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Berkowicz E.W.,University College Dublin | Magee D.A.,University College Dublin | Berry D.P.,Teagasc | Sikora K.M.,University College Cork | And 7 more authors.
Animal Genetics | Year: 2012

The regulation of the bioavailability of insulin-like growth factors (IGFs) is critical for normal mammalian growth and development. The imprinted insulin-like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor that acts to sequester and degrade excess circulating insulin-like growth factor 2 (IGF-II) - a potent foetal mitogen - and is considered an important inhibitor of growth. Consequently, IGF2R may serve as a candidate gene underlying important growth- and body-related quantitative traits in domestic mammalian livestock. In this study, we have quantified genotype-phenotype associations between three previously validated intronic bovine IGF2R single nucleotide polymorphisms (SNPs) (IGF2R:g.64614T>C, IGF2R:g.65037T>C and IGF2R:g.86262C>T) and a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. Notably, all three polymorphisms analysed were associated (P ≥ 0.05) with at least one of a number of performance traits related to animal body size: angularity, body depth, chest width, rump width, and animal stature. In addition, the C-to-T transition at the IGF2R:g.65037T>C polymorphism was positively associated with cow carcass weight and angularity. Correction for multiple testing resulted in the retention of two genotype-phenotype associations (animal stature and rump width). None of the SNPs analysed were associated with any of the milk traits examined. Analysis of pairwise r 2 measures of linkage disequilibrium between all three assayed SNPs ranged between 0.41 and 0.79, suggesting that some of the observed SNP associations with performance may be independent. To our knowledge, this is one of the first studies demonstrating associations between IGF2R polymorphisms and growth- and body-related traits in cattle. These results also support the increasing body of evidence that imprinted genes harbour polymorphisms that contribute to heritable variation in phenotypic traits in domestic livestock species. © 2011 Stichting International Foundation for Animal Genetics.


Cottle D.J.,University College Dublin | Cottle D.J.,University of New England of Australia | Gilmour A.R.,Cargo Inc | Pabiou T.,Bandon Co. | And 2 more authors.
Journal of Animal Breeding and Genetics | Year: 2016

It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records from 4407 ewes collected in 56 flocks. The percentage of pedigreed lambing ewes with singles, twins and triplets was 30, 54 and 14%, respectively, in 2013 and has been relatively constant for the last 15 years. The variance of NLB increases with the mean in this data; the correlation of mean and standard deviation across sires is 0.50. The breeding goal is to increase the mean NLB without unduly increasing the incidence of triplets and higher litter sizes. The heritability estimates for lambing traits were NLB, 0.09; triplet occurrence (TRI) 0.07; and twin occurrence (TWN), 0.02. The highest and lowest twinning flocks differed by 23% (75% versus 52%) in the proportion of ewes lambing twins. Fitting bivariate sire models to NLB and the residual from the NLB model using a double hierarchical generalized linear model (DHGLM) model found a strong genetic correlation (0.88 ± 0.07) between the sire effect for the magnitude of the residual (VE) and sire effects for NLB, confirming the general observation that increased average litter size is associated with increased variability in litter size. We propose a threshold model that may help breeders with low litter size increase the percentage of twin bearers without unduly increasing the percentage of ewes bearing triplets in Belclare sheep. © 2016 Blackwell Verlag GmbH.


Pabiou T.,Bandon Co. | Pabiou T.,Swedish University of Agricultural Sciences | Fikse W.F.,Swedish University of Agricultural Sciences | Amer P.R.,AbacusBio Ltd | And 3 more authors.
Animal | Year: 2012

The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min rg(MVC) = 0.35; max r g(VHVC) = 0.69), and animal price at both weaning (min r g(MVC) = 0.37; max rg(VHVC) = 0.66) and post weaning (min rg(MVC) = 0.50; max rg(VHVC) = 0.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min rg(HVC) = 0.34; max rg(LVC) = 0.45), weanling quality (min rg(MVC) = 0.12; max rg(VHVC) = 0.49), linear scores for muscularity at both weaning (hindquarter development: min rg(MVC) = -0.06; max rg(VHVC) = 0.46), post weaning (hindquarter development: min rg(MVC) = 0.23; max rg(VHVC) = 0.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction prices and weanling quality. Total bone weight was, however, positively correlated with skeletal scores at weaning and post weaning. These results indicate that some traits collected early in life are moderate-to-strongly correlated with carcass cut weights predicted from VIA technology. This information can be used to improve the accuracy of selection for carcass cut weights in national genetic evaluations. © The Animal Consortium 2011.


PubMed | Cargo Inc, University College Dublin, Bandon Co. and AbacusBio Ltd
Type: Journal Article | Journal: Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie | Year: 2016

It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records from 4407 ewes collected in 56 flocks. The percentage of pedigreed lambing ewes with singles, twins and triplets was 30, 54 and 14%, respectively, in 2013 and has been relatively constant for the last 15years. The variance of NLB increases with the mean in this data; the correlation of mean and standard deviation across sires is 0.50. The breeding goal is to increase the mean NLB without unduly increasing the incidence of triplets and higher litter sizes. The heritability estimates for lambing traits were NLB, 0.09; triplet occurrence (TRI) 0.07; and twin occurrence (TWN), 0.02. The highest and lowest twinning flocks differed by 23% (75% versus 52%) in the proportion of ewes lambing twins. Fitting bivariate sire models to NLB and the residual from the NLB model using a double hierarchical generalized linear model (DHGLM) model found a strong genetic correlation (0.880.07) between the sire effect for the magnitude of the residual (VE ) and sire effects for NLB, confirming the general observation that increased average litter size is associated with increased variability in litter size. We propose a threshold model that may help breeders with low litter size increase the percentage of twin bearers without unduly increasing the percentage of ewes bearing triplets in Belclare sheep.


Zhao F.,Chinese Academy of Agricultural Sciences | McParland S.,Teagasc | Kearney F.,Bandon Co. | Du L.,Chinese Academy of Agricultural Sciences | Berry D.P.,Teagasc
Genetics Selection Evolution | Year: 2015

Background: Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs. Results: Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (FST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the FST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global FST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection. Conclusions: This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies. © 2015 Zhao et al.


Berry D.P.,Teagasc | McParland S.,Teagasc | Kearney J.F.,Bandon Co. | Sargolzaei M.,University of Guelph | Mullen M.P.,Teagasc
Animal | Year: 2014

The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the within-animal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ≥96% accuracy. © The Animal Consortium 2014.


Mc Hugh N.,Teagasc | Mc Hugh N.,University College Dublin | Evans R.D.,Bandon Co | Amer P.R.,Abacus Biotech Ltd | And 2 more authors.
Journal of Animal Science | Year: 2011

Beef outputs from dairy farms make an important contribution to overall profitability in Irish dairy herds and are the sole source of revenue in many beef herds. The aim of this study was to estimate genetic parameters for animal BW and price across different stages of maturity. Data originated from 2 main sources: price and BW from livestock auctions and BW from on-farm weighings between 2000 and 2008. The data were divided into 4 distinct maturity categories: calves (n = 24,513), weanlings (n = 27,877), postweanlings (n = 23,279), and cows (n = 4,894). A univariate animal model used to estimate variance components was progressively built up to include a maternal genetic effect and a permanent environmental maternal effect. Bivariate analyses were used to estimate genetic covariances between BW and price per animal within and across maturity category. Direct heritability estimates for price per animal were 0.34 ± 0.03, 0.31 ± 0.05, 0.19 ± 0.04, and 0.10 ± 0.04 for calves, weanling, postweanlings, and cows, respectively. Direct heritability estimates for BW were 0.26 ± 0.03 for weanlings, 0.25 ± 0.04 for postweanlings, and 0.24 ± 0.06 for cows; no BW data were available on calves. Significant maternal genetic and maternal permanent environmental effects were observed for weanling BW only. The genetic correlation between price per animal and BW within each maturity group varied from 0.55 ± 0.06 (postweanling price and BW) to 0.91 ± 0.04 (cow price and BW). The availability of routinely collected data, along with the existence of ample genetic variation for animal BW and price per animal, facilitates their inclusion in Irish dairy and beef breeding objectives to better reflect the profitability of both enterprises. ©2011 American Society of Animal Science.


PubMed | Bandon Co., Teagasc and Chinese Academy of Agricultural Sciences
Type: | Journal: Genetics, selection, evolution : GSE | Year: 2015

Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs.Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (FST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the FST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global FST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection.This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.


PubMed | Teagasc, Bandon Co. and Reprodoc Ltd.
Type: Journal Article | Journal: Theriogenology | Year: 2014

The objective of this study was to estimate the association between detailed reproductive phenotypes for cows categorized as divergent for phenotypic and genetic performance. The hypothesis was that higher yielding animals, either phenotypically or genetically, would have compromised ovarian and uterine reproductive performance. Detailed reproductive traits including multiple ovulations, cystic ovarian structures, corpus luteum (CL) presence, and uterine environment were available on 9675 ultrasound records from 8174 dairy lactating cows, calved between 10 and 70 days. Cows were categorized, within parity, into low, average, or high for each of the performance traits. There was a greater likelihood of multiple ovulations in cows with greater phenotypic yields (odds ratio: 1.53-1.81) and greater genetic merit for yield (odds ratio: 1.31-1.59) relative to lower performing contemporaries. After adjustment for genetic merit, a similar trend of increased odds (odds ratio: 1.29-1.87) of multiple ovulations in higher yielding cows was observed compared with the lowest yielding category. There was no association between either phenotypic milk composition or genetic merit for milk composition with the likelihood of multiple ovulations. The likelihood of cystic ovarian structures was highest in cows with greatest phenotypic milk yields (odds ratio: 2.75-3.24), greater genetic merit for milk yield (odds ratio: 1.30-1.51), and even after adjustment for genetic merit there was a greater likelihood of cystic ovarian structures in cows with the highest milk yields (odds ratio: 2.71-2.95), compared with cows in the lowest category for each of the milk traits. Cows with average phenotypic milk yields were more likely to have a CL, compared with the lowest yielding category (odds ratio: 1.20-1.23), and these associations remained after adjustment for genetic merit of the trait. The likelihood of CL presence was highest in cows with the lowest genetic merit for milk. Lower fat:protein ratio was associated with an increased likelihood of CL presence compared with cows with greater fat:protein ratio and cows with the highest phenotypic milk composition were more likely to have a CL compared with cows in the lowest composition category. Genetic predisposition to higher somatic cell score was associated with a reduced risk of multiple ovulations (odds ratio: 0.69; 95% CI: 0.55-0.87) but an increased likelihood of CL presence (odds ratio: 2.66; 95% CI: 2.09-3.37) and poorer uterine health score (odds ratio: 1.36; 95% CI: 1.20-1.55). There was a lower likelihood of multiple ovulations, cystic ovarian structures, and poorer uterine health and an increased likelihood of CL presence in cows with superior genetic merit for reproductive performance and survival.


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Bandon Corporation | Date: 2015-05-01

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