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Journal of Animal Breeding and Genetics

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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

Estimation of inbreeding and effective population size of full‐blood wagyu cattle registered with the American Wagyu Cattle Association
The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST) and the effective population size (Ne) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle po...
Source: Journal of Animal Breeding and Genetics - December 20, 2013 Category: Genetics & Stem Cells Authors: E. Scraggs, R. Zanella, A. Wojtowicz, J.F. Taylor, C.T. Gaskins, J.J. Reeves, J.M. Avila, H.L. Neibergs Tags: Original Article Source Type: research

Transcript level of the porcine ME1 gene is affected by SNP in its 3′UTR, which is also associated with subcutaneous fat thickness
Summary Pork quality depends on multiple factors, including fatty acid composition in muscle and fat tissues. The ME1 gene is a strong candidate for fat accumulation, as it encodes the malic enzyme, which is required for fatty acid synthesis. We identified seven new polymorphisms in 3′UTR of the ME1 gene and moreover confirmed the presence of 4 polymorphisms detected previously. Interestingly, the studied Duroc pigs were monomorphic at all these polymorphic sites, while in 3 other breeds (Pietrain, Polish Landrace and Polish Large White), the polymorphisms were unevenly distributed. One of the novel SNPs (c.*488A>G) w...
Source: Journal of Animal Breeding and Genetics - December 20, 2013 Category: Genetics & Stem Cells Authors: M. Bartz, B. Kociucka, M. Mankowska, M. Switonski, M. Szydlowski Tags: Original Article Source Type: research

The coefficient of dominance is not (always) estimable with biallelic markers
Summary The genetic relationship among individuals at one locus is characterized by nine coefficients of identity. The coefficients of inbreeding, coancestry and dominance (or fraternity) are just linear functions of them. Here, it is shown how they can be estimated using biallelic and triallelic markers using the method of moments, and comparisons are made with other methods based on molecular coancestry or molecular covariance. It is concluded that in the general case of dominance and inbreeding with biallelic markers, only the coefficients of inbreeding and coancestry can be estimated, but neither the single coefficient...
Source: Journal of Animal Breeding and Genetics - December 1, 2013 Category: Genetics & Stem Cells Authors: L.A. García‐Cortés, A. Legarra, M.A. Toro Tags: Original Article Source Type: research

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations
Summary The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1)...
Source: Journal of Animal Breeding and Genetics - December 1, 2013 Category: Genetics & Stem Cells Authors: L.D. Pham, D.N. Do, L.Q. Nam, N. Van Ba, L.T.A. Minh, T.X. Hoan, V.C. Cuong, H.N. Kadarmideen Tags: Original Article Source Type: research

Within‐ and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium‐ and low‐density genotypes
The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower‐ to higher‐density genotypes in dairy and beef cattle. High‐density genotypes consisting of 777 962 single‐nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein‐Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151...
Source: Journal of Animal Breeding and Genetics - December 1, 2013 Category: Genetics & Stem Cells Authors: D.P. Berry, M.C. McClure, M.P. Mullen Tags: Original Article Source Type: research

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding, extensive loss of genetic diversity and lack of correlation between inbreeding and health
Summary One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid‐20th century and comprise 5–10 generations and 1 000–50 000 individuals per pedigree over our study period of 19...
Source: Journal of Animal Breeding and Genetics - December 1, 2013 Category: Genetics & Stem Cells Authors: M. Jansson, L. Laikre Tags: Original Article Source Type: research

A genome‐wide association study for canine cryptorchidism in Siberian Huskies
Summary Cryptorchidism is a condition whereby one or both testes fail to descend into the scrotal sac. Here, we performed a genome‐wide association study (GWAS) with both a case–control analysis using the GEMMA software accounting for population structure and a BayesB approach in the GenSel software applied to every 1 Mb window of SNPs or haplotypes. The haplotypes were constructed from a genealogical tree using the population of 204 Siberian Huskies. The BayesB analyses identified six putative genomic candidate regions on CFA6, 9, 24, 27 and X. These regions explained a high percentage of genetic variance when compar...
Source: Journal of Animal Breeding and Genetics - November 28, 2013 Category: Genetics & Stem Cells Authors: X. Zhao, S. Onteru, M. Saatchi, D. Garrick, M. Rothschild Tags: Original Article Source Type: research

Cluster and meta‐analyses of genetic parameters for feed intake traits in growing beef cattle
Summary A data set based on 50 studies including feed intake and utilization traits was used to perform a meta‐analysis to obtain pooled estimates using the variance between studies of genetic parameters for average daily gain (ADG); residual feed intake (RFI); metabolic body weight (MBW); feed conversion ratio (FCR); and daily dry matter intake (DMI) in beef cattle. The total data set included 128 heritability and 122 genetic correlation estimates published in the literature from 1961 to 2012. The meta‐analysis was performed using a random effects model where the restricted maximum likelihood estimator was used to eva...
Source: Journal of Animal Breeding and Genetics - November 24, 2013 Category: Genetics & Stem Cells Authors: I.D.P.S. Diaz, D.H. Crews, R.M. Enns Tags: Original Article Source Type: research

Heritabilities and genetic correlations between fetlock, hock and stifle osteochondrosis and fetlock osteochondral fragments in Hanoverian Warmblood horses
Summary The main objective of this study is to estimate genetic parameters for osteochondrosis (OC) and osteochondrosis dissecans (OCD) in fetlock, hock and stifle joints as well as for palmar or plantar osteochondral fragments (POFs) and dorsodistal osteochondral fragments (DOFs) in fetlock joints. For this purpose, the results of a standardized radiographic examination of 7396 Hanoverian Warmblood horses were used. Heritabilities and genetic correlations were estimated using residual maximum likelihood (REML) under a linear animal model. Heritability estimates for OC at the different joints were at 0.17–0.34, for OCD a...
Source: Journal of Animal Breeding and Genetics - November 19, 2013 Category: Genetics & Stem Cells Authors: D. Hilla, O. Distl Tags: Original Article Source Type: research

Acknowledgements to referees
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 17, 2013 Category: Genetics & Stem Cells Tags: Referee List Source Type: research

Exploring the potential of hierarchical generalized linear models in animal breeding and genetics
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 17, 2013 Category: Genetics & Stem Cells Authors: L. Rönnegård, Y. Lee Tags: Editorial Source Type: research

MyoD and Myf6 gene expression patterns in skeletal muscle during embryonic and posthatch development in the domestic duck (Anas platyrhynchos domestica)
The objective of this study was to evaluate MyoD and Myf6 gene expression patterns in the skeletal muscle during early developmental stage of ducks. Gene expression levels were detected using the quantitative RT‐PCR method in the breast muscle (BM) and leg muscle (LM) at embryonic days 13, 17, 21, 25, 27, as well as at 1 week posthatching in Gaoyou and Jinding ducks (Anas platyrhynchos domestica). The MyoD and Myf6 gene profiles in the two duck breeds were consistent during early development, and MyoD gene expression showed a ‘wave’ trend in BM and an approximate ‘anti‐√’ trend in LM. Myf6 gene expression in...
Source: Journal of Animal Breeding and Genetics - October 1, 2013 Category: Genetics & Stem Cells Authors: H. Li, C. Zhu, Z. Tao, W. XU, W. Song, Y. Hu, W. Zhu, C. Song Tags: Original Article Source Type: research