Journal Articles
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Item Fine mapping highlights ITGAL and MUS81 loss-of-function mutations modulating recessive impacts in dairy cattle(John Wiley and Sons Ltd on behalf of Stichting International Foundation for Animal Genetics, 2025-08-01) Duntsch L; Jivanji S; Lopdell T; Reynolds EGM; Williams L; Littlejohn MDWe recently described several major-effect recessive loci impacting anatomical and lactation traits in dairy cattle. Two of these loci in particular presented multiple candidate causative variants, comprising tightly linked coding variants that could not be easily differentiated on a statistical or functional basis. Here, we re-examine the candidacy of these variants by leveraging a dataset of 1 million genotyped animals. Assessing lactation and bodyweight effects in conjunction with rare, recombined genotypes for the IL4R, KIAA0556, ITGAL, DPF2, and MUS81 candidates, we highlight ITGAL and MUS81 as the most likely causative genes for the two QTL. Recombinant homozygotes for these genes present larger, more significant effects than other candidates at the same loci, with both representing premature stop mutations anticipated to inactivate ITGAL and MUS81. We further examined homozygotes for the ITGAL mutation to better understand the range of phenotypes impacted. While outwardly normal, ITGAL mutants showed significant differences in the number and composition of circulating leukocytes, consistent with the role of ITGAL as a key mediator of leukocyte signalling, adhesion, and migration. These results demonstrate how near-perfectly linked candidate mutations can be differentiated given population-scale data, and highlight the ITGAL and MUS81 mutations as diagnostic targets to help manage the frequency of these variants.Item Genetic variation in surface temperature measured using infra-red thermography and genetic associations with production traits in grazing dairy cattle(Taylor and Francis Group, 2024-01-01) Douie JS; Lopez-Villalobos N; Dukkipati VSR; Udy GIncreasing global temperatures and the incidence of extreme weather conditions will result in heat stress becoming a greater issue in production animals. Genetic selection and breeding for heat-tolerant animals have been promoted as a possible mitigation strategy in dairy cattle. The objectives of this study were to obtain in-field skin temperature measurements of the eye, muzzle and udder using infra-red thermography to examine the genetic variation in skin temperature within cows of a dairy herd and to estimate the genetic correlations between skin temperature and production traits. Thermal images and herd test records were obtained for the dairy herd at Massey University’s dairy farm 1. Estimates of (co)variances were obtained using the JWAS program with univariate and bivariate animal models. The heritability estimates for the eye, muzzle and udder temperature were low to moderate at 0.20, 0.24 and 0.39, respectively. All genetic correlations between production and temperature traits were positive except for eye temperature with milk yield and protein yield which was negative and weak. These results indicate that it may be possible to select for a greater skin temperature, however, these results need to be validated using a larger sample size.Item Comparative study of first lactation performance of Norwegian Red crossbred cows with traditional breeds in New Zealand dairy systems(Taylor and Francis Group, 2024-01-01) Curry BA; Dukkipati VSR; López-Villalobos NSome New Zealand dairy farmers are using semen from Norwegian Red (NR) bulls to explore the performance of this breed under local grazing conditions. The objective of this study was to compare the first lactation performance of first cross NR cattle with traditional New Zealand breeds. Data were collected from six dairy farms in Southland, New Zealand, during 2022–2023 milk production seasons. Data were collected from 1178 first lactation cows including herd test of daily yields of milk, fat and protein and somatic cell counts, and persistency. Breeds included 386 NR cross (NRX), 231 Holstein Friesian (F), 84 Holstein Friesian cross (FX), 134 Holstein Friesian x Jersey (FJ) and 58 Jersey cross (JX) cows. Findings indicate F cows produced the greatest cumulative milk yield (3,744 kg), 138.6 kg more than NRX cows. There were no significant differences among the breed groups for milk yield and milk solids yield persistency and SCS (SCS = Log2 SCC). The total lactation milk yield of NRX cows was lower than that of the other breeds, excluding JX. These results pertain specifically to first lactation cows; therefore, it is necessary to undertake further analysis to evaluate the long-term productivity and longevity of NR breeds under New Zealand conditions.Item Repeatability of whole herd lameness scoring: an analysis of a New Zealand dataset(Taylor and Francis Group, 2024-09-03) Laven RA; Mason WA; Laven LJ; Müller KRAIMS: To assess whether a whole-herd lameness score on a New Zealand dairy farm in spring could predict lameness prevalence on the same farm in summer (and vice versa) and whether a single-herd lameness score could be used to determine whether herd lameness prevalence was < 5% in both spring and summer. METHODS: Prevalence data (proportion of the herd with lameness score ≥ 2 and with score 3; 0-3 scale) from a study where 120 dairy farms across New Zealand were scored in spring and in the following summer were analysed using limits-of-agreement analysis. In addition, farms were categorised as having either acceptable welfare (lameness prevalence < 5% in both spring and summer) or not (lameness prevalence ≥ 5% in either spring or summer or both). The accuracy and specificity of a single, whole-herd lameness score at identifying herds with acceptable welfare were then calculated. RESULTS: The limits-of-agreement analysis suggests that 95% of the time, the prevalence of lameness in summer would be expected to be between 0.23 and 4.3 times that of the prevalence in spring. The specificity and accuracy of identifying a farm as acceptable on both occasions from a single observation were, respectively, 74% and 92% in spring, and 59% and 87% in summer. CONCLUSIONS: A single, one-off, whole-herd lameness score does not accurately predict future lameness prevalence. Similarly, acceptable status (lameness prevalence < 5%) in one season is not sufficiently specific to be used to predict welfare status in subsequent seasons. CLINICAL RELEVANCE: Whole-herd lameness scoring should be used principally as a means of detecting lame cows for treatment. A single whole-herd lameness score by an independent assessor should not be used to determine a herd's welfare status.Item The intrauterine effects of a maternal winter diet of either kale or fodder beet on measures of calf stature and bone morphology at birth(Taylor and Francis Group, 2024-10-09) Gibson MJ; Rogers CW; Back PJ; Dittmer KE; Wehrle-Martinez A; Dalley DE; Woods RRFodder beet and kale are commonly used winter crops in New Zealand dairy and dairy support farm systems. Fodder beet (FB) is known to have lower crude protein, phosphorus and calcium content compared to kale. The intrauterine effects of feeding FB during late pregnancy on bone growth and development in calves requires attention. This study aimed to examine the intrauterine effects of a maternal diet of either kale or FB on measures of calf stature and bone morphology at birth. In winters 2019 and 2020, two herds of pregnant Friesian ×Jersey cows were fed either kale (2019, 2020 n = 20) or FB (2019, 2020 n = 20) supplemented with pasture baleage. Calves born from these mobs were euthanised within ten days of birth and a forelimb and section of rib including the costochondral junction were harvested for peripheral quantitative computed tomography and histological analysis. Calves from the FB treatment had reduced bone density and strength compared to calves from the kale treatment (p <.05). The effect of a nutritional deficit on bone morphology at birth emphasises the importance of sufficient nutrition in pre-calving diets. Future research is required to examine the long-term impact of dam undernutrition on calf growth and production.Item The prevalence of damaged tails in New Zealand dairy cattle.(Taylor and Francis Group, 2024-03-11) Cuttance EL; Mason WA; Hea SY; Bryan MA; Laven RAAIMS: To undertake a survey of the prevalence of tail deviations, trauma and shortening on a representative selection of New Zealand dairy farms, and to assess whether sampling based on milking order could be used instead of random sampling across the herd to estimate prevalence. METHODS: This was a cross-sectional observational study, with 200 randomly selected farms enrolled across nine regions of New Zealand via selected veterinary practices (one/region). Veterinary clinics enrolled 20-25 farms each depending on region, with 1-2 trained technicians scoring per region. All cows (n = 92,348) present at a milking or pregnancy testing event were tail scored using a modified version of the New Zealand Veterinary Association Industry Scoring System. Palpated lesions were recorded as deviated (i.e. non-linear deformity), shortened (tail shorter than normal) or traumatic (all other lesions). The location of lesions was defined by dividing the tail into three equal zones: upper, middle and lower. A cow could have more than one lesion type and location, and/or multiple lesions of the same type, but for the prevalence calculation, only the presence or absence of a particular lesion was assessed. Prevalence of tail damage calculated using whole herd scoring was compared to random sampling across the herd and sampling from the front and back of the milking order. Bootstrap sampling with replacement was used to generate the sampling distributions across seven sample sizes ranging from 40-435 cows. RESULTS: When scoring all cows, the median prevalence for deviation was 9.5 (min 0.9, max 40.3)%; trauma 0.9 (min 0, max 10.7)%, and shortening was 4.5 (min 1.3, max 10.8)%. Deviation and trauma prevalence varied between regions; the median prevalence of deviations ranged from 6% in the West Coast to 13% in Waikato, and the median prevalence of all tail damage from 7% in the West Coast to 29% in Southland. Sampling based on milking order was less precise than random sampling across the herd. With the latter and using 157 cows, 95% of prevalence estimates were within 5% of the whole herd estimate, but sampling based on milking order needed > 300 cows to achieve the same precision. CONCLUSIONS AND CLINICAL RELEVANCE: The proportion of cows identified as having damaged tails was consistent with recent reports from New Zealand and Ireland, but at 11.5%, the proportion of cows with trauma or deviation is below acceptable standards. An industry-wide programme is needed to reduce the proportion of affected cows.Item Farm-level risk factors and treatment protocols for lameness in New Zealand dairy cattle.(Taylor and Francis Group, 2024-05-08) Mason WA; Müller KR; Laven LJ; Huxley JN; Laven RAAims To identify farm-level risk factors for dairy cow lameness, and to describe lameness treatment protocols used on New Zealand dairy farms. Methods One hundred and nineteen farms from eight veterinary clinics within the major dairying regions of New Zealand were randomly enrolled into a cross-sectional lameness prevalence study. Each farmer completed a questionnaire on lameness risk factors and lameness treatment and management. Trained observers lameness scored cattle on two occasions, between October–December (spring, coinciding with peak lactation for most farms) and between January–March (summer, late lactation for most farms). A four-point (0–3) scoring system was used to assess lameness, with animals with a lameness score (LS) ≥2 defined as lame. At each visit, all lactating animals were scored including animals that had previously been identified lame by the farmer. Associations between the farmer-reported risk factors and lameness were determined using mixed logistic regression models in a Bayesian framework, with farm and score event as random effects. Results A lameness prevalence of 3.5% (2,113/59,631) was reported at the first LS event, and 3.3% (1,861/55,929) at the second LS event. There was a median prevalence of 2.8% (min 0, max 17.0%) from the 119 farms. Most farmers (90/117; 77%) relied on informal identification by farm staff to identify lame animals. On 65% (75/116) of farms, there was no external provider of lame cow treatments, with the farmer carrying out all lame cow treatments. Most farmers had no formal training (69/112; 62%). Animals from farms that used concrete stand-off pads during periods of inclement weather had 1.45 times the odds of lameness compared to animals on farms that did not use concrete stand-off pads (95% equal-tailed credible interval 1.07–1.88). Animals from farms that reported peak lameness incidence from January to June or all year-round, had 0.64 times odds of lameness compared to animals from farms that reported peak lameness incidence from July to December (95% equal-tailed credible interval 0.47–0.88). Conclusions Lameness prevalence was low amongst the enrolled farms. Use of concrete stand-off pads and timing of peak lameness incidence were associated with odds of lameness. Clinical relevance Veterinarians should be encouraging farmers to have formal lameness identification protocols and lameness management plans in place. There is ample opportunity to provide training to farmers for lame cow treatment. Management of cows on stand-off pads should consider the likely impact on lameness.Item Effect of Breed on the Fatty Acid Composition of Milk from Dairy Cows Milked Once and Twice a Day in Different Stages of Lactation(MDPI (Basel, Switzerland), 2022-09) Sanjayaranj I; Lopez-Villalobos N; Blair HT; Janssen PWM; Holroyd SE; MacGibbon AKH; Ametaj BThe objective of this study was to evaluate the effect of breed on the overall composition and fatty acid composition of milk from cows milked once a day (OAD) and twice a day (TAD) in different stages of lactation. Milk samples were taken from 39 Holstein-Friesian (F), 27 Jersey (J), and 34 Holstein-Friesian × Jersey (F × J) crossbred cows from a OAD milking herd and 104 F and 83 F × J cows from a TAD milking herd in early (49 ± 15 days in milk), mid (129 ± 12 days in milk), and late (229 ± 13 days in milk) lactation. Calibration equations to predict the concentrations of individual fatty acids were developed using mid-infrared (MIR) spectroscopy. There was a significant interaction between breed within the milking frequency and stage of lactation for the production traits and composition traits. Holstein-Friesian cows milked OAD produced milk with lower concentrations of C18:0 in early and mid lactations compared to F × J and J cows. Holstein-Friesian cows milked TAD produced lower concentrations of C18:0 in early lactation and lower concentrations of C16:0 and C18:0 in late lactation compared to F × J. Lower concentrations of these fatty acids would reduce the hardness of the butter when the milk is processed. In the OAD milking herd, F cows were superior for daily milk yield compared to J cows, but Jersey cows produced significantly (p < 0.05) higher percentages of fat and a higher concentration of C18:0 fatty acid. The relative concentrations of C18:0 and C18 cis-9 in F and J cows milked OAD imply there is no breed effect on the activity of delta-9-desaturase, whereas stages of lactation likely have an effect. These results can be used to assist with selecting breeds and cows that are suitable for either OAD or TAD milking, allowing closer alignment with milk processing needs.Item Association of Single Nucleotide Polymorphism in the DGAT1 Gene with the Fatty Acid Composition of Cows Milked Once and Twice a Day(MDPI (Basel, Switzerland), 2023-03-21) Sanjayaranj I; MacGibbon AKH; Holroyd SE; Janssen PWM; Blair HT; Lopez-Villalobos NA single nucleotide polymorphism (SNP) rs109421300 of the diacylglycerol acyltransferase 1 (DGAT1) on bovine chromosome 14 is associated with fat yield, fat percentage, and protein percentage. This study aimed to investigate the effect of SNP rs109421300 on production traits and the fatty acid composition of milk from cows milked once a day (OAD) and twice a day (TAD) under New Zealand grazing conditions. Between September 2020 and March 2021, 232 cows from a OAD herd and 182 cows from a TAD herd were genotyped. The CC genotype of SNP rs109421300 was associated with significantly (p < 0.05) higher fat yield, fat percentage, and protein percentage, and lower milk and protein yields in both milking frequencies. The CC genotype was also associated with significantly (p < 0.05) higher proportions of C16:0 and C18:0, higher predicted solid fat content at 10 °C (SFC10), and lower proportions of C4:0 and C18:1 cis-9 in both milking frequencies. The association of SNP with fatty acids was similar in both milking frequencies, with differences in magnitudes. The SFC10 of cows milked OAD was lower than cows milked TAD for all three SNP genotypes suggesting the suitability of OAD milk for producing easily spreadable butter. These results demonstrate that selecting cows with the CC genotype is beneficial for New Zealand dairy farmers with the current payment system, however, this would likely result in less spreadable butter.Item Genomic Regions Associated with Milk Composition and Fertility Traits in Spring-Calved Dairy Cows in New Zealand(MDPI (Basel, Switzerland), 2023-04-01) Jayawardana JMDR; Lopez-Villalobos N; McNaughton LR; Hickson RE; Ayaz A; Ullah F; Saqib SThe objective of this study was to identify genomic regions and genes that are associated with the milk composition and fertility traits of spring-calved dairy cows in New Zealand. Phenotypic data from the 2014-2015 and 2021-2022 calving seasons in two Massey University dairy herds were used. We identified 73 SNPs that were significantly associated with 58 potential candidate genes for milk composition and fertility traits. Four SNPs on chromosome 14 were highly significant for both fat and protein percentages, and the associated genes were DGAT1, SLC52A2, CPSF1, and MROH1. For fertility traits, significant associations were detected for intervals from the start of mating to first service, the start of mating to conception, first service to conception, calving to first service, and 6-wk submission, 6-wk in-calf, conception to first service in the first 3 weeks of the breeding season, and not in calf and 6-wk calving rates. Gene Ontology revealed 10 candidate genes (KCNH5, HS6ST3, GLS, ENSBTAG00000051479, STAT1, STAT4, GPD2, SH3PXD2A, EVA1C, and ARMH3) that were significantly associated with fertility traits. The biological functions of these genes are related to reducing the metabolic stress of cows and increasing insulin secretion during the mating period, early embryonic development, foetal growth, and maternal lipid metabolism during the pregnancy period.