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The Dutch national breeding programmes have developed to major globally operating companies
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 6, 2015 Category: Genetics & Stem Cells Authors: J. Napel, R.F. Veerkamp Tags: Editorial Source Type: research

Mitogenome revealed multiple postdomestication genetic mixtures of West African sheep
Summary Notable diversity observed within African ovine breeds makes them of great interests, but limited studies on genetic origins and domestications remain poorly understood. Here, we investigate the evolutionary status of West African native breeds, Djallonke and Sahelian sheep using mitogenome sequencing. Compared with other ovine mitogenome sequences, West African sheep were revealed a Eurasian origin, and the initially tamed sheep breeds in West Africa have been genetically mixed with each other and mixed with European breeds. Worldwide domestic sheep is deemed the Eurasian origin and migrated west to Europe and Afr...
Source: Journal of Animal Breeding and Genetics - April 12, 2015 Category: Genetics & Stem Cells Authors: O.H.D. Brahi, H. Xiang, X. Chen, S. Farougou, X. Zhao Tags: Original Article Source Type: research

Genetic management of Dutch golden retriever dogs with a simulation tool
Summary Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each y...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: J.J. Windig, K. Oldenbroek Tags: Original Article Source Type: research

Estimation of indirect genetic effects in group‐housed mink (Neovison vison) should account for systematic interactions either due to kin or sex
Summary Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non‐family members. Here, we investigate kin‐ and sex‐specific non‐genetic social interactions i...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: S.W. Alemu, P. Berg, L. Janss, P. Bijma Tags: Original Article Source Type: research

The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection
Summary The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north‐western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of variou...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Ćurković, J. Ramljak, S. Ivanković, B. Mioč, A. Ivanković, V. Pavić, M. Brka, C. Veit‐Kensch, I. Medugorac Tags: Original Article Source Type: research

Phenotypic and genetic variation in longevity of Polish Landrace sows
Summary The influence of some production traits on the longevity of Polish Landrace sows was evaluated using survival analysis. Estimates of genetic parameters were obtained from the sire and animal components in linear and survival methodologies. Comparison between survival and linear models was based on heritabilities and ranking of estimated breeding values of sires. The same data set, 13 031 sows, was used for both methodologies, even in the presence of censored observations. The effects of herd*year and year*season of the first farrowing had the largest influence on the risk of culling of sows. Sows born in spring se...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Sobczyńska, T. Blicharski Tags: Original Article Source Type: research

Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium
Summary The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP‐LD). In the three GBLUP‐LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP‐LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation da...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Nishio, M. Satoh Tags: Original Article Source Type: research

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study
Summary The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G−1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, di...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: B.O. Fragomeni, D.A.L. Lourenco, S. Tsuruta, Y. Masuda, I. Aguilar, I. Misztal Tags: Original Article Source Type: research

Relationship between perilipin genes polymorphisms and growth, carcass and meat quality traits in pigs
Summary The perilipins (PLIN) belong to a family of structural proteins that play a role regulating intracellular lipid storage and mobilization. Here, PLIN1 and PLIN2 have been evaluated as candidate genes for growth, carcass and meat quality traits in pigs. A sample of 607 Duroc pigs were genotyped for two single‐nucleotide polymorphisms, one in intron 2 of the PLIN1 gene (JN860199:g.173G>A) and the other at the 3′ untranslated region of the PLIN2 gene (GU461317:g.98G>A). Using a Bayesian approach, we have been able to find evidence of additive, dominant and epistatic associations of the PLIN1 and PLIN2 polymor...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: S. Gol, R. Ros‐Freixedes, P. Zambonelli, M. Tor, R.N. Pena, S. Braglia, M. Zappaterra, J. Estany, R. Davoli Tags: Original Article Source Type: research

The biodiversity and genetic structure of Balearic sheep breeds
Summary The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was foun...
Source: Journal of Animal Breeding and Genetics - March 31, 2015 Category: Genetics & Stem Cells Authors: A.L. Pons, V. Landi, A. Martinez, J.V. Delgado Tags: Original Article Source Type: research

Quantitative genetics of disease traits
Summary John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James’ most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this r...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: N.R. Wray, P.M. Visscher Tags: Invited Review Source Type: research

Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits
Summary Linkage disequilibrium (LD) influences the genetic variation in a quantitative trait contributed by two or more loci, with positive LD increasing the variance. The magnitude of LD also affects the relative magnitude of dominance and epistatic variation. We quantify the extent of the non‐additive variance expected within populations, deriving analytical expressions for simple models and using numerical simulation in finite population more generally. As LD generates non‐independence among loci, a simple partition into additive, dominance and epistatic components is not possible, so we merely distinguish between a...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: W.G. Hill, A. Mäki‐Tanila Tags: Original Article Source Type: research

Some aspects of design and analysis of selection programmes in aquaculture species
In this study, we focus on a few aspects of aquaculture genetics to which Professor James made substantial contributions. His outstanding ability to comprehend, clarify and simplify complex problems with easy‐to‐understand mathematical derivations is clearly demonstrated in the areas of large‐scale strain comparisons, genotype‐by‐environment interactions (GxE), transformations and interpretation of selection response, as well as in the treatment of economic aspects of designing breeding programmes. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: Y. Li, R.W. Ponzoni Tags: Invited Review Source Type: research

Community‐based livestock breeding programmes: essentials and examples
Summary Breeding programmes described as community‐based (CBBP) typically relate to low‐input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low‐input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin‐America, Africa and Asia hi...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.P. Mueller, B. Rischkowsky, A. Haile, J. Philipsson, O. Mwai, B. Besbes, A. Valle Zárate, M. Tibbo, T. Mirkena, G. Duguma, J. Sölkner, M. Wurzinger Tags: Invited Review Source Type: research

Comparison of breeding objectives across countries with application to sheep indexes in New Zealand and Ireland
The objective of this study was to describe the methodology to calculate correlations between national selection indexes and gain a deeper understanding of the factors influencing responses in economically important traits in both the New Zealand and Irish sheep industries. Moderate to strong correlations were calculated among indexes within and between countries, with the strongest correlation (0.86) between the New Zealand and Irish maternal indexes. In both countries, responses to selection in the maternal indexes are largely driven by growth traits; each index, however, has a different balance of traits. Ewe mature wei...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: B.F.S. Santos, N. McHugh, T.J. Byrne, D.P. Berry, P.R. Amer Tags: Original Article Source Type: research

How old are quantitative trait loci and how widely do they segregate?
Summary The mutations that cause genetic variation in quantitative traits could be old and segregate across many breeds or they could be young and segregate only within one breed. This has implications for our understanding of the evolution of quantitative traits and for genomic prediction to improve livestock. We investigated the age of quantitative trait loci (QTL) for milk production traits identified as segregating in Holstein dairy cattle. We use a multitrait method and found that six of 11 QTL also segregate in Jerseys. Variants identified as Holstein‐only QTL were fixed or rare [minor allele frequency (MAF) <...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: K.E. Kemper, B.J. Hayes, H.D. Daetwyler, M.E. Goddard Tags: Original Article Source Type: research

Managing the rate of increase in average co‐ancestry in a rolling front tree breeding strategy
Summary In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long‐ and short‐term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by ...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R.J. Kerr, T.A. McRae, G.W. Dutkowski, B. Tier Tags: Invited Review Source Type: research

grain: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach
Summary GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the ‘classical’ inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC), defined here for the first time. AHC is defined as the numbe...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R. Baumung, J. Farkas, D. Boichard, G. Mészáros, J. Sölkner, I. Curik Tags: Original Article Source Type: research

Genetic contributions and their optimization
Summary Genetic contributions were first formalized in 1958 by James and McBride (Journal of Genetics, 56, 55–62) and have since been shown to provide a unifying framework for theories of gain and inbreeding. As such they have underpinned the development of methods that provide the most effective combination of maximizing gain whilst managing inbreeding and loss of genetic variation. It is shown how this optimum contribution technology can be developed from theory and adapted to provide practical selection protocols for a wide variety of situations including overlapping generations and multistage selection. The natural d...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.A. Woolliams, P. Berg, B.S. Dagnachew, T.H.E. Meuwissen Tags: Invited Review Source Type: research

Quantitative genetics, spread of genes and genetic improvement: papers in honour of John James
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: F.W. Nicholas, C.M. Wade, L. Ollivier, J. Sölkner Tags: Introduction Source Type: research

A 57‐bp deletion in the ovine KAP6‐1 gene affects wool fibre diameter
In this study, we used polymerase chain reaction – single‐strand conformational polymorphism (PCR‐SSCP) analysis to screen for variation in a gene encoding the ovine HGT‐KAP6‐1 protein. We identified three gene variants (A, B and C). Variants A and B were similar to each other, with only three nucleotide differences occurring downstream of the coding sequence. However, variant C had a 57‐bp deletion that would notionally result in a loss of 19 amino acids in the protein. The presence of C was found to be associated with an increase in mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), coeffici...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: H. Zhou, H. Gong, S. Li, Y. Luo, J.G.H. Hickford Tags: Original Article Source Type: research

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs
Summary The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotype...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: T. Aasmundstad, I. Andersen‐Ranberg, Ø. Nordbø, T. Meuwissen, O. Vangen, E. Grindflek Tags: Original Article Source Type: research

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds
In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out‐of‐bag (OOB) error rate for both ranking met...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: F. Bertolini, G. Galimberti, D.G. Calò, G. Schiavo, D. Matassino, L. Fontanesi Tags: Original Article Source Type: research

Y‐chromosomal variation of local goat breeds of Turkey close to the domestication centre
In this study, the male‐specific region markers, sex‐determining region‐Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honamlı, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illus...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: B. Cinar Kul, N. Bilgen, J.A. Lenstra, O. Korkmaz Agaoglu, B. Akyuz, O. Ertugrul Tags: Original Article Source Type: research

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls
The objectives of this study were to characterize the genetic variability of village chickens from three agro‐ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of F...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: F. Z. Mahammi, S. B. S. Gaouar, D. Laloë, R. Faugeras, N. Tabet‐Aoul, X. Rognon, M. Tixier‐Boichard, N. Saidi‐Mehtar Tags: Original Article Source Type: research

Genetic parameters for different growth scales in GIFT strain of Nile tilapia (Oreochromis niloticus)
Summary Body weight, length, width and depth at two growth stages were observed for a total of 5015 individuals of GIFT strain, along with a pedigree including 5588 individuals from 104 sires and 162 dams was collected. Multivariate animal models and a random regression model were used to genetically analyse absolute and relative growth scales of these growth traits. In absolute growth scale, the observed growth traits had moderate heritabilities ranging from 0.321 to 0.576, while pairwise ratios between body length, width and depth were lowly inherited and maximum heritability was only 0.146 for length/depth. All genetic ...
Source: Journal of Animal Breeding and Genetics - March 6, 2015 Category: Genetics & Stem Cells Authors: J. He, H. Gao, P. Xu, R. Yang Tags: Original Article Source Type: research

Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes
Summary Heritabilities and genetic correlations for milk production traits were estimated from first‐parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Legm) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and ...
Source: Journal of Animal Breeding and Genetics - March 2, 2015 Category: Genetics & Stem Cells Authors: E.B. Flores, J. Werf Tags: Original Article Source Type: research

A retrospective analysis of allele frequency changes of major genes during 20 years of selection in the Italian Large White pig breed
In this study, we investigated whether a selection programme based on boar genetic evaluation obtained with a classical BLUP animal model can change allele frequencies in a pig population. All Italian Large White boars born from 1992 to 2012 with estimated breeding value reliability >0.85 (n = 200) were selected among all boars of this breed. Boars were genotyped with markers in major genes (IGF2 intron3‐g.3072G>A, MC4R p.D298N, VRTN PRE1 insertion, PRKAG3 p.I199V and FTO g.276T>G). Genotyping data were analysed grouping boars in eight classes according to their year of birth. To evaluate the influence of time...
Source: Journal of Animal Breeding and Genetics - March 1, 2015 Category: Genetics & Stem Cells Authors: L. Fontanesi, G. Schiavo, E. Scotti, G. Galimberti, D.G. Calò, A.B. Samorè, M. Gallo, V. Russo, L. Buttazzoni Tags: Original Article Source Type: research

Assessment of bagging GBLUP for whole‐genome prediction of broiler chicken traits
Summary Bootstrap aggregation (bagging) is a resampling method known to produce more accurate predictions when predictors are unstable or when the number of markers is much larger than sample size, because of variance reduction capabilities. The purpose of this study was to compare genomic best linear unbiased prediction (GBLUP) with bootstrap aggregated sampling GBLUP (Bagged GBLUP, or BGBLUP) in terms of prediction accuracy. We used a 600 K Affymetrix platform with 1351 birds genotyped and phenotyped for three traits in broiler chickens; body weight, ultrasound measurement of breast muscle and hen house egg production. ...
Source: Journal of Animal Breeding and Genetics - March 1, 2015 Category: Genetics & Stem Cells Authors: R. Abdollahi‐Arpanahi, G. Morota, B.D. Valente, A. Kranis, G.J.M. Rosa, D. Gianola Tags: Original Article Source Type: research

Genetic heteroscedasticity of teat count in pigs
Summary The genetic improvement in pig litter size has been substantial. The number of teats on the sow must thus increase as well to meet the needs of the piglets, because each piglet needs access to its own teat. We applied a genetic heterogeneity model to teat counts in pigs, and estimated a medium heritability for teat counts (0.35), but found a low heritability for residual variance (0.06), indicating that selection for reduced residual variance might have a limited effect. A numerically positive correlation (0.8) was estimated between the breeding values for the mean and the residual variance. However, because of the...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: M. Felleki, N. Lundeheim Tags: Original Article Source Type: research

Genetic analysis of river, swamp and hybrid buffaloes of north‐east India throw new light on phylogeography of water buffalo (Bubalus bubalis)
This study analysed buffaloes from north‐east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South‐East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north‐east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp‐type buffaloes of north‐east India with Lower Assamese (significantly hybrid type) buffaloes in one plane...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: B.P. Mishra, P.K. Dubey, B. Prakash, P. Kathiravan, S. Goyal, D.K. Sadana, G.C. Das, R.N. Goswami, V. Bhasin, B.K. Joshi, R.S. Kataria Tags: Original Article Source Type: research

Additive and epistatic genome‐wide association for growth and ultrasound scan measures of carcass‐related traits in Brahman cattle
This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three‐stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome‐wide epistasis analysis. We fitted these three‐stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits ...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: A.A. Ali, M.S. Khatkar, H.N. Kadarmideen, P.C. Thomson Tags: Invited Review Source Type: research

Sustainable dairy cattle selection in the genomic era
Summary Genomic selection offers considerable flexibility to increase genetic trends in dairy cattle breeding. It is also an opportunity for more sustainable breeding, in terms of breeding goal and genetic variability. With a shorter generation interval, there is a big risk of increasing inbreeding if semen dissemination policy of elite bulls is not changed. However, using a large number of young bulls as service bulls and bull sires is a solution for both maximizing genetic trend while reducing inbreeding trend. Female genotyping is a key challenge for within‐herd selection but, more importantly, for selection of new tr...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: D. Boichard, V. Ducrocq, S. Fritz Tags: Invited Review Source Type: research

Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits
We examined a range of traits in six populations amounting to 173 population‐trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree‐based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as ...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: A. Loberg, J. W. Dürr, W.F. Fikse, H. Jorjani, L. Crooks Tags: Original Article Source Type: research

Genetic conditions of joint Nordic genetic evaluations of lifetime competition performance in warmblood sport horses
Summary Breeding programmes for warmblood sport horses are similar in the Nordic countries Sweden, Denmark, Finland and Norway, and stallions of same origin are used. The aim was to investigate whether a joint Nordic genetic evaluation based on lifetime competition performance is feasible and beneficial for breeding competitive sport horses in the Nordic countries. Results for almost 45 000 horses in show jumping and 30 000 horses in dressage were available. The larger populations in Sweden and Denmark contributed with 85% of the results. Heritabilities and genetic correlations between performances in the different count...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: Å. Viklund, S. Furre, S. Eriksson, O. Vangen, J. Philipsson Tags: Original Article Source Type: research

Polynomial order selection in random regression models via penalizing adaptively the likelihood
Summary Orthogonal Legendre polynomials (LP) are used to model the shape of additive genetic and permanent environmental effects in random regression models (RRM). Frequently, the Akaike (AIC) and the Bayesian (BIC) information criteria are employed to select LP order. However, it has been theoretically shown that neither AIC nor BIC is simultaneously optimal in terms of consistency and efficiency. Thus, the goal was to introduce a method, ‘penalizing adaptively the likelihood’ (PAL), as a criterion to select LP order in RRM. Four simulated data sets and real data (60 513 records, 6675 Colombian Holstein cows) were em...
Source: Journal of Animal Breeding and Genetics - January 27, 2015 Category: Genetics & Stem Cells Authors: J.D. Corrales, S. Munilla, R.J.C. Cantet Tags: Original Article Source Type: research

Resemblance between two relatives – animal and plant breeding
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 26, 2015 Category: Genetics & Stem Cells Authors: C.C. Schön, H. Simianer Tags: Editorial Source Type: research

A method to approximate the inverse of a part of the additive relationship matrix
The objective of this study is to present a modification of the SP algorithm (RSP algorithm) and to assess its use in approximating when the actual is dense. The RSP algorithm sets up a restricted sparsity pattern of by limiting the pedigree search to a maximum number of searched branches. We have tested its use on four different simulated genotyped populations, from 10 000 to 75 000 genotyped animals. Accuracy of approximation is tested by replacing the actual by its approximation in an equivalent mixed model including only genotyped animals. Results show that limiting the pedigree search to four branches is enough to p...
Source: Journal of Animal Breeding and Genetics - December 1, 2014 Category: Genetics & Stem Cells Authors: P. Faux, N. Gengler Tags: Original Article Source Type: research

Genetic parameters for litter size, piglet growth and sow's early growth and body composition in the Chinese–European line Tai Zumu
Summary Genetics of piglet growth in association with sow's early growth and body composition were estimated in the Tai Zumu line. Piglet and sow's litter growth traits were calculated from individual weights collected at birth and at 3 weeks of age. Sow's litter traits included the number of piglets born alive (NBA), the mean piglet weight (MW) and the standard deviation of weights within the litter (SDW). Sow's early growth was measured by the age at 100 kg (A100), and body composition included backfat thickness (BF100). A main objective of this study was to estimate separately the direct genetic effect (d) and the mat...
Source: Journal of Animal Breeding and Genetics - November 26, 2014 Category: Genetics & Stem Cells Authors: M. Banville, J. Riquet, D. Bahon, M. Sourdioux, L. Canario Tags: Original Article Source Type: research

Acknowledgements to referees
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 14, 2014 Category: Genetics & Stem Cells Authors: Asko Mäki‐Tanila, Rodolfo Cantet, Ignacy Misztal, Miguel Pérez‐Enciso, Henner Simianer, Julius Werf Tags: Acknowledgements to Referees Source Type: research

Livestock genetic improvement in New Zealand – a world apart but a part of the world
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 14, 2014 Category: Genetics & Stem Cells Authors: P. Amer Tags: Editorial Source Type: research

Is the use of formulae a reliable way to predict the accuracy of genomic selection?
In conclusion, no rules can be applied to predict the reliability of genomic selection using these formulae. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - October 1, 2014 Category: Genetics & Stem Cells Authors: S. Brard, A. Ricard Tags: Original Article Source Type: research

An overview of animal science research 1945–2011 through science mapping analysis
Summary The conceptual structure of the field of Animal Science (AS) research is examined by means of a longitudinal science mapping analysis. The whole of the AS research field is analysed, revealing its conceptual evolution. To this end, an automatic approach to detecting and visualizing hidden themes or topics and their evolution across a consecutive span of years was applied to AS publications of the JCR category ‘Agriculture, Dairy & Animal Science’ during the period 1945–2011. This automatic approach was based on a coword analysis and combines performance analysis and science mapping. To observe the concept...
Source: Journal of Animal Breeding and Genetics - October 1, 2014 Category: Genetics & Stem Cells Authors: A. Rodriguez‐Ledesma, M.J. Cobo, C. Lopez‐Pujalte, E. Herrera‐Viedma Tags: Original Article Source Type: research

Accounting for unknown foster dams in the genetic evaluation of embryo transfer progeny
We present a method that allows including records of calves with unknown age of dam. Assumptions are as follows: (i) foster cows belong to the same breed being evaluated, (ii) there is no correlation between the breeding value (BV) of the calf and the maternal BV of the recipient cow, and (iii) cows of all ages are used as recipients. We examine the issue of bias for the fixed level of unknown age of dam (AOD) and propose an estimator of the effect based on classical measurement error theory (MEM) and a Bayesian approach. Using stochastic simulation under random mating or selection, the MEM estimating equations were compar...
Source: Journal of Animal Breeding and Genetics - October 1, 2014 Category: Genetics & Stem Cells Authors: M.J. Suárez, S. Munilla, R.J.C. Cantet Tags: Original Article Source Type: research

Estimates of genetic parameters associated with lactation feed intake and growth and composition traits measured during a performance test
Summary Days to reach 113.4 kg, adjusted backfat depth and adjusted loin muscle area to 113.4 kg were evaluated on pure‐bred Landrace (n = 15 660) and Yorkshire (n = 14 808) boars and gilts. Daily lactation feed intake (LFI) was recorded within parity records from pure‐bred Yorkshire (n = 1587) and Landrace (n = 2197) females during day 1–22 of lactation, and LFI curves were predicted using a mixed model. Evaluation of feed intake differences between 2 consecutive days of lactation resulted in the following periods: day 1–6 (PB1), day 7–10 (PB2) and day 11–18 (PB3). Average rate of change in intake ...
Source: Journal of Animal Breeding and Genetics - October 1, 2014 Category: Genetics & Stem Cells Authors: C.L. Yoder, V.M. Duttlinger, T.J. Baas Tags: Original Article Source Type: research

10th WCGALP in beautiful Vancouver
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 16, 2014 Category: Genetics & Stem Cells Authors: R.J.C. Cantet, O.F. Christensen, M. Pérez‐Enciso, J.H.J. Werf Tags: Review Source Type: research

Animal breeding strategies in Africa: current issues and the way forward
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 16, 2014 Category: Genetics & Stem Cells Authors: M. Wurzinger, T. Mirkena, J. Sölkner Tags: Editorial Source Type: research

Increasing imputation and prediction accuracy for Chinese Holsteins using joint Chinese–Nordic reference population
This study investigated the effect of including Nordic Holsteins in the reference population on the imputation accuracy and prediction accuracy for Chinese Holsteins. The data used in this study include 85 Chinese Holstein bulls genotyped with both 54K chip and 777K (HD) chip, 2862 Chinese cows genotyped with 54K chip, 510 Nordic Holstein bulls genotyped with HD chip, and 4398 Nordic Holstein bulls genotyped with 54K chip and with deregressed proofs for five milk production traits. Based on these data, the accuracy of imputation from 54K to HD marker data and the accuracy of genomic predictions in Chinese Holstein were ass...
Source: Journal of Animal Breeding and Genetics - August 6, 2014 Category: Genetics & Stem Cells Authors: P. Ma, M.S. Lund, X. Ding, Q. Zhang, G. Su Tags: Original Article Source Type: research

Estimation of ancestral inbreeding effects on stillbirth, calving ease and birthweight in German Holstein dairy cattle
In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction ...
Source: Journal of Animal Breeding and Genetics - August 6, 2014 Category: Genetics & Stem Cells Authors: D. Hinrichs, J. Bennewitz, R. Wellmann, G. Thaller Tags: Original Article Source Type: research

Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis
Summary The aim of this study was to compare correlation matrices between direct genomic predictions for 31 traits at the genomic and chromosomal levels in US Holstein bulls. Multivariate factor analysis carried out at the genome level identified seven factors associated with conformation, longevity, yield, feet and legs, fat and protein content traits. Some differences were found at the chromosome level; variations in covariance structure on BTA 6, 14, 18 and 20 were interpreted as evidence of segregating QTL for different groups of traits. For example, milk yield and composition tended to join in a single factor on BTA 1...
Source: Journal of Animal Breeding and Genetics - August 6, 2014 Category: Genetics & Stem Cells Authors: N.P.P. Macciotta, C. Dimauro, D.J. Null, G. Gaspa, M. Cellesi, J.B. Cole Tags: Original Article Source Type: research