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Genome ‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle
Summary We performed a genome‐wide mapping for the age at first calving (AFC) with the goal of annotating candidate genes that regulate fertility in Nellore cattle. Phenotypic data from 762 cows and 777k SNP genotypes from 2,992 bulls and cows were used. Single nucleotide polymorphism (SNP) effects based on the single‐step GBLUP methodology were blocked into adjacent windows of 1 Megabase (Mb) to explain the genetic variance. SNP windows explaining more than 0.40% of the AFC genetic variance were identified on chromosomes 2, 8, 9, 14, 16 and 17. From these windows, we identified 123 coding protein genes that were used ...
Source: Journal of Animal Breeding and Genetics - October 1, 2017 Category: Genetics & Stem Cells Authors: R.R. Mota, S.E.F. Guimar ães, M.R.S. Fortes, B. Hayes, F.F. Silva, L.L. Verardo, M.J. Kelly, C.F. Campos, J.D. Guimarães, R.R. Wenceslau, J.M. Penitente‐Filho, J.F. Garcia, S. Moore Tags: ORIGINAL ARTICLE Source Type: research

Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality
Summary Data of 127,800 Iberian piglets were used to study genetic parameters of mortality at birth at the piglet level. These records proceed from three data sets: 4,987 litter of 2,156 sows of a dam line, 2,768 litter of 817 sows of a complete diallel cross between four Iberian strains and 7,153 litter of 2,113 sows of the Torbiscal composite line. Perinatal mortality was considered as a binary trait, and Bayesian threshold animal models were fitted to separately analyse the three data sets. The posterior means of direct heritability were 0.010, 0.004 and 0.003, and those of maternal heritability were 0.03...
Source: Journal of Animal Breeding and Genetics - September 28, 2017 Category: Genetics & Stem Cells Authors: M. Mu ñoz, M.C. Rodríguez, L.A. García‐Cortes, A. González, J.M. García‐Casco, L. Silió Tags: ORIGINAL ARTICLE Source Type: research

Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs
In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p‐value threshold of 1 × 10−6 among which 42 associations in low linkage disequilibrium (r2 
Source: Journal of Animal Breeding and Genetics - September 21, 2017 Category: Genetics & Stem Cells Authors: J. Zhang, Y. Zhang, H. Gong, L. Cui, T. Huang, H. Ai, J. Ren, L. Huang, B. Yang Tags: ORIGINAL ARTICLE Source Type: research

Correction for adipocyte size and number in the analysis of differences in gene expression in fat tissues
Summary In gene expression studies of candidate genes related to fat deposition, accounting for differences in cell number using reference genes could be not sufficient when cell transcriptional levels are related to cell size, or the tissues are constituted by different types of cells where candidate genes could be differentially expressed. In these situations, mixed model can be applied giving the possibility to take into account the effects of adipocyte size and number on gene expression. The inclusion in the models of analysis of adipocyte size and number, previously estimated taking into account the possible bimodalit...
Source: Journal of Animal Breeding and Genetics - September 20, 2017 Category: Genetics & Stem Cells Authors: L. Alfonso Tags: ORIGINAL ARTICLE Source Type: research

Revolutionary leaps in the development of agriculture
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 6, 2017 Category: Genetics & Stem Cells Authors: J.J. Lauvergne Tags: EDITORIAL Source Type: research

Implications of SNP weighting on single ‐step genomic predictions for different reference population sizes
Summary We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single‐step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage...
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: D. A. L. Lourenco, B. O. Fragomeni, H. L. Bradford, I. R. Menezes, J. B. S. Ferraz, I. Aguilar, S. Tsuruta, I. Misztal Tags: ORIGINAL ARTICLE Source Type: research

Genomic estimation of additive and dominance effects and impact of accounting for dominance on accuracy of genomic evaluation in sheep populations
This study showed a substantial dominance genetic variance for weight and ultrasound scanned body composition traits particularly in cross‐bred population; however, improvement in the accuracy of genomic breeding values was small and statistically not significant. Dominance variance estimates in combined cross‐bred population could be overestimated if heterosis is not fitted in the model. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: N. Moghaddar, J. H. J. Werf Tags: ORIGINAL ARTICLE Source Type: research

Gaussian covariance graph models accounting for correlated marker effects in genome ‐wide prediction
In this study, methods adapting the theory of GCovGM to genome‐wide prediction were developed (Bayes GCov, Bayes GCov‐KR and Bayes GCov‐H). In simulated data sets, improvements in correlation between phenotypes and predicted breeding values and accuracies of predicted breeding values were found. Our models account for correlation of marker effects and permit to accommodate general structures as opposed to models proposed in previous studies, which consider spatial correlation only. In addition, they allow incorporation of biological information in the prediction process through its use when constructing graph G, and ...
Source: Journal of Animal Breeding and Genetics - August 1, 2017 Category: Genetics & Stem Cells Authors: C.A. Mart ínez, K. Khare, S. Rahman, M.A. Elzo Tags: ORIGINAL ARTICLE Source Type: research

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population
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 ...
Source: Journal of Animal Breeding and Genetics - July 27, 2017 Category: Genetics & Stem Cells Authors: K. Martikainen, A. M. Tyrisev ä, K. Matilainen, J. Pösö, P. Uimari Tags: ORIGINAL ARTICLE Source Type: research

Can we make genomic selection 100% accurate?
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 11, 2017 Category: Genetics & Stem Cells Authors: M.E. Goddard Tags: EDITORIAL Source Type: research

Correlated response in litter size components in rabbits selected for litter size variability
In conclusion, a decrease in litter size variability showed a favourable effect on ES and led to a higher litter size at birth. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 1, 2017 Category: Genetics & Stem Cells Authors: M.J. Argente, E.W. Calle, M.L. Garc ía, A. Blasco Tags: ORIGINAL ARTICLE Source Type: research

Contemporary group estimates adjusted for climatic effects provide a finer definition of the unknown environmental challenges experienced by growing pigs
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. Data were recorded from 1999 to 2013 at a piggery in south‐east Queensland, Australia (n = 31,230). Firstly, CG estimates of average daily gain ...
Source: Journal of Animal Breeding and Genetics - June 1, 2017 Category: Genetics & Stem Cells Authors: S.Z.Y. Guy, L. Li, P.C. Thomson, S. Hermesch Tags: ORIGINAL ARTICLE Source Type: research

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‐g...
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...
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...
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 usin...
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

A genetic analysis of meat compositions in Japanese Black cattle: Genetic parameters and sex influence
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. Genetic correlations between free amino acids, peptides and sugars and carcase traits were often negative, suggesting a trade‐off between traits. Using two‐trait animal models that treat records from the two sexes as different traits, we estimated sex‐specific heritabilities ...
Source: Journal of Animal Breeding and Genetics - April 1, 2017 Category: Genetics & Stem Cells Authors: A. Onogi, S. Sasaki, M. Kobayashi, A. Ogino, T. Nozaki, K. Kurogi, T. Yasumori, K. Togashi, H. Iwata Tags: ORIGINAL ARTICLE Source Type: research

Selection of core animals in the Algorithm for Proven and Young using a simulation model
Summary 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 ...
Source: Journal of Animal Breeding and Genetics - April 1, 2017 Category: Genetics & Stem Cells Authors: H.L. Bradford, I. Pocrni ć, B.O. Fragomeni, D.A.L. Lourenco, I. Misztal Tags: ORIGINAL ARTICLE Source Type: research

Genetic relationships among female fertility disorders, female fertility traits and productivity of Holstein dairy cows in the early lactation period
Summary Fertility health disorders from the early lactation period including retained placenta (REPLA), metritis (MET), corpus luteum persistence (CLP), anoestria/acyclia (AOEAC) and ovarial cysts (OC), as well as overall disease categories (disorders during the postpartal period (DPP), ovary infertility (OINF), overall trait definition “fertility disorders” (FD)), were used to estimate genetic (co)variance components with female fertility and test‐day traits. The disease data set comprised 25,142 Holstein cows from parities 1, 2 and 3 resulting in 43,584 lactations. For disease traits, we used the binary tra...
Source: Journal of Animal Breeding and Genetics - April 1, 2017 Category: Genetics & Stem Cells Authors: E. Gernand, S. K önig Tags: ORIGINAL ARTICLE Source Type: research

Purebreeding of Red Maasai and crossbreeding with Dorper sheep in different environments in Kenya
Summary The aim of this article was to study opportunities for improvement of the indigenous and threatened Red Maasai sheep (RM) in Kenya, by comparing purebreeding with crossbreeding with Dorper sheep (D) as a terminal breed, in two different environments (Env. A and a harsher Env. B), assuming different levels of genotype‐by‐environment interaction (G × E). Breeding goals differed between environments and breeds. Four scenarios of nucleus breeding schemes were stochastically simulated, with the nucleus in Env. A. Overall, results showed an increase in carcass weight produced per ewe by more than 10% ...
Source: Journal of Animal Breeding and Genetics - March 27, 2017 Category: Genetics & Stem Cells Authors: E. Zonabend K önig, E. Strandberg, J.M.K. Ojango, T. Mirkena, A.M. Okeyo, J. Philipsson Tags: ORIGINAL ARTICLE Source Type: research

Estimation of genetic parameters for functional longevity in the South African Holstein cattle using a piecewise Weibull proportional hazards model
Summary Non‐genetic factors influencing functional longevity and the heritability of the trait were estimated in South African Holsteins using a piecewise Weibull proportional hazards model. Data consisted of records of 161,222 of daughters of 2,051 sires calving between 1995 and 2013. The reference model included fixed time‐independent age at first calving and time‐dependent interactions involving lactation number, region, season and age of calving, within‐herd class of milk production, fat and protein content, class of annual variation in herd size and the random herd–year effect. Random sire and maternal g...
Source: Journal of Animal Breeding and Genetics - March 14, 2017 Category: Genetics & Stem Cells Authors: V.E. Imbayarwo ‐Chikosi, V. Ducrocq, C.B. Banga, T.E. Halimani, J.B. Wyk, A. Maiwashe, K. Dzama Tags: ORIGINAL ARTICLE Source Type: research

Animal Breeding learning from machine learning
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 13, 2017 Category: Genetics & Stem Cells Authors: M. P érez‐Enciso Tags: Editorial Source Type: research

Genome ‐wide association study of cell‐mediated immune response in chicken
In this study, a genome‐wide association study (GWAS) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high‐density single nucleotide polymorphism (SNP) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome‐wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model (MLM) had better inflation rate, and therefore the results from MLM were used for s...
Source: Journal of Animal Breeding and Genetics - March 9, 2017 Category: Genetics & Stem Cells Authors: V. Raeesi, A. Ehsani, R.V. Torshizi, M. Sargolzaei, A.A. Masoudi, R. Dideban Tags: ORIGINAL ARTICLE Source Type: research

Genetic parameters for fur quality graded on live animals and dried pelts of American mink (Neovison vison)
In this study, we evaluated traits assessed during live grading and pelt traits examined on dried skins to determine correlation between live and pelt traits. Grading traits and body weight were measured during live animal grading for 9,539 Brown American mink, and pelt quality traits and skin size were evaluated on 8,385 dried mink skins after pelting. Data were sampled from 2 yearly production cycles. Genetic parameters were estimated using the REML method implemented in the DMU package. Heritabilities and proportions of litter variance were calculated from estimated variance components for all traits, and genetic a...
Source: Journal of Animal Breeding and Genetics - March 9, 2017 Category: Genetics & Stem Cells Authors: J.P. Thirstrup, J. Jensen, M.S. Lund Tags: ORIGINAL ARTICLE Source Type: research

Founder representation and effective population size in old versus young breeds —genetic diversity of Finnish and Nordic Spitz
Summary Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks result...
Source: Journal of Animal Breeding and Genetics - January 31, 2017 Category: Genetics & Stem Cells Authors: M. Kumpulainen, H. Anderson, T. Svevar, I. Kangasvuo, J. Donner, J. Pohjoism äki Tags: ORIGINAL ARTICLE Source Type: research

Genomic and single ‐step evaluations of carcass traits of young bulls in dual‐purpose cattle
Summary Genetic evaluations for carcass traits of young bulls in Normande and Montbeliarde breeds are currently being developed in France. In order to determine a suitable genomic evaluation for three carcass traits of young bulls, genomic breeding values were estimated for young candidates to selection using different approaches. Records of 111,789 Normande and 118,183 Montbeliarde were used. Average progeny pre‐adjusted performances (DYD) were calculated for sires. Evaluation approaches were compared based on an assessment of their accuracy (correlation between DYD and estimated breeding values [EBVs]) and bias (regres...
Source: Journal of Animal Breeding and Genetics - January 31, 2017 Category: Genetics & Stem Cells Authors: I. Crou é, V. Ducrocq Tags: ORIGINAL ARTICLE Source Type: research

Genetic trends for fertility, udder health and protein yield in Swedish red cattle estimated with different models
Summary The aim of this study was to estimate and compare genetic trends in Swedish Red cattle using a full multiple‐trait (MT) model and trait‐group‐wise models for female fertility, udder health and protein yield. Field data for maiden heifers from 1989 and cows with a first and second lactation between 1990 and 2007 were included. (Co)variance components were estimated prior to prediction of breeding values. The estimated genetic trends were clearly favourable for protein yield and udder conformation, and in most cases neutral to favourable for clinical mastitis and calving to first insemination. In maiden heifers...
Source: Journal of Animal Breeding and Genetics - January 31, 2017 Category: Genetics & Stem Cells Authors: S. Eriksson, K. Johansson, H. Hansen Axelsson, W.F. Fikse Tags: ORIGINAL ARTICLE Source Type: research

The legacy of Columbus in American horse populations assessed by microsatellite markers
In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of “all other Criollo breeds” had the closest genetic relationship with breeds originating from the Iberian Peninsula, specificall...
Source: Journal of Animal Breeding and Genetics - January 31, 2017 Category: Genetics & Stem Cells Authors: O. Cort és, S. Dunner, L.T. Gama, A.M. Martínez, J.V. Delgado, C. Ginja, L.M. Jiménez, J. Jordana, C. Luis, M.M. Oom, D.P. Sponenberg, P. Zaragoza, , J.L. Vega‐Pla Tags: ORIGINAL ARTICLE Source Type: research

Performance of genomic selection under a single ‐step approach in autochthonous Spanish beef cattle populations
This study evaluated different strategies for implementing a single‐step genomic selection programme in two autochthonous Spanish beef cattle populations (Pirenaica—Pi and Rubia Gallega—RG). The strategies were compared in terms of accuracy attained under different scenarios by simulating genomic data over the known genealogy. Several genotyping approaches were tested, as well as, other factors like marker density, effective population size, mutation rate and heritability of the trait. The results obtained showed gains in accuracy with respect to pedigree BLUP evaluation in all cases. The greatest benefit was...
Source: Journal of Animal Breeding and Genetics - January 31, 2017 Category: Genetics & Stem Cells Authors: E. ‐F. Mouresan, J. Altarriba, C. Moreno, S. Munilla, A. González‐Rodríguez, L. Varona Tags: ORIGINAL ARTICLE Source Type: research

Daniel Gianola's contributions to animal breeding and quantitative genetics, a vuelo de p ájaro
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 30, 2017 Category: Genetics & Stem Cells Authors: D. Sorensen, G. Campos Tags: ORIGINAL ARTICLE Source Type: research

Effective breeding programmes down under
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 9, 2017 Category: Genetics & Stem Cells Authors: J. Werf, R. Banks Tags: EDITORIAL Source Type: research

Mitochondrial DNA D ‐loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia
Summary To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D‐loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231–1232 bp D‐loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusi...
Source: Journal of Animal Breeding and Genetics - December 17, 2016 Category: Genetics & Stem Cells Authors: A.G. Dyomin, M.I. Danilova, J.M. Mwacharo, A.E. Masharsky, A.V. Panteleev, A.S. Druzhkova, V.A. Trifonov, S.A. Galkina Tags: Original Article Source Type: research

Genetic diversity of the Mexican Lidia bovine breed and its divergence from the Spanish population
In conclusion, as the Mexican Lidia population had initially a small number of founders and its current population has been reared isolated from their Spanish ancestors since a long time, these bottleneck effects and a combination of mixed cattle origin are the factors that might erase any trace of the Spanish origin of this population. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 30, 2016 Category: Genetics & Stem Cells Authors: P.G. Eusebi, O. Cort és, S. Dunner, J. Cañón Tags: ORIGINAL ARTICLE Source Type: research

Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes
Summary We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross‐breed. Elite nucleus herds had access to high‐quality feed, and production herds were fed low‐quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (rg = 0.2), medium (rg = 0.5) and high (rg = 0.8). In our alternative breeding schemes, different proportion of productio...
Source: Journal of Animal Breeding and Genetics - November 30, 2016 Category: Genetics & Stem Cells Authors: K.G. Nirea, T.H.E. Meuwissen Tags: Original Article Source Type: research

Genomic evaluation of regional dairy cattle breeds in single ‐breed and multibreed contexts
Summary An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic ev...
Source: Journal of Animal Breeding and Genetics - November 30, 2016 Category: Genetics & Stem Cells Authors: D. J ónás, V. Ducrocq, S. Fritz, A. Baur, M.‐P. Sanchez, P. Croiseau Tags: Original Article Source Type: research

Genetic parameter estimates for prenatal and postnatal mortality in Nellore cattle
Summary The aim of this study was to estimate genetic parameters for prenatal (PRE) and postnatal (POS) mortality in Nellore cattle. A total of 13 141 (PRE) and 17 818 (POS) records from Nellore females were used. PRE and POS were recorded using binary scale scores: a score of ‘1’ was given to calves that were born alive (PRE) and those that were alive at weaning (POS), and a score of ‘0’ was given to calves that were not alive at or around birth (PRE), as well as to those weighed at birth but not at weaning (POS). The relationship matrix included 698 sires, 107 paternal grandsires and 69 ...
Source: Journal of Animal Breeding and Genetics - November 30, 2016 Category: Genetics & Stem Cells Authors: L.C. Magalh ães Silva, F. Baldi, C. Aboujaoude, G.C. Venturini, L.G. Albuquerque, M.J.R. Paranhos da Costa Tags: Original Article Source Type: research

Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism, using pedigree or genomic information
Summary Mortality of laying hens due to cannibalism is a major problem in the egg‐laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire‐family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of...
Source: Journal of Animal Breeding and Genetics - November 23, 2016 Category: Genetics & Stem Cells Authors: T. Brinker, B. Raymond, P. Bijma, A. Vereijken, E.D. Ellen Tags: Original Article Source Type: research

Acknowledgements to referees
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 15, 2016 Category: Genetics & Stem Cells Tags: Acknowledgements to Referees Source Type: research

The frontier spirit and reproducible research in animal breeding
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 15, 2016 Category: Genetics & Stem Cells Authors: R. J. Tempelman Tags: Editorial Source Type: research