Browsing by Author "Lopez-Villalobos, Nicolas"

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    Accounting for scale effects in genetic evaluation of New Zealand dairy cattle : a thesis presented in partial fulfilment for the degree of Master of Agricultural Science in Animal Science at Massey University
    (Massey University, 1994) Lopez-Villalobos, Nicolas
    It is well known that variation in lactation yields tends to increase with average production. Failure to account for this scale effect may cause overestimation of genetic merit for sires with a majority of daughters in high-variation herds and vice-versa. The current system of sire evaluation in New Zealand overcomes this problem by expressing daughters performance as a proportion of contemporary average performance. The objectives of this study were to quantify the magnitude of scaling (heterogeneous variance), and to identify methods to stabilise the variance of milkfat yields for use in the genetic evaluation system of dairy cattle through best linear unbiased prediction (BLUP) using an animal model across breeds. Lactation records of dairy cows calving between 1986 and 1989 were obtained from the Livestock Improvement Corporation of the New Zealand Dairy Board. There were milkfat yields from 2,004,854 lactations in 83,805 contemporary groups (herdyear- age; HYA). The data were divided into three equal-sized subsets based on HYA mean; these being (kg milkfat ± sd) High (H), 172 ± 28; Medium (M), 152 ± 26; and Low (L), 139 ± 25. The methods investigated for the accounting of scaling were: adjustment by the HYA sd (SD-adjustment); scaling by the HYA mean (MEAN-correction); and natural logarithmic transformation (LOG-transformation) of milkfat yield. The overall correlation between HY A means and HYA sd's was 0.44. This value was reduced to 0.31 in SD-adjusted, -0.27 in the MEAN-corrected and -0.24 in the LOG-transformed data. Ideally, the transformed data should exhibit independence between the mean and standard deviation. Breeding values of sires were separately estimated from each data subset using a mixed model. Product-moment and rank correlations between breeding values for sires estimated from the independent subsets and with variable minimum number of daughters were in the overall comparisons (L-M, L-H and M-H) lower than expected correlations, reflecting inaccuracies in sire evaluation when scaling is ignored. Product-moment and rank correlations were similar for SD-adjustment and MEAN-correction, but LOGtransformation reduced the calculated correlations in the L-M, L-H and M-H comparisons. Estimates of the genetic correlations between production in pairs of environments were obtained from the ratio of observed to expected correlations. These estimates ranged from 0.82 to 1.01 for the linear yields. Estimates of genetic correlations were similar for SD-adjusted and MEAN-corrected data, but for LOG-transformed data these were reduced, especially in the L-H comparison which ranged from 0.77 to 0.87. Results confirm the problem of scaling on genetic evaluation of New Zealand dairy cattle. MEAN-correction and LOG-transformation methods are not appropriate because they tend to overcorrect the scaling problem. SD-adjustment is not satisfactory but seems to be more appropriate than no adjustment. An alternative method is proposed based on a Bayesian approach, which takes into account any relationship between variance and mean.
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    Dietary crude protein and nitrogen utilisation in two contrasting dairy systems : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
    (Massey University, 2020) Correa-Luna, Martin
    This thesis evaluated the efficiency of crude protein utilisation (ECPU) in dairy cows and nitrogen (N) utilisation efficiency (NUE) of two pasture-based dairy systems differing in intensification levels in New Zealand. During two consecutive seasons, in the low-intensity production system (LIPS), 257 cows were milked once-daily with low supplementation, and in the high-intensity production system (HIPS), 210 cows were milked twice-daily with higher supplementation. At every herd test, ECPU was calculated as protein yield (PY) divided by crude protein intake (CPI), estimated from feed intake. Milk urea (MU) was measured in early-, mid-, and late-lactation. Urinary N was estimated by back-calculation from estimated faecal N, taking into consideration N contained in milk and in body tissues. Pasture allocation represented 93% and 65% of the total intake for LIPS and HIPS cows, respectively, resulting in higher CPI for LIPS cows throughout the lactation. Compared to HIPS cows, LIPS cows produced 22% and 16% less milk and protein, with 32% higher MU, and 25% lower ECPU. Urine N was 34% higher in LIPS cows but faecal N was 5% higher for HIPS cows. A multivariate predictive model of ECPU was developed, including milk production performance, live weight variation, diet composition and quality along with climatic variables. The model accurately predicted the ECPU in an internal validation dataset (RPE = 6.96%, R2 = 0.95). Milk urea was not selected as a predictive variable of ECPU, considering that cows of higher ECPU also had higher MU. Compared with cows of high MU genetic merit, cows of lower MU genetic merit had lower milk production and similar ECPU. A whole-farm assessment of NUE, N losses and financial analysis was undertaken. On whole-farm level, LIPS produced 23% less milk and NUE was 31% lower when compared to HIPS. The lower MY along with the 35% higher N fertiliser applied on LIPS produced a higher N surplus per ha causing higher N losses when compared to HIPS. Despite the higher feed costs of HIPS, profitability was 16% higher because of milking more cows with higher MY when compared to LIPS.
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    Genetic and genomic studies of animal welfare and environmental traits in dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
    (Massey University, 2020) Ariyarathne, Hewa Bahithige Pavithra Chathurangi
    New Zealand dairy cows graze outdoors throughout the year and are exposed to a wide range of weather conditions also their excreta are dispersed in the paddock. There is an emerging interest in whether between-cow genetic variation could contribute to environmental sustainability and improved animal welfare. The initial objectives of the study were 1) to estimate genetic parameters of rectal temperature (RT) as an indicator of heat stress (HS), 2) to identify gene regions associated with HS through genome-wide association studies (GWAS), and 3) to estimate response of genetic selection for low HS on milk production using conventional selection in grazing dairy cows of New Zealand. The genetic variance of RT estimated in 776 mixed-breed cows at two Massey University experimental dairy farms was very low due to insufficient environmental stress on sampling days. This outcome diverted the topic of study to the genetic basis of milk urea concentration (MU) and efficiency crude protein utilisation (ECPU) and their potential role in improved environmental sustainability. The new study was conducted considering MU as the trait of interest. Additionally, the possible reduction of urinary nitrogen (N) excretion by genetic selection for low milk urea N concentration (MUN) was determined. The heritability estimated for MU (from 0.27 to 0.49) and ECPU (from 0.02 to 0.41) using a random regression model in 634 mixed-breed cows indicated that these traits can be genetically manipulated by direct selection. Estimates of genetic correlations between MU and yield of milk, fat, crude protein, lactose, and liveweight (LWT) in each day of ii lactation were mostly positive and imply that selection for reduced MU would result in reduced production and LWT of cows. The GWAS identified six novel genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, ASS1) associated with MU that function in protein catabolism, urea cycle, ion transportation and N excretion. This suggests that genomic selection for MU is possible, however, the results should be validated with a larger sample size. Selection index theory was used to estimate correlated responses for different selection indices including MUN with different relative emphasis (RE). The predicted genetic responses per cow per year of the current index were 16.4 kg milk yield (MY), 2.0 kg fat yield (FY), 1.4 kg crude protein yield (CPY), -0.4 kg LWT and -0.05 mg/dl MUN. Including MUN in the selection index with 20% negative RE resulted in annual responses of 5.4 kg MY, 1.6 kg FY, 1.0 kg CPY, -1.1 kg LWT and -0.17 mg/dl MUN. The total N predicted to be excreted in the base year was 336.5 kg/ha. When stocking rate was adjusted by changes in milk production and cow feed requirements, 10 years of selection with a selection index not including MUN increased total N excretion to 338.9 kg/ha. A selection index with 20% negative RE for MUN increased total N excretion to 341.6 kg/ha, and genetic gain in production of milk protein per hectare was reduced, thereby reducing farm profits. The results of this thesis indicate that inclusion of MUN in a selection index with negative RE is not an effective pathway to reduce farm-level N leaching and carbon footprint.
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    Genetic and genomic studies on milk production and composition, and longevity in New Zealand dairy goats : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatu, New Zealand
    (Massey University, 2020) Scholtens, Megan
    The New Zealand dairy goat industry is important for producing and exporting high-quality specialised dairy products aimed at niche markets. Efforts to increase the quantity and composition of goat milk will improve profits for farmers and deliver significant economic benefits to New Zealand. However, no formal program exists for the genetic improvement of dairy goats. Therefore, the general aim of this thesis was to perform genetic and genomic studies that contribute to the design of the breeding program for New Zealand dairy goats. The first studies estimated variance components and genetic parameters of total lactation yields of milk, fat and protein, somatic cell score and longevity. The main findings suggest sufficient variation and favourable genetic correlations between these traits, supporting their inclusion into a selection index that predicts profit per animal. A random regression test-day model was then used to predict lactation curves of milk, fat, protein and somatic cell score. Using this model for genetic evaluation will enable the dairy goat industry to move from total yields into the prediction of lactation curves, enabling more accurate predictions and the opportunity of selecting for extended lactations. The first genome-wide association study of dairy goats in New Zealand was conducted using 3,732 animals genotyped with the Caprine 50K SNP chip. A highly significant region on chromosome 19 was associated with yields of milk, fat and protein, and somatic cell score, and a region on chromosome 29 was associated with somatic cell score. A prototype single-step BayesC model was developed to predict genomic breeding values and demonstrated that including genomic information into the evaluation can increase the accuracy of predictions compared to the traditional methods based on pedigrees alone, which is currently implemented in the New Zealand dairy goat industry. This thesis demonstrates that a single-step prediction model that uses genomic information would put the New Zealand dairy goat industry in a very good position to implement a genomic selection scheme. Further studies are required to define clearer breeding objectives and to systematically design a breeding program for the genetic improvement of New Zealand dairy goats.
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    Genetic parameters of fertility traits of cows milked once daily versus twice daily in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2023) Jayawardana, Jayawardana Mudiyanselage Dinesha Rajinee
    In New Zealand about 55% of dairy herds are milked twice daily (TAD) and about 9% of herds are milked once daily (OAD) for their entire lactation, with the balance of herds using variable milking frequencies across the lactation. The general aim of this thesis was to estimate genetic parameters for fertility traits of spring-calved OAD and TAD milking cows in New Zealand. Cows milked OAD for the entire lactation were more fertile than cows milked TAD for the entire lactation. Heritability and repeatability estimates for milk production and fertility traits were broadly consistent for cows that were milked either OAD or TAD for their entire lactation. Though genetic correlations between milk production and fertility were antagonistic in both milking systems, correlations between milk production and the key reproductive metrics of 6 wk in-calf, not in-calf rate and 6 wk calving were less strong in cows milked OAD compared with TAD. In both OAD and TAD milking populations, individual breed effects for milk, fat, protein and lactose yields were in favor of Friesian (F) cows; however, maternal breed effects for yields were in favor of Jersey (J) dams. Jersey cows were more fertile than the F cows in both milking populations, but maternal breed effects for fertility traits were in favour of F dams. Favourable F×J heterosis for milk production and fertility traits were significant in both milking cow populations. Recombination loss effects were sometimes favorable for production and fertility traits, but most estimates were small with larger standard errors. A genome-wide association study (GWAS) was conducted using 1,537 spring-calved dairy cows genotyped with Bovine Illumina 50K single nucleotide polymorphisms (SNPs) chips in two Massey University dairy herds. Four SNPs on chromosome 14 were highly significant for fat and protein percentages and associated genes were DGAT1, SLC52A2, CPSF1 and MROH1. The GWAS identified 10 candidate genes (KCNH5, HS6ST3, GLS, ENSBTAG00000051479, STAT1, STAT4, GPD2, SH3PXD2A, EVA1C and ARMH3) associated with fertility traits, which relate to functions, reduced metabolic stress and increased insulin secretion during the mating period, early embryonic development, fetal growth, and maternal lipid metabolism during the pregnancy period. Overall, the results of this thesis indicate milking OAD for the entire lactation improves the fertility performance of dairy cows but reduces milk production. The antagonistic genetic correlations between milk yield and key fertility measures were weaker in the OAD milking population than in the TAD milking population. The findings of this thesis can be used to develop a selection index for production and fertility traits in OAD milking cow population in New Zealand.
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    The gross composition, fatty acid composition, and processability of milk from cows milked once and twice a day under New Zealand grazing conditions : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science, Massey University, Palmerston North, New Zealand
    (Massey University, 2023) Sanjayaranj, Inthujaa
    In New Zealand, milking once a day (OAD) is practised by some farmers, with the majority of farmers milking twice a day (TAD). Once-a-day milking provides several benefits such as reduced labour cost, improved labour efficiency, improved health and reproductive performance of cows, and additional employment opportunities for farmers. Once-a-day milking causes a reduction in milk yield and modifies milk composition by increasing the fat and protein percentages. The main aim of this thesis was to study the effect of OAD milking on the gross composition, fatty acids composition, and processability of milk. To achieve this, the milk from 232 cows from a OAD herd and 182 cows from a TAD herd were collected in a full season in early, mid-, and late lactation. The samples were analysed for milk composition and fatty acid composition using Fourier-transform mid-infrared (FT-MIR) spectroscopy. Calibration equations for individual and grouped fatty acids were developed using FT-MIR calibrator software. Milk coagulation properties (rennet coagulation time, curd firming rate, and curd firmness) were analysed using a Formagraph. In addition, a SNP (rs109421300) in the diacylglycerol acyltransferase 1 (DGAT1) region on bovine chromosome 14, which is associated with a higher fat percentage in milk, was selected to study its association with fatty acid composition. Solid fat content at 10°C (SFC₁₀), a parameter that predicts butter hardness, was calculated using an equation developed from the proportions of fatty acids. The proportions of de novo synthesised fatty acids (C8:0-C14:0) were significantly higher, and the proportions of preformed, long-chain fatty acids (mainly C16:0 and C18:0) were lower in milk from cows milked OAD compared with cows milked TAD. Milk coagulation properties were superior for Jersey cows compared with Holstein-Friesian and Holstein-Friesian × Jersey cows milked OAD and TAD. The CC genotype of SNP rs109421300 was associated with higher fat yield, fat percentage, protein percentage, and SFC₁₀. Milk from OAD cows had lower proportions of C16:0 suggesting it would produce more easily spreadable butter. Selecting cows with the CC genotype would be suitable for the New Zealand dairy industry with the current payment system, however, the CC genotype was less suitable for making more easily spreadable butter. Overall, there were some significant differences noted between milk from cows milked OAD and TAD in terms of fatty acid composition and processability.
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    Investigation of lameness and claw disorders in New Zealand dairy goats : a multidisciplinary approach : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Jaques, Natasha
    New Zealand dairy goat farmers have problems preventing and treating lameness caused by claw disorders within their herds. There is scarce information about lameness and claw disorders in commercial dairy goat herds nationally and internationally. The two aims of this thesis were: to acquire information on the level of clinical lameness and the types and level of claw disorders present on three dairy goat farms in New Zealand and to explore the epidemiological, productivity, and genetic aspects of lameness and claw disorders. Information on lameness and claw disorders was collected on herds 4 or 5 times between July 2019 and June 2020. Additional information collected were age, stage of lactation, milk production, pedigree, kidding date, and lactation type. The prevalence of clinical lameness and claw disorders fluctuated across the production year at levels that differed on each farm. Farm A had the highest average of clinical lameness (23%), followed by farms B and C (12 and 10%, respectively). For the investigation of claw disorders, the main claw disorders studied were horn separation, granulomas, and rot. Farm C had the highest prevalence of horn separation (83%), while farm A had the highest prevalence of rot and granulomas (19 and 14%). Rot and granulomas increased the odds of clinical lameness (OR= 2.10-7.02). Compared to goats walking normally, severe lameness had the highest milk production losses of 7.10% and 8.56% in extended and seasonal lactation goats, respectively. The average income losses ranged from NZD 26 to 104 per goat. The heritability (h2) estimates for lameness occurrence and susceptibility were 0.07 and 0.13, respectively, and the h2 estimates of claw disorder susceptibilities ranged from 0.02 to 0.23. This thesis identified that clinical lameness caused by claw disorders is a problem on dairy goat farms in New Zealand and reported the negative impact of severe lameness on milk production. Additionally, breeding for resistance or tolerance of clinical lameness and claw disorder may be possible. Further large-scale studies are needed to understand the risk factors of clinical lameness and claw disorders. Small-scale studies are required to investigate effective treatments to manage claw disorders in dairy goats.
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    Unveiling the potential of proximal hyperspectral sensing for measuring herbage nutritive value in a pasture-based dairy farm system : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Agriculture and Horticulture at Massey University, Manawatū, New Zealand
    (Massey University, 2020) Duranovich, Federico Nicolás
    The aim of this thesis was to unveil the potential of proximal hyperspectral sensing for measuring herbage nutritive value in a pasture based-dairy farm system. Hyperspectral canopy reflectance and herbage cuts as well as data on herbage and supplement allocation, and milk production were collected regularly from Dairy 1 farm at Massey University during the 2016-17 and 2017-18 production seasons. Milk, fat and protein yields and body condition score of cows were measured at monthly herd tests while live weights were recorded daily. Calibration equations determining herbage the nutritive value traits digestible organic matter in dry matter, metabolisable energy (ME), crude protein, neutral detergent fibre and acid detergent fibre from hyperspectral canopy reflectance data were developed and validated using partial least squares regression. Canopy reflectance calibration models were able to determine the various herbage nutritive value traits with R2 values ranging from 0.57 to 0.78. Variation of herbage nutritive value traits were mostly explained by month within production season (42.7% of variance among traits) followed by random error (33.4%), production season (13.1%) and paddock (10.7%). The relative importance of herbage nutritive value and other herbage quantity and climate-related variables in driving performance per cow in the herd was determined using multiple linear regression. Herbage metabolizable energy explained 20% to 30% of milk, fat and protein production per cow while herbage quantity and climate- related factors were relatively less important (below 15%). Random regression models were used to model lactation curves of milk, fat, protein and live weight to estimate daily ME requirements of individual cows. The daily ME estimated requirements was nearly a fifth above or below the daily mean ME supplied. The deviation of the daily ME estimated requirements of a cow from the actual ME supplied per cow in the herd was mostly explained by the observations made within a cow rather than between cows or breeds. Variation in herbage nutritive value in addition to the within and between cow variation of ME estimated requirements were high enough to justify the use of proximal hyperspectral sensing as measurement tool to assist with feed allocation decision-making. However, the potential of this technology could be further enhanced using more precise technologies to allocate herbage to individual cows or groups of cows. The potential benefits of more precise feed allocation will result in more efficient grazing management and thus improved utilisation of herbage and hence milk production.