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Journal of Animal Breeding and Genetics

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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

Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries
Summary Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population‐wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome‐wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount o...
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: E.C. Akanno, F.S. Schenkel, M. Sargolzaei, R.M. Friendship, J.A.B. Robinson Tags: Original Article Source Type: research

Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia
Summary Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high‐ versus low‐altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed usin...
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: Z. Edea, H. Dadi, S.‐W. Kim, J.‐H. Park, G.‐H. Shin, T. Dessie, K.‐S. Kim Tags: Original Article Source Type: research

Genome‐wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)
This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: M.H.A. Santana, Y.T. Utsunomiya, H.H.R. Neves, R.C. Gomes, J.F. Garcia, H. Fukumasu, S.L. Silva, P.R. Leme, L.L. Coutinho, J.P. Eler, J.B.S. Ferraz Tags: Original Article Source Type: research

Comparison of multiplicative heterogeneous variance adjustment models for genetic evaluations
Summary Two heterogeneous variance adjustment methods and two variance models were compared in a simulation study. The method used for heterogeneous variance adjustment in the Nordic test‐day model, which is a multiplicative method based on Meuwissen (J. Dairy Sci., 79, 1996, 310), was compared with a restricted multiplicative method where the fixed effects were not scaled. Both methods were tested with two different variance models, one with a herd‐year and the other with a herd‐year‐month random effect. The simulation study was built on two field data sets from Swedish Red dairy cattle herds. For both data sets, ...
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: Sz. Márkus, E.A. Mäntysaari, I. Strandén, J‐Å. Eriksson, M.H. Lidauer Tags: Original Article Source Type: research

Validation of biomarkers for loin meat quality (M. longissimus) of pigs
Summary The aim of this study was to validate previously reported associations between microarray gene expression levels and pork quality traits using real‐time PCR. Meat samples and meat quality data from 100 pigs were collected from a different pig breed to the one tested by microarray (Large White versus Pietrain) and a different country of origin (Denmark versus Germany). Ten genes (CARP, MB, CSRP3, TNNC1, VAPB, TNNI1, HSPB1, TNNT1, TIMP‐1, RAD‐like) were chosen from the original microarray study on the basis of the association between gene expression levels and the meat quality traits meat %, back fat, pH24, dri...
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: M. Pierzchala, A.J.W. Hoekman, P. Urbanski, L. Kruijt, L. Kristensen, J.F. Young, N. Oksbjerg, D. Goluch, M.F.W. te Pas Tags: Original Article Source Type: research

Investigating maternal effects on production traits in Duroc pigs using animal and sire models
Summary Variance components for production traits were estimated using different models to evaluate maternal effects. Data analysed were records from the South African pig performance testing scheme on 22 224 pigs from 18 herds, tested between 1990 and 2008. The traits analysed were backfat thickness (BFAT), test period weight gain (TPG), lifetime weight gain (LTG), test period feed conversion ratio (FCR) and age at slaughter (AGES). Data analyses were performed by REML procedures in ASREML, where random effects were successively fitted into animal and sire models to produce different models. The first animal model had on...
Source: Journal of Animal Breeding and Genetics - February 1, 2014 Category: Genetics & Stem Cells Authors: B. Dube, S.D. Mulugeta, K. Dzama Tags: Original Article Source Type: research

Optimizing the use of breed types in developing country livestock production systems: a neglected research area
Summary Developing country livestock production systems are diverse and dynamic, and include those where existing indigenous breeds are currently optimal and likely to remain so, those where non‐indigenous breed types are already in common use, and systems that are changing, such as by intensification, where the introduction of new breed types represents significant opportunities. These include opportunities to improve the livelihood of the world's poor, increase food and nutrition security and enhance environmental sustainability. At present, very little research has focused on this issue, such that significant knowledg...
Source: Journal of Animal Breeding and Genetics - January 28, 2014 Category: Genetics & Stem Cells Authors: K. Marshall Tags: Original Article Source Type: research

Dissection of additive genetic variability for quantitative traits in chickens using SNP markers
Summary The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The ...
Source: Journal of Animal Breeding and Genetics - January 25, 2014 Category: Genetics & Stem Cells Authors: R. Abdollahi‐Arpanahi, A. Pakdel, A. Nejati‐Javaremi, M. Moradi Shahrbabak, G. Morota, B.D. Valente, A. Kranis, G.J.M. Rosa, D. Gianola Tags: Original Article Source Type: research

Bioeconomic model and selection indices in Aberdeen Angus cattle
Summary A bioeconomic model was developed to calculate economic values for biological traits in full‐cycle production systems and propose selection indices based on selection criteria used in the Brazilian Aberdeen Angus genetic breeding programme (PROMEBO). To assess the impact of changes in the performance of the traits on the profit of the production system, the initial values ​​of the traits were increased by 1%. The economic values for number of calves weaned (NCW) and slaughter weight (SW) were, respectively, R$ 6.65 and R$ 1.43/cow/year. The selection index at weaning showed a 44.77% emphasis on body weight, 1...
Source: Journal of Animal Breeding and Genetics - January 20, 2014 Category: Genetics & Stem Cells Authors: G.S. Campos, J. Braccini Neto, R.P. Oaigen, F.F. Cardoso, J.A. Cobuci, E.L. Kern, L.T. Campos, C.D. Bertoli, C.M. McManus Tags: Original Article Source Type: research

Marbled Japanese Black cattle
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 12, 2014 Category: Genetics & Stem Cells Authors: H. Hirooka Tags: Editorial Source Type: research

Model averaging for genome‐enabled prediction with reproducing kernel Hilbert spaces: a case study with pig litter size and wheat yield
Summary Predictive ability of yet‐to‐be observed litter size (pig) grain yield (wheat) records of several reproducing kernel Hilbert spaces (RKHS) regression models combining different number of Gaussian or t kernels was evaluated. Predictive performance was assessed as the average (over 50 replicates) predictive correlation in the testing set. Predictions from these models were combined using three different types of model averaging: (i) mean of predicted phenotypes obtained in each model, (ii) weighted average using mean squared error as weight or (iii) using the marginal likelihood as weight. (ii) and (iii) were obt...
Source: Journal of Animal Breeding and Genetics - January 8, 2014 Category: Genetics & Stem Cells Authors: L. Tusell, P. Pérez‐Rodríguez, S. Forni, D. Gianola Tags: Original Article Source Type: research

A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations
Summary Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)‐analysis is a tool for aggregating information from multiple independent studies. The aim of this study was to identify loci underlying variation in FEC, as an indicator of nematode resistance, in a joint analysis using data from three populations (Scottish Blackface, Sarda × Lacaune and Martinik Black‐Belly × Romane), geno...
Source: Journal of Animal Breeding and Genetics - January 8, 2014 Category: Genetics & Stem Cells Authors: V. Riggio, R. Pong‐Wong, G. Sallé, M.G. Usai, S. Casu, C.R. Moreno, O. Matika, S.C. Bishop Tags: Original Article Source Type: research

Genomic relationships computed from either next‐generation sequence or array SNP data
Summary The use of sequence data in genomic prediction models is a topic of high interest, given the decreasing prices of current ‘next’‐generation sequencing technologies (NGS) and the theoretical possibility of directly interrogating the genomes for all causal mutations. Here, we compare by simulation how well genetic relationships (G) could be estimated using either NGS or ascertained SNP arrays. DNA sequences were simulated using the coalescence according to two scenarios: a ‘cattle’ scenario that consisted of a bottleneck followed by a split in two breeds without migration, and a ‘pig’ model where Chines...
Source: Journal of Animal Breeding and Genetics - January 8, 2014 Category: Genetics & Stem Cells Authors: M. Pérez‐Enciso Tags: Original Article Source Type: research

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans
Summary Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst S...
Source: Journal of Animal Breeding and Genetics - January 8, 2014 Category: Genetics & Stem Cells Authors: E. Ceh, P. Dovc Tags: Original Article Source Type: research

Effect of allele frequencies, effect sizes and number of markers on prediction of quantitative traits in chickens
The objective was to assess goodness of fit and predictive ability of subsets of single nucleotide polymorphism (SNP) markers constructed based on minor allele frequency (MAF), effect sizes and varying marker density. Target traits were body weight (BW), ultrasound measurement of breast muscle (BM) and hen house egg production (HHP) in broiler chickens. We used a 600 K Affymetrix platform with 1352 birds genotyped. The prediction method was genomic best linear unbiased prediction (GBLUP) with 354 564 single nucleotide polymorphisms (SNPs) used to derive a genomic relationship matrix (G). Predictive ability was assessed a...
Source: Journal of Animal Breeding and Genetics - January 8, 2014 Category: Genetics & Stem Cells Authors: R. Abdollahi‐Arpanahi, A. Nejati‐Javaremi, A. Pakdel, M. Moradi‐Shahrbabak, G. Morota, B.D. Valente, A. Kranis, G.J.M. Rosa, D. Gianola Tags: Original Article Source Type: research