2W (putative), nuclear receptor coactivator 2, serum/glucocorticoid regulated kinase family, member 3, opioid receptor, kappa 1, proenkephalin, corticotropin releasing hormone. A major finding of this study was that there were very few chromosomal regions in which metabolic and milk production QTL were co-located. This is likely to be due to the highly complex and integrated molecular networks controlled by many genes that influence milk production traits. The data generated in this thesis will be suitable for more advanced examinations of the genetic control of milk production using the new generations of single nucleotide polymorphism chips.Item A comparison of reproductive performance and physiology of three genotypes of Holstein Friesian dairy cattle : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2003) McNaughton, Lorna RachelIt is important to achieve a consistently high reproductive performance in the seasonal, pastoral-based dairy production systems found in New Zealand. A decline in dairy cattle reproductive performance has been reported in many countries and this decline has been suggested to be due to the incorporation of Holstein genetics into the Friesian populations. The use of Holstein genetics (referred to as overseas genetics) has increased rapidly in New Zealand in the past 10 years. This thesis investigates the reproductive performance and physiology of animals in the Dexcel Holstein Friesian Strain Trial, from the onset of puberty, through to the end of the second lactation in a pasture-based dairy production system (total 272 animals). Two strains of New Zealand genetic origin, of either high (NZH) or low (NZL) genetic merit were compared to high genetic merit Holstein-Friesian animals of overseas genetic origin (predominantly North American and Dutch origin, OS). Differences in live weight at puberty were identified between NZ and overseas strains. Nulliparous OS heifers were found to have longer oestrous cycles and luteal phases than NZ heifers, but pregnancy rates between the strains were not different. Body condition score at calving was found to be an important predictor of the length of the postpartum anovulatory interval. Postpartum anovulatory intervals were significantly shorter (p<0.05) in OS than NZH animals. Final pregnancy rates were not different between the strains. The timing of luteal regression, following an unsuccessful first insemination was found to be more variable in OS than NZH cows, with some OS cows initiating luteal regression prior to the timing of maternal recognition of pregnancy. The results from this thesis showed that there are differences in reproductive performance between the strains and that some OS animals are able to perform well in pasture-based dairy production systems. In conclusion, provided OS genetics are proven in New Zealand before they are widely used, there is no reason to recommend against the use of OS Holstein Friesian genetics. Further investigations should focus on the area of body condition score mobilisation and the control of the timing of luteolysis, which are areas where differences between the strains were identified.Item Quantifying genetic variation in environmental sensitivity of New Zealand dairy cattle to apply in the development of a dairy cattle simulation model for pastoral systems : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2006) Bryant, JeremyThe objectives of this research were firstly, to investigate if dairy cattle genotypes in NZ exhibit genetic variation in environmental sensitivity and to determine if this genetic variation is statistically significant from a genetic evaluation perspective, and secondly, to use genetic information including environmental sensitivity data to simulate dairy cattle responses to changes in nutritional regime and variation in climate. A comprehensive review identified that simulation models either overlook, or do not represent environmental sensitivity information where genotypes and breeds respond differently when exposed to variations in environment. A large dataset of daily and total lactation records (yields of milk, fat and protein) from herds participating in the progeny testing of sires from 1989 to 2002 was obtained to test for differences in the environmental sensitivity of dairy cattle in New Zealand. Production data was matched with environmental data relating to climate, herd size, altitude and herd average production levels (a proxy for feeding level). The statistical analyses applying univariate and bivariate multibreed models to environmental character states identified minimal sire re-ranking between environmental character states as measured by genetic and rank correlations. However, differences in yields of milk, fat and protein between New Zealand Jersey and overseas Holstein Friesian systematically diverged with production level, in herds expected to use different levels of supplements. These results suggest New Zealand Jersey cattle are best suited to a grassland-type environment, and overseas Holstein Friesian cattle are more suited to an intensive-type environment. A phenotypic analysis identified thermal environment (cold and hot conditions) significantly affected the expression of production traits in Holstein Friesian, New Zealand Jersey and Holstein Friesian x New Zealand Jersey cattle. Holstein Friesian dairy cattle were more susceptible to the effects of heat conditions than New Zealand Jersey cattle with yields of milk, and concentrations of fat and protein of the former compromised at a lower value for temperature humidity index. Dairy cattle performance is likely to be compromised by heat more frequently than cold conditions in New Zealand. A simulation model that considers how dairy cow genotypes respond to different environments, incorporating the results presented above, was then developed. An initial estimate of feed intake is used to define cow genetic potential based on estimated breeding values for total yields milk, fat and protein, and environmental sensitivity information. A mammary gland module then predicts daily yields of milk, fat and protein based on the cow's genetic potential after considering her age, stage of lactation, body condition score, nutritional status and thermal environment. Live weight change is also predicted via a body energy stores module, which considers the effect of age, stage of lactation, current body condition score, nutritional status, and an estimated breeding value for body condition score. Feed intake is predicted from the requirements for maintenance, growth and pregnancy, and the genetic drive for yields of milk, fat and protein and body fat change. The predictive ability of the model was tested using information from a prior study with two Holstein Friesian genotypes managed in a pasture-based system. The model simulated to a high degree of accuracy, mean values for yields of milk, fat and protein, and concentrations of fat and protein of each genotype. Various tests identified the major source of error between simulated and observed values were due to a lack of simulated variation. In conclusion, the extent of genetic variation in environmental sensitivity for total lactation yields of milk, fat and protein within the range of New Zealand environments are not sufficient to warrant the formation of separate breeding schemes for distinct environments. However, New Zealand Jersey cattle are best suited to a grassland-type environment, and overseas Holstein Friesian cattle are more suited to an intensive-type environment. Genetic variation in the suitability of different breeds for specific environments existed within breeds. A simulation model was developed that was able to simulate the effect of genotype, environment and genotypic differences in environmental sensitivity on daily cow performance.