• Characterization of best linear unbiased estimates generated from national genetic evaluations of reproductive performance, survival, and milk yield in dairy cows

      Dunne, F. L.; Kelleher, Margaret M.; Walsh, S.W.; Berry, Donagh; MultiRepro project; Department of Agriculture, Food and the Marine (Elsevier, 2018-05-16)
      Genetic evaluations decompose an observed phenotype into its genetic and nongenetic components; the former are termed BLUP with the solutions for the systematic environmental effects in the statistical model termed best linear unbiased estimates (BLUE). Geneticists predominantly focus on the BLUP and rarely consider the BLUE. The objective of this study, however, was to define and quantify the association between 8 herd-level characteristics and BLUE for 6 traits in dairy herds, namely (1) age at first calving, (2) calving to first service interval (CFS), (3) number of services, (4) calving interval (CIV), (5) survival, and (6) milk yield. Phenotypic data along with the fixed and random effects solutions were generated from the Irish national multi-breed dairy cow fertility genetic evaluations on 3,445,557 cows; BLUE for individual contemporary groups were collapsed into mean herd-year estimates. Data from 5,707 spring-calving herds between the years 2007 and 2016 inclusive were retained; association analyses were undertaken using linear mixed multiple regression models. Pearson coefficient correlations were used to quantify the relationships among individual trait herd-year BLUE, and transition matrices were used to understand the dynamics of mean herd BLUE estimates over years. Based on the mean annual trends in raw, BLUP, and BLUE, it was estimated that BLUE were associated with at least two-thirds of the improvement in CIV and milk production over the past 10 yr. Milk recording herds calved heifers for the first time on average 15 d younger, had an almost 2 d longer CFS but 2.3 d shorter CIV than non-milk-recording herds. Larger herd sizes were associated with worse BLUE for both CFS and CIV. Expanding herds and herds that had the highest proportion of cows born on the farm itself, on average, calved heifers younger and had shorter CIV. By separating the raw performance of a selection of herds into their respective BLUE and BLUP, it was possible to identify herds with inferior management practices that were being compensated by superior genetics; similarly, herds were identified with superior BLUE, but because of their inferior genetic merit, were not reaching their full potential. This suggests that BLUE could have a pivotal role in a tailored decision support tool that would enable producers to focus on the most limiting factor hindering them from achieving their maximum performance.
    • Comparison of breed of dairy cow under grass-based spring milk production systems

      Buckley, Frank; Walsh, S.W.; Dillon, Pat; National Development Plan (NDP) (Teagasc, 2006-01-01)
      The objective of this study was to investigate the potential differences among different dairy cow breeds across two feeding systems on milk production, udder health, milking characteristics, body weight, body condition score, hormone parameters, ovarian function, survival and overall reproductive efficiency. The breeds investigated included Holstein-Friesian (HF), Montbéliarde (MB), Normande (NM), Norwegian Red (NRF) and Holstein- Friesian × Montbéliarde (MBX) and Holstein- Friesian × Normande (NMX). Selection within the HF breed has, until recently, been predominantly for milk production with little or no direct selection for functional traits other than those correlated with superior type. The MB and the NM have been simultaneously selected for both milk and beef production in the past. The NRF were imported as calves and come from a more balanced total merit index incorporating production and cow functionality since the early 1970s. The dairy cow breeds were grouped into blocks of two within breed groups and randomized across two spring-calving grass-based feeding systems: low concentrate feeding system (LC) and high concentrate feeding system (HC). Those on LC feeding system were offered approximately 530 kg/cow over the total lactation, while those on HC feeding system were offered approximately 1030 kg/cow.
    • Comparison of breed of dairy cow under grass-based spring milk production systems.

      Buckley, Frank; Walsh, S.W.; Dillon, Pat (Teagasc, 2006-01)
      The objective of this study was to investigate the potential differences among different dairy cow breeds across two feeding systems on milk production, udder health, milking characteristics, body weight, body condition score, hormone parameters, ovarian function, survival and overall reproductive efficiency. The breeds investigated included Holstein-Friesian (HF), Montbéliarde (MB), Normande (NM), Norwegian Red (NRF) and Holstein- Friesian × Montbéliarde (MBX) and Holstein- Friesian × Normande (NMX). Selection within the HF breed has, until recently, been predominantly for milk production with little or no direct selection for functional traits other than those correlated with superior type. The MB and the NM have been simultaneously selected for both milk and beef production in the past. The NRF were imported as calves and come from a more balanced total merit index incorporating production and cow functionality since the early 1970s. The dairy cow breeds were grouped into blocks of two within breed groups and randomized across two spring-calving grass-based feeding systems: low concentrate feeding system (LC) and high concentrate feeding system (HC). Those on LC feeding system were offered approximately 530 kg/cow over the total lactation, while those on HC feeding system were offered approximately 1030 kg/cow. There was no genotype by environment interaction observed for any of the milk production, BCS, BW, udder health, milking characteristics, reproductive performance or feed intake/efficiency parameters investigated. Compared to the MB and NM, all other breeds had higher total lactation milk, fat, protein and lactose yield, with the HF having the highest. Animals on the HC feeding system had higher total lactation milk, fat, protein and lactose yield. Compared to the NRF, SCS was higher for the HF, NM, MBX and NMX breed groups, while SCS of the MB was not different. The NM and MB had lower AMF compared to all breeds. The crossbreds achieved the higher AMF. The NM had the lowest PMF, while that of the crossbreds were higher compared to all breeds. Milking duration was not affected by breed. Differences between breeds for AMF, PMF and MD were not apparent after adjustment for milk yield. Animals offered a HC diet had higher AMF, PMF and MD compared to those on the LC feeding system. Somatic cell score did not differ between the feeding systems. The interaction between breed and milk yield influenced SCS, AMF, PMF and MD thus implying that for each unit increase of milk yield by breed, the response in SCS, AMF, PMF and MD was different for some breeds. The response in SCS was similar for the NRF, MBX and NMX, while MD was similar for the MB and MBX. The effect of one unit increase in daily average milk yield caused a favourable decrease in SCS; however a one unit increase in PMF and MD did not influence SCS. No interactions were observed for breed with any milking characteristic on SCS. The HF had the lowest BCS, the MB and NM the highest, while the NRF, MBX and NMX were intermediate. The NRF had the lowest BW; the NM had the highest while the other breeds were intermediate. The NRF had increased likelihood of SR24, PREG1, PREG42 and FINALPR and greater survival compared to the HF. Both MBX and NMX had shorter CSI and CCI and were more likely to be pregnant at the end of the breeding season, thus had higher survival rates compared to the HF; however heterosis estimates for these traits was not significant, likely due to the small data size. Feed system did not influence reproductive performance of the different breeds. Breed of dairy cow did not influence any of the ovarian parameters studied. Breed of dairy cow did not influence insulin or IGF-1 concentrations at any sampling period. Breed significantly effected gestation length, calf birth weight and calving ease score. The NRF had the shortest gestation, lightest calves and least calving difficulty. Genotype had a significant effect on estimated dry matter intake, being highest with the HF, MBX, NMX and lowest with NM and NRF. Genotype also had a significant effect on yield of milk solids per kg of DMI. The highest yield of milk solids per kg of DMI was achieved with the NRF, HF and MBX. Comparisons between genotypes reveal that estimated residual feed intake estimates were lowest (most favourable) for the NRF, compared to other genotypes with the exception of HF.
    • Formulation of a decision support tool incorporating both genetic and non-genetic effects to rank young growing cattle on expected market value

      Dunne, F.L.; Evans, R.D.; Kelleher, M.M.; Walsh, S.W.; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and Marine; European Union; 16/RC/3835; MultiRepro; et al. (Elsevier BV, 2021-02)
      While breeding indexes exist globally to identify candidate parents of the next generation, fewer tools exist that provide guidance on the expected monetary value of young animals. The objective of the present study was therefore to develop the framework for a cattle decision-support tool which incorporates both the genetic and non-genetic information of an animal and, in doing so, better predict the potential market value of an animal, whatever the age. Two novel monetary indexes were constructed and their predictive ability of carcass value was compared to that of the Irish national Terminal breeding index, typical of other terminal indexes used globally. A constructed Harvest index was composed of three carcass-related traits [i.e., 1) carcass weight, 2) carcass conformation and 3) carcass fat, each weighted by their respective economic value] and aimed at purchasers of animals close to harvest; the second index, termed the Calf index, also included docility and feed intake (weighted by their respective economic value), thus targeting purchasers of younger calves for growing (and eventually harvesting). Genetic and non-genetic fixed and random effect model solutions fromthe Irish national genetic evaluations underpinned all indexes. The two novel indexes were formulated using three alternative estimates of an animal's total merit for comparative purposes: 1) an index based solely on the animal's breed solutions, 2) an index which also included within-breed animal differences, and 3) an index which, as well as considering additive and non-additive genetic effects, also included non-genetic effects (referred to as production values [PVs]). As more information (i.e., within breed effects and subsequently non-genetic effects) was included in the total merit estimate, the correlations strengthened between the two proposed indexes and the animal's calculated carcass market value; the correlation coefficients almost doubled in strength when total merit was based on PV-based estimates as compared to the breed solutions alone. Including phenotypic liveweight data, collected during the animal's life, strengthened the predictive ability of the indexes further. Based on the results presented, the proposed indexes may fill the void in decision support when purchasing or selling cattle. In addition, given the dynamic nature of indexes, they have the potential to be updated in real-time as information becomes available.
    • Heritability and impact of environmental effects during pregnancy on antral follicle count in cattle

      Walsh, S.W.; Mossa, F.; Butler, Stephen T.; Berry, Donagh; Scheetz, D.; Jimenez-Krassel, F.; Templeman, R.J.; Cater, F.; Lonergan, P.; Evans, A.C.O.; et al. (Elsevier for American Dairy Science Association, 2014-07)
      Previous studies have documented that ovarian antral follicle count (AFC) is positively correlated with number of healthy follicles and oocytes in ovaries (ovarian reserve), as well as ovarian function and fertility in cattle. However, environmental factors (e.g., nutrition, steroids) during pregnancy in cattle and sheep can reduce AFC in offspring. The role that genetic and environmental factors play in influencing the variability in AFC and, correspondingly, the size of the ovarian reserve, ovarian function, and fertility, are, however, poorly understood. The present study tests the hypothesis that variability in AFC in offspring is influenced not only by genetic merit but also by the dam age and lactation status (lactating cows vs. nonlactating heifers) and milk production during pregnancy. Antral follicle count was assessed by ultrasonography in 445 Irish Holstein-Friesian dairy cows and 522 US Holstein-Friesian dairy heifers. Heritability estimates for AFC (± standard error) were 0.31 ± 0.14 and 0.25 ± 0.13 in dairy cows and heifers, respectively. Association analysis between both genotypic sire data and phenotypic dam data with AFC in their daughters was performed using regression and generalized linear models. Antral follicle count was negatively associated with genetic merit for milk fat concentration. Also, AFC was greater in offspring of dams that were lactating (n = 255) compared with nonlactating dams (n = 89) during pregnancy and was positively associated with dam milk fat concentration and milk fat-to-protein ratio. In conclusion, AFC in dairy cattle is a moderately heritable genetic trait affected by age or lactation status and milk quality but not by level of dam’s milk production during pregnancy.
    • How herd best linear unbiased estimates affect the progress achievable from gains in additive and nonadditive genetic merit

      Dunne, F. L.; McParland, Sinead; Kelleher, Margaret M.; Walsh, S.W.; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier, 2019-04-10)
      Sustainable dairy cow performance relies on coevolution in the development of breeding and management strategies. Tailoring breeding programs to herd performance metrics facilitates improved responses to breeding decisions. Although herd-level raw metrics on performance are useful, implicitly included within such statistics is the mean herd genetic merit. The objective of the present study was to quantify the expected response from selection decisions on additive and nonadditive merit by herd performance metrics independent of herd mean genetic merit. Performance traits considered in the present study were age at first calving, milk yield, calving to first service, number of services, calving interval, and survival. Herd-level best linear unbiased estimates (BLUE) for each performance trait were available on a maximum of 1,059 herds, stratified as best, average, and worst for each performance trait separately. The analyses performed included (1) the estimation of (co)variance for each trait in the 3 BLUE environments and (2) the regression of cow-level phenotypic performance on either the respective estimated breeding value (EBV) or the heterosis coefficient of the cow. A fundamental assumption of genetic evaluations is that 1 unit change in EBV equates to a 1 unit change in the respective phenotype; results from the present study, however, suggest that the realization of the change in phenotypic performance is largely dependent on the herd BLUE for that trait. Herds achieving more yield, on average, than expected from their mean genetic merit, had a 20% greater response to changes in EBV as well as 43% greater genetic standard deviation relative to herds within the worst BLUE for milk yield. Conversely, phenotypic performance in fertility traits (with the exception of calving to first service) tended to have a greater response to selection as well as a greater additive genetic standard deviation within the respective worst herd BLUE environments; this is suggested to be due to animals performing under more challenging environments leading to larger achievable gains. The attempts to exploit nonadditive genetic effects such as heterosis are often the basis of promoting cross-breeding, yet the results from the present study suggest that improvements in phenotypic performance is largely dependent on the environment. The largest gains due to heterotic effects tended to be within the most stressful (i.e., worst) BLUE environment for all traits, thus suggesting the heterosis effects can be beneficial in mitigating against poorer environments.
    • Low numbers of ovarian follicles ≥3 mm in diameter are associated with low fertility in dairy cows

      Mossa, F.; Walsh, S.W.; Butler, Stephen T.; Berry, Donagh; Carter, F.; Lonergan, P.; Smith, G.W.; Ireland, J.J.; Evans, A.C.O. (American Dairy Science Association, 2012-05-01)
      The total number of ovarian follicles ≥3 mm in diameter (antral follicle count, AFC) during follicular waves varies among cattle of similar age, but AFC is highly repeatable within individuals. We hypothesized that lower AFC could be associated with reduced fertility in cattle. The AFC was assessed by ultrasonography for 2 d consecutively during the first wave of follicular growth of the estrous cycle, 4.6 ± 1.43 d (mean ± SD) after estrus, in 306 Holstein-Friesian dairy cows approximately 70 d postpartum. Cows were classified into 3 groups based on AFC: low (AFC ≤15), intermediate (AFC = 16 to 24), and high (AFC ≥25). During the cycle in which AFC was assessed and in subsequent cycles, cows were artificially inseminated (AI) following detection of estrus, and pregnancy status was assessed using ultrasonography. Cows with high AFC had 3.34 times greater odds of being pregnant at the end of the breeding season compared with cows with low AFC; the odds of a successful pregnancy at first service were 1.75 times greater in the intermediate compared with the low group. The predicted probability of a successful pregnancy by the end of the breeding period (length of breeding season was 86 ± 16.3 d) was 94, 88, and 84% for the high, intermediate, and low AFC groups, respectively. No difference was evident among groups in 21-d submission rate (proportion of all cows detected in estrus and submitted for AI in the first 21 d of the breeding season), but the interval from calving to conception was shorter in the high (109.5 ± 5.1 d) versus low (117.1 ± 4 d) group, and animals with intermediate AFC received fewer services during the breeding season (2.3 ± 0.1) compared with animals with low AFC (2.7 ± 0.1). Lactating cows with ≤15 ovarian follicles have lower reproductive performance compared with cows with higher numbers of follicles, but the existence of a positive association between high numbers of ovarian follicles and fertility is yet to be established.