Journal of Animal Breeding and Genetics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Role of inbreeding depression, non ‐inbred dominance deviations and random year‐season effect in genetic trends for prolificacy in closed rabbit lines
Summary 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. This paper fits different genetic evaluation models to data of these line...
Source: Journal of Animal Breeding and Genetics - June 1, 2017 Category: Genetics & Stem Cells Authors: E.N. Fern ández, J.P. Sánchez, R. Martínez, A. Legarra, M. Baselga Tags: ORIGINAL ARTICLE Source Type: research

Prediction of whole ‐genome risk for selection and management of hyperketonemia in Holstein dairy cattle
This study demonstrates the feasibility of using repeated cowside measurement of blood BHB concentration in early lactation to construct a reference population that can be used to estimate HYK breeding values for genomic selection programmes and predict HYK phenotypes for genome‐guided management decisions. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: K.A. Weigel, R. S. Pralle, H. Adams, K. Cho, C. Do, H.M. White Tags: ORIGINAL ARTICLE Source Type: research

Solving efficiently large single ‐step genomic best linear unbiased prediction models
Summary 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 where Aij, i, j = 1,2, are sparse sub‐matrices of A−1, and numbers 1 and 2 refer to non‐genotyped and...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: I. Strand én, K. Matilainen, G.P. Aamand, E.A. Mäntysaari Tags: ORIGINAL ARTICLE Source Type: research

Accuracy of genomic within ‐family selection in aquaculture breeding programmes
Summary 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. Here, we compare by computer simulation: (i) within‐family and population‐wide LD; and (ii...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: M.A. Toro, M. Saura, J. Fernandez, B. Villanueva Tags: ORIGINAL ARTICLE Source Type: research

Accuracy of genomic breeding values revisited: Assessment of two established approaches and a novel one to determine the accuracy in two ‐step genomic prediction
Summary 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 ...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: G. Ni, S. Kipp, H. Simianer, M. Erbe Tags: ORIGINAL ARTICLE Source Type: research

Genomic variance estimates: With or without disequilibrium covariances?
Summary 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 ...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: C. Lehermeier, G. Campos, V. Wimmer, C. ‐C. Schön Tags: ORIGINAL ARTICLE Source Type: research

Beyond genomic selection: The animal model strikes back (one generation)!
Summary 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. The resulting covariance structure (Σ) is Mark...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: R.J.C. Cantet, C.A. Garc ía‐Baccino, A. Rogberg‐Muñoz, N.S. Forneris, S. Munilla Tags: ORIGINAL ARTICLE Source Type: research

A comparison of identity ‐by‐descent and identity‐by‐state matrices that are used for genetic evaluation and estimation of variance components
The objective here is to recognize the difference between these covariance matrices and its implications. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: R. L. Fernando, H. Cheng, X. Sun, D. J. Garrick Tags: ORIGINAL ARTICLE Source Type: research

Modelling female fertility traits in beef cattle using linear and non ‐linear models
Summary 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. Inspired in the methodological developments made by Prof. Daniel Gianola and co‐wor...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: H. Naya, F. Pe ñagaricano, J.I. Urioste Tags: ORIGINAL ARTICLE Source Type: research

“Conversion” of epistatic into additive genetic variance in finite populations and possible impact on long‐term selection response
Summary 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 indirec...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: W.G. Hill Tags: ORIGINAL ARTICLE Source Type: research

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
Summary 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...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: E.N. Fern ández, A. Legarra, R. Martínez, J.P. Sánchez, M. Baselga Tags: ORIGINAL ARTICLE Source Type: research

Prediction of complex traits: Conciliating genetics and statistics
Summary 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, mach...
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: E. Manfredi, L. Tusell, Z.G. Vitezica Tags: ORIGINAL ARTICLE Source Type: research

Special Issue: Quantitative and statistical genetics —papers in honour of Daniel Gianola
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 15, 2017 Category: Genetics & Stem Cells Authors: H. Simianer, G. J. M. Rosa, A. M äki‐Tanila Tags: EDITORIAL Source Type: research

Differences in genetic structure assessed using Y ‐chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires
Summary Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y‐specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y‐chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty‐five Y‐chromosome and 71 mtDNA haplotypes were identified. Most Y‐chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty‐two Y‐haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotype...
Source: Journal of Animal Breeding and Genetics - May 2, 2017 Category: Genetics & Stem Cells Authors: I. Álvarez, L. Pérez‐Pardal, A. Traoré, D.O. Koudandé, I. Fernández, A. Soudré, S. Diarra, M. Sanou, H. Boussini, F. Goyache Tags: ORIGINAL ARTICLE Source Type: research

Geno ‐Diver: A combined coalescence and forward‐in‐time simulator for populations undergoing selection for complex traits
Summary Geno‐Diver is a combined coalescence and forward‐in‐time simulator designed to simulate complex traits with a quantitative and/or fitness component and implement multiple selection and mating strategies utilizing pedigree or genomic information. The simulation is carried out in two steps. The first step generates whole‐genome sequence data for founder individuals. A variety of trait architectures can be generated for quantitative and fitness traits along with their covariance. The second step generates new individuals forward‐in‐time based on a variety of selection and mating scenarios. Genetic values a...
Source: Journal of Animal Breeding and Genetics - May 2, 2017 Category: Genetics & Stem Cells Authors: J. T. Howard, F. Tiezzi, J. E. Pryce, C. Maltecca Tags: ORIGINAL ARTICLE Source Type: research