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Berry D.P.,Animal and Grassland Research and Innovation Center | Mcclure M.C.,Irish Cattle Breeding Federation | Mullen M.P.,Animal and Grassland Research and Innovation Center
Journal of Animal Breeding and Genetics | Year: 2014

Summary: The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777 962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD. © 2013 Blackwell Verlag GmbH.

Berry D.P.,Teagasc | McCarthy J.,Irish Cattle Breeding Federation
Applied Animal Behaviour Science | Year: 2012

The ability to rapidly identify temporal deviations of an animal from its norm will be important in the management of individual cows in large herds. Furthermore, predictors of genetic merit for especially health traits are useful to augment the accuracy of selection, and thus genetic gain, in breeding programs. The objective of this study was to estimate the repeatability of milking order and to quantify the contribution of differences in additive genetic variation to phenotypic differences (i.e., heritability). The data used in this study included 9813 herd milk recording test-day records with time of milking from 85,532 cows in 1143 herds across an 8-year period. Milking order was available for both morning and evening milking for each cow with, on average, 3.33 milk test-day records (i.e., 6.66 milking events) per lactation, and on average 1.62 lactations per cow. Variance components for milking order were estimated using animal linear mixed models; covariance components between milking order and milk yield, milk composition and somatic cell score (i.e., logarithm 10 somatic cell count) were estimated also using animal linear mixed models. The heritability of milking order was 0.20 indicating partial genetic control of milking order. The repeatability of milking order within test-day, within lactation, and across lactations was 0.63, 0.51, and 0.47, respectively. Milking order was positively (P<0.001), but weakly, phenotypically correlated with milk yield (r=0.04), and milk fat concentration (r=0.01) and negatively (P<0.001), but weakly, correlated with milk protein concentration (r=-0.02) and somatic cell score (r=-0.05). Milking order was positively (P<0.05), although weakly, genetically correlated with milk yield (r=0.07) and negatively (P<0.05), but also weakly, genetically correlated with somatic cell score (r=-0.08). This study is the first to show a contribution of additive genetics to milking order in dairy cattle but the genetic correlation between milking order and somatic cell score was weak. © 2011 Elsevier B.V.

Berry D.P.,Teagasc | Evans R.D.,Irish Cattle Breeding Federation
Journal of Animal Science | Year: 2014

Due primarily to a lack of phenotypic data, little research has been undertaken on the genetics of reproductive performance in beef cattle. The objective of this study was to quantify, using data from the Irish national cattle herd, the contribution of additive genetics to phenotypic differences in reproductive performance in beef cattle and to investigate whether routinely available early predictors of genetic merit for reproductive performance exist. Up to 218,718 parity records from 156,506 animals were used to estimate variance components for a range of reproductive traits using repeatability animal linear mixed models. Covariances with performance traits were estimated using bivariate sire linear mixed models. The reproductive traits were age at first calving, calving in the first 42 d of the calving seasons (defined separately in heifers and cows), calving interval between consecutive calving events, and survival to the next lactation. Performance traits included calving dystocia, linear type traits describing the skeletal, muscular, and functional characteristics of an animal, live weight and price, carcass traits, and producer subjectively scored traits of weanling quality and docility. Heritability for age at first calving was 0.31 while the heritability of the remaining reproductive traits ranged from 0.01 to 0.06; repeatability estimates varied from 0.02 to 0.06. Increased muscularity, measured either by trained assessors or producers on live animals, or by mechanical grading machines on slaughtered animals (i.e., carcass conformation), was genetically correlated with reduced reproductive performance for some of the reproductive variables assessed. This is one of the largest studies undertaken on the genetics of reproduction in beef herds and clearly shows that genetic selection for improved reproductive performance in beef herds is feasible. However, breeding goals that select for muscularity and live weight or growth rate should be cognizant of indirect response to selection that may cause any deterioration in reproductive performance. © 2014 American Society of Animal Science. All rights reserved.

Berry D.P.,Teagasc | Crowley J.J.,Irish Cattle Breeding Federation
Journal of Animal Science | Year: 2012

Interest in improving feed efficiency in cattle is intensifying. Residual feed intake (RFI), which is the difference between expected intake and that predicted based on energy demands, is now the most commonly used measure of feed efficiency over a given time period. However, RFI, as commonly defined, is independent of growth rate, which may affect its acceptance by industry. Residual BW gain (RG) has also been proposed as a measure of feed efficiency and is represented as the residuals from a multiple regression model regressing ADG on both DMI and BW. In this study, we propose a new trait, residual intake and BW gain (RIG), which retains the favorable characteristic of both RFI and RG being independent of BW, but animals superior for RIG have, on average, both greater ADG and reduced DMI. Phenotypic and genetic analyses were undertaken on up to 2,605 purebred performance-tested bulls. Clear phenotypic differences in DMI and ADG existed between animals divergent for RIG. The heritability of RIG was 0.36 ± 0.06, which is consistent with the heritability estimates of RFI and other feed efficiency traits measured in the study. The RIG trait was both phenotypically and genetically negatively correlated with DMI and positively correlated with ADG; no correlation existed between RIG and BW. The advantages of both reduced daily DMI and greater ADG in animals superior for RIG are demonstrated compared with animals superior for either RFI or RG. © 2012 American Society of Animal Science.

Finlay E.K.,Trinity College Dublin | Berry D.P.,Teagasc | Wickham B.,Irish Cattle Breeding Federation | Gormley E.P.,University College Dublin | Bradley D.G.,Trinity College Dublin
PLoS ONE | Year: 2012

Background: Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study. Methodology/Principal Findings: We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p<10 -5, peaking at position 59588069, p = 4.02×10 -6) with tuberculosis susceptibility. Conclusions/Significance: A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection. © 2012 Finlay et al.

Berry D.P.,Teagasc | Evans R.D.,Irish Cattle Breeding Federation | Mc Parland S.,Teagasc
Theriogenology | Year: 2011

A successful outcome to a given service is a combination of both male and female fertility. Despite this, most national evaluations for fertility are generally confined to female fertility with evaluations for male fertility commonly undertaken by individual breeding organisations and generally not made public. The objective of this study was to define a pertinent male fertility trait for seasonal calving production systems, and to develop a multiple regression mixed model that may be used to evaluate male fertility at a national level. The data included in the study after editing consisted of 361,412 artificial inseminations from 206,683 cow-lactations (134,911 cows) in 2,843 commercial dairy and beef herds. Fixed effects associated with whether a successful pregnancy ensued (pregnant = 1) or not (pregnant = 0) from a given service were year by month of service, day of the week, days since calving, cow parity, level of calving difficulty experienced, whether or not the previous calving was associated with perinatal mortality, and age of the service bull at the date of insemination. Non-additive genetic effects such as heterosis and recombination loss as well as inbreeding level of the service bull, dam or mating were not associated with a successful pregnancy; there was no difference in pregnancy rate between fresh or frozen semen. Random effects included in the model were the additive genetic effect of the cow, as well as a within lactation and across lactation permanent environmental effect of the cow; pedigree group effects based on cow breed were also included via the relationship matrix. Temporal differences in the AI technician and service bull were also included as random effects. A difference in five percentage units in male fertility was evident between the average effects of different dairy and beef breeds. The correlation between raw pregnancy rates for bulls with more than 100 services (n = 431) and service bull solutions from the mixed model analysis was 0.66. The correlation between the raw pregnancy rates of 288 technicians with more than 100 services and their respective solutions from the mixed model was 0.35. These low to moderate correlations suggest considerable re-ranking among both service bulls and technicians and suggest possibly a benefit of using a statistical model to better estimate the performance of both service bulls and technicians. © 2011 Elsevier Inc.

Mee J.F.,Teagasc | Berry D.P.,Teagasc | Cromie A.R.,Irish Cattle Breeding Federation
Veterinary Journal | Year: 2011

The incidence of and risk factors associated with calving assistance and dystocia in pasture-based dairy herds were determined from analysis of 152,641 records of full-term calvings from Holstein-Friesian dams served by artificial insemination (AI) sires of seven breeds in herds of 20 calvings or more per year over 4. years.The overall incidence of calving assistance and dystocia was 31.1% and 6.8%, respectively. The incidence in primiparae and pluriparae was 40.0% and 28.2% for assistance, and 9.3% and 5.8% for dystocia, respectively. Association analyses were undertaken using generalised estimating equations using a logit link function. The likelihood of calving assistance or dystocia did not change over time but was greatest in autumn and in spring. The likelihood of calving assistance or dystocia was greater for males in primiparae and males sired by Charolais sires. The odds of calving assistance and dystocia were greater in twin calves (OR 2.0 and 2.4; P< 0.001) and in dams that had dystocia at the previous calving (OR 1.65 and 2.9; P< 0.001). The logit of the probability of calving assistance and dystocia increased linearly per unit increase in sire predicted transmitting ability for direct calving difficulty. The probability of assisted calving, but not dystocia, increased linearly in primiparae as animals calved at a younger age relative to the median age at first calving. Herd size and day of the week of calving were not associated with the odds of dystocia. Stakeholders must focus on identified modifiable risk factors to control the incidence of dystocia in dairy herds. © 2009 Elsevier Ltd.

Berry D.P.,Teagasc | Kearney J.F.,Irish Cattle Breeding Federation
Animal | Year: 2011

The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein-Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein-Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection. © 2011 The Animal Consortium.

McCarthy J.,Irish Cattle Breeding Federation | Veerkamp R.F.,Animal Science Group
Journal of Dairy Science | Year: 2012

Variance components for test-day milk yield were estimated for primiparous animals in a seasonal calving system where 80% of calvings occur within a 5-mo period in the spring. The objective was to investigate if the variance components of milk production were affected by seasonality via month in milk and test month (TM). These effects were, therefore, fitted for both the permanent environment effect and additive genetic effect. Estimates of heritability (0.14-0.27) were found to be lowest during early and late lactation for all calving months. The peak in heritability (0.22-0.27) occurred later in lactation for animals that calved toward the end of the spring calving season. Genetic variance of test day milk yield for all calving months was found to be highest at the beginning of the lactation (2.23-3.36kg2), with a plateau toward the middle of the lactation. Genetic variance was found to be highest (2.98-3.36kg2) for animals calving early in the season. Genetic correlations between corresponding stages of lactation were strongest (0.99-1.00) between consecutive calving months. Genetic correlations were slightly weaker when intervals between calving months increased; however, they remained above 0.96 in all cases. Akaike's information criterion values from models both inclusive and exclusive of TM, suggest that the model exclusive of TM is the preferred model. Estimated breeding values of lactation milk yield from bulls with 20 or more daughters, predicted for a full 305-d lactation, were used to compare the model with the standard test-day model (i.e., exclusive of TM), based on DIM. Correlations were higher than 0.995 for milk yield (and higher than 0.930 for persistency) between models inclusive and exclusive of TM, suggesting that given the straightforward approach taken in the current study, an apparent benefit for including seasonality in the evaluation of test-day milk yield was not found; however, there may be benefits of including it in the estimation of persistency. © 2012 American Dairy Science Association.

Berry D.P.,Moorepark Dairy Production Research Center | Kearney J.F.,Irish Cattle Breeding Federation | Roche J.R.,DairyNZ Ltd.
Theriogenology | Year: 2011

There is a paucity of estimates of genetic variation for secondary sex ratio (i.e., sex ratio at birth) in dairy cattle. The objective of this study was to estimate the direct and maternal genetic variance as well as maternal permanent environmental variance for offspring sex in dairy herds. The data consisted of 77,508 births from 61,963 dams and 2,859 sires in 1,369 Irish dairy herds across the years 2003 to 2008, inclusive. Mixed models were used to estimate all parameters. Significant genetic variation in sex ratio existed, with a heritability for secondary sex ratio estimated at 0.02; the genetic standard deviation was 0.07 percentage units. No maternal genetic effects on secondary sex ratio were identified but the proportion of phenotypic variance in secondary sex ratio attributable to maternal permanent environmental effects was similar to that attributable to the additive genetic variance (i.e., 0.02). These results, therefore, suggest that the paternal (genetic) influence on secondary sex ratio is just as large as the maternal (non-genetic) influence, both of which are biologically substantial. The results from this study will be useful in generating a sample population of divergent animals for inclusion in a controlled experiment to elucidate the physiological mechanism underpinning differences in secondary sex ratio. © 2011 Elsevier Inc.

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