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Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie

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https://www.readbyqxmd.com/read/28804930/gaussian-covariance-graph-models-accounting-for-correlated-marker-effects-in-genome-wide-prediction
#1
C A Martínez, K Khare, S Rahman, M A Elzo
Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G...
August 13, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28748554/estimation-of-inbreeding-depression-on-female-fertility-in-the-finnish-ayrshire-population
#2
K Martikainen, A M Tyrisevä, K Matilainen, J Pösö, P Uimari
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (FPH ), runs of homozygosity (FROH ) and pedigree (FPED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows...
July 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28695620/correlated-response-in-litter-size-components-in-rabbits-selected-for-litter-size-variability
#3
M J Argente, E W Calle, M L García, A Blasco
A divergent selection experiment for the environmental variability of litter size (Ve) over seven generations was carried out in rabbits at the University Miguel Hernández of Elche. The Ve was estimated as the phenotypic variance within the female, after correcting for year-season and parity-lactation status. The aim of this study was to analyse the correlated responses to selection in litter size components. The ovulation rate (OR) and number of implanted embryos (IE) in females were measured by laparoscopy at 12 day of the second gestation...
July 11, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28691230/contemporary-group-estimates-adjusted-for-climatic-effects-provide-a-finer-definition-of-the-unknown-environmental-challenges-experienced-by-growing-pigs
#4
S Z Y Guy, L Li, P C Thomson, S Hermesch
Environmental descriptors derived from mean performances of contemporary groups (CGs) are assumed to capture any known and unknown environmental challenges. The objective of this paper was to obtain a finer definition of the unknown challenges, by adjusting CG estimates for the known climatic effects of monthly maximum air temperature (MaxT), minimum air temperature (MinT) and monthly rainfall (Rain). As the unknown component could include infection challenges, these refined descriptors may help to better model varying responses of sire progeny to environmental infection challenges for the definition of disease resilience...
July 10, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28685498/role-of-inbreeding-depression-non-inbred-dominance-deviations-and-random-year-season-effect-in-genetic-trends-for-prolificacy-in-closed-rabbit-lines
#5
E N Fernández, J P Sánchez, R Martínez, A Legarra, M Baselga
In closed rabbit lines selected for prolificacy at the Polytechnic University of Valencia, genetic responses are predicted using BLUP. With a standard additive BLUP model and year-season (YS) effects fitted as fixed, genetic trends were overestimated compared to responses estimated using control populations obtained from frozen embryos. In these lines, there is a confounding between genetic trend, YS effects and inbreeding, and the role of dominance is uncertain. This is a common situation in data from reproductively closed selection lines...
July 6, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28699266/can-we-make-genomic-selection-100-accurate
#6
EDITORIAL
M E Goddard
No abstract text is available yet for this article.
August 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508489/prediction-of-whole-genome-risk-for-selection-and-management-of-hyperketonemia-in-holstein-dairy-cattle
#7
K A Weigel, R S Pralle, H Adams, K Cho, C Do, H M White
Hyperketonemia (HYK), a common early postpartum health disorder characterized by elevated blood concentrations of β-hydroxybutyrate (BHB), affects millions of dairy cows worldwide and leads to significant economic losses and animal welfare concerns. In this study, blood concentrations of BHB were assessed for 1,453 Holstein cows using electronic handheld meters at four time points between 5 and 18 days postpartum. Incidence rates of subclinical (1.2 ≤ maximum BHB ≤ 2.9 mmol/L) and clinical ketosis (maximum BHB ≥ 3...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508488/modelling-female-fertility-traits-in-beef-cattle-using-linear-and-non-linear-models
#8
H Naya, F Peñagaricano, J I Urioste
Female fertility traits are key components of the profitability of beef cattle production. However, these traits are difficult and expensive to measure, particularly under extensive pastoral conditions, and consequently, fertility records are in general scarce and somehow incomplete. Moreover, fertility traits are usually dominated by the effects of herd-year environment, and it is generally assumed that relatively small margins are kept for genetic improvement. New ways of modelling genetic variation in these traits are needed...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508487/accuracy-of-genomic-breeding-values-revisited-assessment-of-two-established-approaches-and-a-novel-one-to-determine-the-accuracy-in-two-step-genomic-prediction
#9
G Ni, S Kipp, H Simianer, M Erbe
Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508486/pedigree-based-estimation-of-covariance-between-dominance-deviations-and-additive-genetic-effects-in-closed-rabbit-lines-considering-inbreeding-and-using-a-computationally-simpler-equivalent-model
#10
E N Fernández, A Legarra, R Martínez, J P Sánchez, M Baselga
Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508485/-conversion-of-epistatic-into-additive-genetic-variance-in-finite-populations-and-possible-impact-on-long-term-selection-response
#11
W G Hill
The role of epistasis in understanding the genetic architecture and variation of quantitative traits and its role, if any, in artificial selection and livestock improvement more generally has a long and sometimes controversial history. Its presence has been clearly demonstrated in, for example, laboratory experiments, but the amount of variation it contributes is likely to be small in outbred populations. In a finite population, although additive x additive epistatic variance is lost by genetic drift, it also contributes by conversion to additive variance through drift sampling and therefore has a potential indirect role in medium and long-term selection response, with superficial similarity to and hard to distinguish from mutation...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508484/special-issue-quantitative-and-statistical-genetics-papers-in-honour-of-daniel-gianola
#12
EDITORIAL
H Simianer, G J M Rosa, A Mäki-Tanila
No abstract text is available yet for this article.
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508483/genomic-variance-estimates-with-or-without-disequilibrium-covariances
#13
C Lehermeier, G de Los Campos, V Wimmer, C-C Schön
Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508482/solving-efficiently-large-single-step-genomic-best-linear-unbiased-prediction-models
#14
I Strandén, K Matilainen, G P Aamand, E A Mäntysaari
Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) and pedigree (A22 ). Different approaches were used to ease computations, reduce computing time and improve numerical stability. Inverse of A22 can be computed as A22-1=A22-A21A11-1A12 where A(ij) , i, j = 1,2, are sparse sub-matrices of A(-1) , and numbers 1 and 2 refer to non-genotyped and genotyped animals, respectively...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508481/a-comparison-of-identity-by-descent-and-identity-by-state-matrices-that-are-used-for-genetic-evaluation-and-estimation-of-variance-components
#15
R L Fernando, H Cheng, X Sun, D J Garrick
The genetic covariance matrix conditional on pedigree is proportional to the pedigree-based additive relationship matrix (PARM), which is twice the matrix of identity-by-descent (IBD) probabilities. In genomic prediction, IBD probabilities in the PARM, which are expected genetic similarities between relatives that are derived from the pedigree, are substituted by realized similarities that are derived from genotypes to obtain a genomic additive relationship matrix (GARM). Different definitions of similarity lead to different GARMs, and two commonly used GARMS are the matrix G, which is based on an allele substitution effect model, and the matrix T, which is based on an allele effect model...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508480/beyond-genomic-selection-the-animal-model-strikes-back-one-generation
#16
R J C Cantet, C A García-Baccino, A Rogberg-Muñoz, N S Forneris, S Munilla
Genome inheritance is by segments of DNA rather than by independent loci. We introduce the ancestral regression (AR) as a recursive system of simultaneous equations, with grandparental path coefficients as novel parameters. The information given by the pedigree in the AR is complementary with that provided by a dense set of genomic markers, such that the resulting linear function of grandparental BV is uncorrelated to the average of parental BV in the absence of inbreeding. AR is then connected to segmental inheritance by a causal multivariate Gaussian density for BV...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508479/prediction-of-complex-traits-conciliating-genetics-and-statistics
#17
E Manfredi, L Tusell, Z G Vitezica
This review focuses on methods used to predict complex traits. Main characteristics of prediction approaches are given: the deterministic or stochastic nature of prediction, the objects of prediction, the sources of information and the main statistical methods. Sources of information discussed are the traditional genealogies and phenotypes, nucleotide sequences, expression data and epigenetics marks. Statistical methods are presented as successive degrees of generalization from the definition of the conditional expectation as the prediction rule, to best linear unbiased prediction, then Bayesian and, recently, machine learning methods, including meta-methods...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508478/accuracy-of-genomic-within-family-selection-in-aquaculture-breeding-programmes
#18
M A Toro, M Saura, J Fernandez, B Villanueva
In aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28470817/a-genetic-analysis-of-meat-compositions-in-japanese-black-cattle-genetic-parameters-and-sex-influence
#19
A Onogi, S Sasaki, M Kobayashi, A Ogino, T Nozaki, K Kurogi, T Yasumori, K Togashi, H Iwata
Meat composition in beef is related to eating quality and food functionality. Genetic parameters for several meat compositions including free amino acid, peptide and sugar, however, remain poorly described. In this study, we estimated genetic parameters for 51 meat components, including free amino acids, peptides, sugars and fatty acid compositions, and two carcase traits in 1,354 heifers and 1,797 steers of Japanese Black cattle. Heritability estimates were generally equivalent to or moderately greater than those in previous studies of this breed...
May 3, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28464315/selection-of-core-animals-in-the-algorithm-for-proven-and-young-using-a-simulation-model
#20
H L Bradford, I Pocrnić, B O Fragomeni, D A L Lourenco, I Misztal
The Algorithm for Proven and Young (APY) enables the implementation of single-step genomic BLUP (ssGBLUP) in large, genotyped populations by separating genotyped animals into core and non-core subsets and creating a computationally efficient inverse for the genomic relationship matrix (G). As APY became the choice for large-scale genomic evaluations in BLUP-based methods, a common question is how to choose the animals in the core subset. We compared several core definitions to answer this question. Simulations comprised a moderately heritable trait for 95,010 animals and 50,000 genotypes for animals across five generations...
May 2, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
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