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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

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

A reaction norm model approach to estimate the genetic effect of temperature on sportive performance of trotter horses
Summary The performance results of Spanish Trotter Horses were merged with the information from the nearest official weather stations, to estimate the effects of temperature (T) on speed during the day of the race. The resulting data set included: 104 125 individual results from 7653 races with 3772 participant horses and driven by 1402 jockeys. After a classical repeatability animal model in which the effects of T were assumed null, a total of five different random regression models (RRM) with the same fixed part were applied in a parsimonious nested process in which the (co)variance components for each random effect wer...
Source: Journal of Animal Breeding and Genetics - August 1, 2014 Category: Genetics & Stem Cells Authors: M. Dolores Gómez, A. Menéndez‐Buxadera, M. Valera, A. Molina Tags: Original Article Source Type: research

Genetic associations between temperament and performance traits in Nellore beef cattle
Summary The aim of this study was to estimate genetic associations between temperament and performance traits. Temperament was evaluated in yearling male and female Nellore cattle, using four traits: temperament score (TS), for assessing animals’ reactions in a corral pen (n = 25 691); movement score (MOV), for animals’ movements recorded inside the crush; crush score (CS), for animal's general reactivity inside the crush; and flight speed (FS), for the speed (in m/s) at which the animals exited the crush (n = 11 697, for the last three methods); for all the temperament traits, lower scores indicate animals with ...
Source: Journal of Animal Breeding and Genetics - August 1, 2014 Category: Genetics & Stem Cells Authors: A.C. Sant'Anna, F. Baldi, T.S. Valente, L.G. Albuquerque, L.M. Menezes, A.A. Boligon, M.J.R. Paranhos da Costa Tags: Original Article Source Type: research

Breakeven prices for recording of indicator traits to reduce the environmental impact of milk production
Summary A breeding scheme using genomic selection and an indicator trait for environmental impact (EI) was studied to find the most effective recording strategy in terms of annual monetary genetic gain and breakeven price for the recording of indicator traits. The breakeven price shows the investment space for developing a recording system for an indicator trait. The breeding goal consisted of three traits – milk production, functional trait and environmental impact – with economic values of €83, €82 and €−83, respectively. The first scenario included only breeding goal traits and no indicator traits (NoIT). Th...
Source: Journal of Animal Breeding and Genetics - August 1, 2014 Category: Genetics & Stem Cells Authors: H. Hansen Axelsson, J.R. Thomasen, A.C. Sørensen, L. Rydhmer, M. Kargo, K. Johansson, W.F. Fikse Tags: Original Article Source Type: research

Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models
This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49 583 female calves born during 1998 and 2009 were considered in five age periods as days 1–30, 31–180, 181–365, 366–760 and full period (day 1–760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd‐year, genetic effect of sire or animal and residual). Rates of death ...
Source: Journal of Animal Breeding and Genetics - August 1, 2014 Category: Genetics & Stem Cells Authors: M. Forutan, S. Ansari Mahyari, M. Sargolzaei Tags: Original Article Source Type: research

Effective population size and inbreeding depression on litter size in rabbits. A case study
Summary The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some prac...
Source: Journal of Animal Breeding and Genetics - August 1, 2014 Category: Genetics & Stem Cells Authors: M. Ragab, J.P. Sánchez, M. Baselga Tags: Original Article Source Type: research

The effect of the ‘Gait keeper’ mutation in the DMRT3 gene on gaiting ability in Icelandic horses
Summary A nonsense mutation in DMRT3 (‘Gait keeper’ mutation) has a predominant effect on gaiting ability in horses, being permissive for the ability to perform lateral gaits and having a favourable effect on speed capacity in trot. The DMRT3 mutant allele (A) has been found in high frequency in gaited breeds and breeds bred for harness racing, while other horse breeds were homozygous for the wild‐type allele (C). The aim of this study was to evaluate further the effect of the DMRT3 nonsense mutation on the gait quality and speed capacity in the multigaited Icelandic horse and demonstrate how the frequencies of the A...
Source: Journal of Animal Breeding and Genetics - July 31, 2014 Category: Genetics & Stem Cells Authors: T. Kristjansson, S. Bjornsdottir, A. Sigurdsson, L.S. Andersson, G. Lindgren, S.J. Helyar, A.M. Klonowski, T. Arnason Tags: Original Article Source Type: research

Evaluation of the length of competitive life in Hungarian sport horses
Summary The aim of this study was to analyse the duration of the competitive life of jumping horses in Hungary to assess the potential for genetic evaluation and to get information about the risk factors affecting jumping performance of sport horses. The data set included lifetime performance in jumping competitions for 8475 horses born from 1992 onwards with records between 1996 and 2011 (32.7% were right‐censored). Longevity was measured as the number of years spent in the competition. Discrete time survival model included fixed effects of gender, age at first competition, and the time‐dependent effect of competition...
Source: Journal of Animal Breeding and Genetics - July 30, 2014 Category: Genetics & Stem Cells Authors: J. Posta, A. Rudiné Mezei, S. Mihók, G. Mészáros Tags: Original Article Source Type: research

Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs
Summary The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the PorcineSNP60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome‐wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis we...
Source: Journal of Animal Breeding and Genetics - July 22, 2014 Category: Genetics & Stem Cells Authors: P. Stratz, K. Wimmers, T.H.E. Meuwissen, J. Bennewitz Tags: Original Article Source Type: research

Differences between genomic‐based and pedigree‐based relationships in a chicken population, as a function of quality control and pedigree links among individuals
Summary This work studied differences between expected (calculated from pedigree) and realized (genomic, from markers) relationships in a real population, the influence of quality control on these differences, and their fit to current theory. Data included 4940 pure line chickens across five generations genotyped for 57 636 SNP. Pedigrees (5762 animals) were available for the five generations, pedigree starting on the first one. Three levels of quality control were used. With no quality control, mean difference between realized and expected relationships for different type of relationships was ≤ 0.04 with standard devia...
Source: Journal of Animal Breeding and Genetics - July 15, 2014 Category: Genetics & Stem Cells Authors: H. Wang, I. Misztal, A. Legarra Tags: Original Article Source Type: research

Genetic parameters for direct and maternal calving ease in Walloon dairy cattle based on linear and threshold models
Summary Calving ease scores from Holstein dairy cattle in the Walloon Region of Belgium were analysed using univariate linear and threshold animal models. Variance components and derived genetic parameters were estimated from a data set including 33 155 calving records. Included in the models were season, herd and sex of calf × age of dam classes × group of calvings interaction as fixed effects, herd × year of calving, maternal permanent environment and animal direct and maternal additive genetic as random effects. Models were fitted with the genetic correlation between direct and maternal additive genetic effects eith...
Source: Journal of Animal Breeding and Genetics - June 26, 2014 Category: Genetics & Stem Cells Authors: S. Vanderick, T. Troch, A. Gillon, G. Glorieux, N. Gengler Tags: Original Article Source Type: research

Sequence diversity and molecular evolutionary rates between buffalo and cattle
In this study, gene diversity between buffalo and cattle was determined using 86 gene orthologues. There was approximately 3% difference in all genes in terms of nucleotide diversity and 0.267 ± 0.134 in amino acids, indicating the possibility for successfully using cross‐species strategies for genomic studies. There were significantly higher non‐synonymous substitutions both in cattle and buffalo; however, there was similar difference in terms of dN– dS (4.414 versus 4.745) in buffalo and cattle, respectively. Higher rate of non‐synonymous substitutions at similar level in buffalo and cattle indicated a similar...
Source: Journal of Animal Breeding and Genetics - June 19, 2014 Category: Genetics & Stem Cells Authors: M. Moaeen‐ud‐Din, G. Bilal Tags: Original Article Source Type: research

Mitochondrial DNA diversity of Anatolian indigenous domestic goats
In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phyl...
Source: Journal of Animal Breeding and Genetics - June 18, 2014 Category: Genetics & Stem Cells Authors: I. Akis, K. Oztabak, A. Mengi, C. Un Tags: Original Article Source Type: research

North American animal breeding and production: meeting the needs of a changing landscape
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 18, 2014 Category: Genetics & Stem Cells Authors: H. Blackburn, Y. Plante Tags: Editorial Source Type: research

Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes
Summary Village‐ and central nucleus‐based schemes were simulated and evaluated for their relative bio‐economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village‐based 2‐tier (Scheme‐1) and 1‐tier (Scheme‐2) cooperative village breeding schemes, dispersed village‐based nuclei scheme (Scheme‐3), conventional 2‐tier central nucleus‐based scheme (Scheme‐4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme‐5) or in both central and village nuclei (Scheme‐6). Among village‐based schemes, Scheme‐1 gave the...
Source: Journal of Animal Breeding and Genetics - June 18, 2014 Category: Genetics & Stem Cells Authors: S. Gizaw, B. Rischkowsky, A. Valle‐Zárate, A. Haile, J.A.M. Arendonk, A.O. Mwai, T. Dessie Tags: Original Article Source Type: research

Supervised independent component analysis as an alternative method for genomic selection in pigs
The objective of this work was to evaluate the efficiency of the supervised independent component regression (SICR) method for the estimation of genomic values and the SNP marker effects for boar taint and carcass traits in pigs. The methods were evaluated via the agreement between the predicted genetic values and the corrected phenotypes observed by cross‐validation. These values were also compared with other methods generally used for the same purposes, such as RR‐BLUP, SPCR, SPLS, ICR, PCR and PLS. The SICR method was found to have the most accurate prediction values. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 1, 2014 Category: Genetics & Stem Cells Authors: C.F. Azevedo, F.F. Silva, M.D.V. Resende, M.S. Lopes, N. Duijvesteijn, S.E.F. Guimarães, P.S. Lopes, M.J. Kelly, J.M.S. Viana, E.F. Knol Tags: Original Article Source Type: research

Genomic additive and dominance variance of milk performance traits
The objective of this study was to estimate genetic variance components of production and milk component traits (e.g. acetone, fatty acids), which are particularly important for milk processing or which can provide information on the health status of cows. A genomic relationship approach was applied to phenotypic and genetic information of 1295 Holstein cows for estimating additive genetic and dominance variance components. Most of the 17 investigated traits were mainly affected by additive genetic effects, but protein content and casein content also showed a significant contribution of dominance. The ratio of dominance to...
Source: Journal of Animal Breeding and Genetics - June 1, 2014 Category: Genetics & Stem Cells Authors: D. Wittenburg, N. Melzer, N. Reinsch Tags: Original Article Source Type: research

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle
This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p‐value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p‐value for daily gain 0.007 and p‐value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additi...
Source: Journal of Animal Breeding and Genetics - June 1, 2014 Category: Genetics & Stem Cells Authors: S. Hartwig, R. Wellmann, H. Hamann, J. Bennewitz Tags: Original Article Source Type: research

Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes
This study showed that farmer cooperation is crucial to effect genetic improvement under smallholder low‐input sheep farming systems. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - June 1, 2014 Category: Genetics & Stem Cells Authors: S. Gizaw, J.A.M. Arendonk, A. Valle‐Zárate, A. Haile, B. Rischkowsky, T. Dessie, A.O. Mwai Tags: Original Article Source Type: research

Genetic variation in the ovine uncoupling protein 1 gene: association with carcass traits in New Zealand (NZ) Romney sheep, but no association with growth traits in either NZ Romney or NZ Suffolk sheep
Summary The uncoupling protein 1 (UCP1) plays an important role in the regulation of lipolysis and thermogenesis in adipose tissues. Genetic variation within three regions (the promoter, intron 2 and exon 5) of the ovine UCP1 gene (UCP1) was investigated using polymerase chain reaction‐single‐strand conformational polymorphism (PCR‐SSCP) analyses. These revealed three promoter variants (designated A, B and C) and two intron 2 variants (a and b). The association of this genetic variation with variation in lamb carcass traits and postweaning growth was investigated in New Zealand (NZ) Romney and Suffolk sheep. The pres...
Source: Journal of Animal Breeding and Genetics - June 1, 2014 Category: Genetics & Stem Cells Authors: G. Yang, R. Forrest, H. Zhou, S. Hodge, J. Hickford Tags: Original Article Source Type: research

Identification of the putative ancestral allele of bovine single‐nucleotide polymorphisms
We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19 551 488 SNPs and identified the putative ancestral allele for 14 339 107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic‐based approach to identify putative ancestral alleles is reliable. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 26, 2014 Category: Genetics & Stem Cells Authors: D. Rocha, C. Billerey, F. Samson, D. Boichard, M. Boussaha Tags: Original Article Source Type: research

On the genomic analysis of data from structured populations
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 18, 2014 Category: Genetics & Stem Cells Authors: G. Campos, D. Sorensen Tags: Editorial Source Type: research

Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle
Summary Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy‐tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy‐tail distributions (multivariate Student's t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle usi...
Source: Journal of Animal Breeding and Genetics - May 16, 2014 Category: Genetics & Stem Cells Authors: S.O. Peters, K. Kizilkaya, D.J. Garrick, R.L. Fernando, E.J. Pollak, R.M. Enns, M. De Donato, O.O. Ajayi, I.G. Imumorin Tags: Original Article Source Type: research

Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers
In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab‐Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab‐Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab‐Barb), respecti...
Source: Journal of Animal Breeding and Genetics - April 1, 2014 Category: Genetics & Stem Cells Authors: N. Berber, S. Gaouar, G. Leroy, S. Kdidi, N. Tabet Aouel, N. Saïdi Mehtar Tags: Original Article Source Type: research

Estimates of genetic parameters associated with lactation feed intake and reproductive performance in purebred and F1 sows
Summary Daily feed intake during lactation was recorded in parity records from purebred Yorkshire (n = 1587), Landrace (n = 2197) and reciprocal cross F1 (n = 6932) females, and lactation feed intake (LFI) curves were predicted using a mixed model. Evaluation of the difference in feed intake between two consecutive days of lactation resulted in the following classifications: three periods for purebreds, days 1–6, days 7–10 and days 11–18, and two periods for F1 sows, days 1–5 and days 6–18. Average rate of change in intake (ARC), average daily intake (ADI) and variation from predicted LFI values (VAR) were ...
Source: Journal of Animal Breeding and Genetics - April 1, 2014 Category: Genetics & Stem Cells Authors: C.L. Yoder, V.M. Duttlinger, T.J. Baas Tags: Original Article Source Type: research

Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices
This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G‐matrices) across these two breeds. Single‐trait genomic best linear unbiased prediction (GBLUP) model and two‐trait GBLUP model were used for single‐breed and two‐breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedi...
Source: Journal of Animal Breeding and Genetics - April 1, 2014 Category: Genetics & Stem Cells Authors: L. Zhou, M.S. Lund, Y. Wang, G. Su Tags: Original Article Source Type: research

BSE‐associated polymorphisms in the prion protein gene: an investigation
Summary The aim of this study was to determine the frequency of the 12‐bp and 23‐bp indel polymorphisms in the prion protein gene (PRNP) in cattle and to investigate the association between these frequencies and the occurrence of bovine spongiform encephalopathy (BSE). There was no significant difference in the 12‐bp indel frequency between the BSE animals and control group. For the 23‐bp indel, the BSE animals had a significantly lower + + (insins) genotype frequency and + allele frequency compared with the control animals. The − − / − − genotype frequency in the BSE animals was not significantly higher wh...
Source: Journal of Animal Breeding and Genetics - April 1, 2014 Category: Genetics & Stem Cells Authors: K. Vernerova, L. Tothova, A. Mikova, P. Vodrazka, B. Simek, L. Hanusova, J. Citek Tags: Original Article Source Type: research

Modelling genetic evaluation for dressage in Pura Raza Español horses with focus on the rider effect
Summary The most popular use of the Pura Raza Español horse in sport is for dressage competitions. Tests on young sport horses were first established in 2004 in Spain to collect data for the genetic evaluation of this breed's suitability for dressage. The aim of this study was to compare eight different models to find out the most appropriate way to include the rider in the genetic evaluation of dressage. A progressive removal of systematic effects from model was also analysed. A total of 8867 performance records collected between 2004 and 2011 from 1234 horses aged between 4 and 6 years old were used. The final score in...
Source: Journal of Animal Breeding and Genetics - March 28, 2014 Category: Genetics & Stem Cells Authors: M.J. Sánchez Guerrero, I. Cervantes, M. Valera, J.P. Gutiérrez Tags: Original Article Source Type: research

Genetic parameters for chronic progressive lymphedema in Belgian Draught Horses
Summary Genetic parameters for chronic progressive lymphedema (CPL)‐associated traits in Belgian Draught Horses were estimated, using a multitrait animal model. Clinical scores of CPL in the four limbs/horse (CPLclin), skinfold thickness and hair samples (hair diameter) were studied. Due to CPLclin uncertainty in younger horses (progressive CPL character), a restricted data set (D_3+) was formed, excluding records from horses under 3 years from the complete data set (D_full). Age, gender, coat colour and limb hair pigmentation were included as fixed, permanent environment and date of recording as random effects. Higher ...
Source: Journal of Animal Breeding and Genetics - March 20, 2014 Category: Genetics & Stem Cells Authors: K. De Keyser, S. Janssens, L.M. Peeters, N. Foqué, F. Gasthuys, M. Oosterlinck, N. Buys Tags: Original Article Source Type: research

Genome‐wide association study for egg production and quality in layer chickens
The objective of this study was to find genomic regions associated with egg production and quality traits in layers using analysis methods developed for the purpose of whole genome prediction. Genotypes on over 4500 birds and phenotypes on over 13 000 hens from eight generations of a brown egg layer line were used. Birds were genotyped with a custom 42K Illumina SNP chip. Recorded traits included two egg production and 11 egg quality traits (puncture score, albumen height, yolk weight and shell colour) at early and late stages of production, as well as body weight and age at first egg. Egg weight was previously analysed b...
Source: Journal of Animal Breeding and Genetics - March 17, 2014 Category: Genetics & Stem Cells Authors: A. Wolc, J. Arango, T. Jankowski, I. Dunn, P. Settar, J.E. Fulton, N.P. O'Sullivan, R. Preisinger, R.L. Fernando, D.J. Garrick, J.C.M. Dekkers Tags: Original Article Source Type: research

Genetics, genomics, breeding – why scale matters
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 16, 2014 Category: Genetics & Stem Cells Authors: H. Simianer, M. Erbe Tags: Editorial Source Type: research