Cork, Ireland
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Cottle D.J.,University of New England of Australia | Gilmour A.R.,CargoVale Cargo | Pabiou T.,Sheep Ireland | Amer P.R.,AbacusBio Ltd Dunedin New Zealand | Fahey A.G.,University College Dublin
Journal of Animal Breeding and Genetics | Year: 2015

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. © 2015 Blackwell Verlag GmbH.

Mchugh N.,Teagasc | Berry D.P.,Teagasc | Pabiou T.,Sheep Ireland
Animal | Year: 2015

The objective of this study was to establish the risk factors associated with both lambing difficulty and lamb mortality in the Irish sheep multibreed population. A total of 135 470 lambing events from 42 675 ewes in 839 Irish crossbred and purebred flocks were available. Risk factors associated with producer-scored ewe lambing difficulty score (scale of one (no difficulty) to four (severe difficulty)) were determined using linear mixed models. Risk factors associated with the logit of the probability of lamb mortality at birth (i.e. binary trait) were determined using generalised estimating equations. For each dependent variable, a series of simple regression models were developed as well as a multiple regression model. In the simple regression models, greater lambing difficulty was associated with quadruplet bearing, younger ewes, of terminal breed origin, lambing in February; for example, first parity ewes experienced greater (P<0.001) lambing difficulty (1.56±0.02) than older ewes. The association between lambing difficulty and all factors persisted in the multiple regression model, and the trend in fixed effects level solutions did not differ from the trend observed in the simple regression models. In the simple regression analyses, a greater odds of lamb mortality was associated with male lambs (1.31 times more likely of death than females), lambs of very light (2 to 3 kg) and very heavy (>7.0 kg) birth weights, quadruplet born lambs and lambs that experienced a more difficult lambing (predicted probability of death for lambs that required severe and veterinary assistance of 0.15 and 0.32, respectively); lambs from dual-purpose breeds and born to younger ewes were also at greater risk of mortality. In the multiple regression model, the association between ewe parity, age at first lambing, year of lambing and lamb mortality no longer persisted. The trend in solutions of the levels of each fixed effect that remained associated with lamb mortality in the multiple regression model, did not differ from the trends observed in the simple regression models although the differential in relative risk between the different lambing difficulty scores was greater in the multiple regression model. Results from this study show that many common flock- and animal-level factors are associated with both lambing difficulty and lamb mortality and management of different risk category groups (e.g. scanned litter sizes, ewe age groups) can be used to appropriately manage the flock at lambing to reduce their incidence. © The Animal Consortium 2015.

PubMed | Weatherbys Ltd, Sheep Ireland, IdentiGEN, Teagasc and A Neogen Company
Type: Journal Article | Journal: Genetics, selection, evolution : GSE | Year: 2016

Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms.Genotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates.A mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes.Our results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.

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