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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

Application of supernodal sparse factorization and inversion to the estimation of (co)variance components by residual maximum likelihood
Summary We demonstrated that supernodal techniques were more efficient than traditional methods for factorization and inversion of a coefficient matrix of mixed model equations (MME), which are often required in residual maximum likelihood (REML). Supernodal left‐looking and inverse multifrontal algorithms were employed for sparse factorization and inversion, respectively. The approximate minimum degree or multilevel nested dissection was used for ordering. A new computer package, Yet Another MME Solver (yams), was developed and compared with fspak with respect to computing time and size of temporary memory for 13 test m...
Source: Journal of Animal Breeding and Genetics - October 1, 2013 Category: Genetics & Stem Cells Authors: Y. Masuda, T. Baba, M. Suzuki Tags: Original Article Source Type: research

Assessing the impact of genomic selection against hip dysplasia in the Labrador Retriever dog
In this study, we have compared the utilities and performances of both genomic and phenotypic selection against hip dysplasia in a simulated population with the characteristics of the British Veterinary Association and Kennel Club (BVA/KC) hip dysplasia scheme. The results confirm the potential benefits of genomic selection by showing a moderate increase of 1.15‐fold (assuming a realistic accuracy of r2 = 0.5) in response to selection due to the higher accuracy (between 0.96‐ and 1.32‐fold, considering 0.35 ≤ r2 ≤ 0.7) and more than a threefold increase when all the offspring in each litter are tested (betw...
Source: Journal of Animal Breeding and Genetics - October 1, 2013 Category: Genetics & Stem Cells Authors: E. Sánchez‐Molano, J.A. Woolliams, S.C. Blott, P. Wiener Tags: Original Article Source Type: research

Analyses of genetic diversity in five Canadian dairy breeds using pedigree data
The objective of this study was to analyze the trend in within‐breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective populat...
Source: Journal of Animal Breeding and Genetics - October 1, 2013 Category: Genetics & Stem Cells Authors: M.G. Melka, K. Stachowicz, F. Miglior, F.S. Schenkel Tags: Original Article Source Type: research

Sequencing millions of animals for genomic selection 2.0
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 15, 2013 Category: Genetics & Stem Cells Authors: J. M. Hickey Tags: Editorial Source Type: research

Inheritance of ectopic ureters in Entlebucher Mountain Dogs
Summary To test the hypothesis of a heritable base of ectopic ureters (EU) in Entlebucher Mountain Dogs (EMD) and to elucidate associated risk factors and mode of inheritance of the disease, 565 EMD were clinically investigated and population genetic analyses performed. Based on the location of the most caudal termination of the ureteral openings, 552 EMD were classified into three phenotype groups trigone, intravesically and extravesically ectopic based on results of abdominal sonography, urethra‐cystoscopy and/or contrast‐enhanced computed tomography. One‐third (32.9%) of the phenotyped animals had normal terminati...
Source: Journal of Animal Breeding and Genetics - September 10, 2013 Category: Genetics & Stem Cells Authors: R. Fritsche, G. Dolf, C. Schelling, S. O. Hungerbuehler, R. Hagen, I. M. Reichler Tags: Original Article Source Type: research

Interplay between heritability, genetic correlation and economic weighting in a selection index with and without genomic information
Summary The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h2), genetic correlation () and economic weighting of traits with regard to the standard deviation of the index (σI). As σI is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. In...
Source: Journal of Animal Breeding and Genetics - August 29, 2013 Category: Genetics & Stem Cells Authors: A.M. Haberland, E.C.G. Pimentel, F. Ytournel, M. Erbe, H. Simianer Tags: Original Article Source Type: research

Genomewide association for a dominant pigmentation gene in sheep
The objective here was to assess the feasibility of performing GWAS for a dominant trait for which the genetic basis was already known. A total of 42 Manchega and Rasa Aragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP50 BeadChip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC1R gene, setting an a priori expectation for GWAS. Multiple methods were used to identify and quantify the strength of population substructure between black and white animals, before allelic association testing was performed for 49...
Source: Journal of Animal Breeding and Genetics - August 26, 2013 Category: Genetics & Stem Cells Authors: J.W. Kijas, M. Serrano, R. McCulloch, Y. Li, J. Salces Ortiz, J.H. Calvo, M.D. Pérez‐Guzmán, Tags: Original Article Source Type: research

Genetic background of claw disorders in the course of lactation and their relationships with type traits
Summary Random regression threshold animal models were applied to binary longitudinal claw disorder data for studying genetic parameters of all claw disorders (ACD), as well as to claw disorders divided into different categories: non‐purulent claw disorders (NPCD), purulent claw disorders (PCD), dermatitis digitalis (DD), sole ulcer (SU), phlegmona (PH), laminitis (LAM) and interdigital hyperplasia (IH) in the course of lactation. Claw disorder data were obtained from 26 651 Holstein cows kept in 15 large‐scale contract herds in the region of Thuringia over a period of 5 years from 2007 to 2012. If a cow had one or m...
Source: Journal of Animal Breeding and Genetics - August 5, 2013 Category: Genetics & Stem Cells Authors: E. Gernand, D.A. Döhne, S. König Tags: Original Article Source Type: research

Analyzes of genetic diversity in five Canadian dairy breeds using pedigree data
The objective of this study was to analyze the trend in within‐breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective populat...
Source: Journal of Animal Breeding and Genetics - August 1, 2013 Category: Genetics & Stem Cells Authors: M.G. Melka, K. Stachowicz, F. Miglior, F.S. Schenkel Tags: Original Article Source Type: research

Polymorphisms in the promoter region of myostatin gene are associated with carcass traits in pigs
This study confirmed evidence that MSTN g.435G>A and g.447A>G affected carcass traits in pigs. The effects of the mutated alleles were additive with the maximal effects resulting from two copies of the mutated allele. Selection for MSTN g.435A/g.447G allele is expected to increase muscle of limb and total meat production and decrease backfat thickness. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - August 1, 2013 Category: Genetics & Stem Cells Authors: P.‐A. Tu, L.‐L. Lo, Y.‐C. Chen, C.‐C. Hsu, J.‐W. Shiau, E.‐C. Lin, R.‐S. Lin, P.‐H. Wang Tags: Original Article Source Type: research

Genetic parameters for linear type traits in the Rendena dual‐purpose breed
Summary The aim of the study was to estimate the genetic parameters for five composite traits and 20 individual type traits on 10 735 first‐parity Rendena dual‐purpose cows. Fixed effects included in the linear animal mixed models were herd‐year‐classifier, days in milk and age at first calving; the additive genetic effect of the animal was included as a random effect. Heritability estimates varied from 0.12 (feet) to 0.52 (stature). Genetic correlations between the individual body size traits were all ≥0.69; similar strong genetic correlations existed between traits describing similar morphological characterist...
Source: Journal of Animal Breeding and Genetics - August 1, 2013 Category: Genetics & Stem Cells Authors: S. Mazza, N. Guzzo, C. Sartori, D.P. Berry, R. Mantovani Tags: Original Article Source Type: research

Consequences for diversity when animals are prioritized for conservation of the whole genome or of one specific allele
Summary When animals are selected for one specific allele, for example for inclusion in a gene bank, this may result in the loss of diversity in other parts of the genome. The aim of this study was to quantify the risk of losing diversity across the genome when targeting a single allele for conservation when storing animals in a gene bank. From a small Holstein population, genotyped for 54 001 SNP loci, animals were prioritized for a single allele while maximizing the genomewide diversity using optimal contribution selection. Selection for a single allele was done for five different target frequencies: (i) no restriction ...
Source: Journal of Animal Breeding and Genetics - August 1, 2013 Category: Genetics & Stem Cells Authors: K.A. Engelsma, R.F. Veerkamp, M.P.L. Calus, J.J. Windig Tags: Original Article Source Type: research

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red
Summary Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well‐documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, b...
Source: Journal of Animal Breeding and Genetics - August 1, 2013 Category: Genetics & Stem Cells Authors: T.C. Bray, S.J.G. Hall, M.W. Bruford Tags: Original Article Source Type: research

Livestock development in China: animal production, consumption and genetic resources
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 15, 2013 Category: Genetics & Stem Cells Authors: H. Yang Tags: Editorial Source Type: research

Genetic parameters of pelt character, feed efficiency and size traits in Finnish blue fox (Vulpes lagopus)
Summary Pelt character traits (size, quality, colour clarity, darkness) are important economic traits in blue fox breeding. Better feed efficiency (FE) is another economically important and new breeding goal for fur animals. The purpose of this study was to determine the correlations between pelt character traits, FE and size traits and to estimate genetic parameters for pelt character traits. Pelt size (pSIcm) had a high positive genetic correlation with animal grading size (gSI), final body weight (BWFin), body length and daily gain (DG), and a moderate correlation with body condition score (BCS). Animal body length and ...
Source: Journal of Animal Breeding and Genetics - June 17, 2013 Category: Genetics & Stem Cells Authors: R. Kempe, N. Koskinen, I. Strandén Tags: Original Article Source Type: research

Implementation of genetic evaluation and mating designs for the endangered local pig breed ‘Bunte Bentheimer’
Summary A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an eff...
Source: Journal of Animal Breeding and Genetics - June 6, 2013 Category: Genetics & Stem Cells Authors: A.D.M. Biermann, E.C.G. Pimentel, M. Tietze, T. Pinent, S. König Tags: Original Article Source Type: research

Allelic frequencies of PRKAG3 in several pig breeds and its technological consequences on a Duroc × Landrace‐Large White cross
Summary The allelic frequencies of PRKAG3 gene (the RN gene) have been investigated in several pig breeds. R200Q mutation appear only in Hampshire pigs, whereas V199I mutation is most abundant in Iberian, Porco Celta or Bizaro, and less in breeds selected for muscularity as Duroc, Landrace and Pietrain. A thorough study of phenotypic effects of V1991 has been performed in a Duroc × Landrace‐Large White cross. 199I homozygous pigs show increased pH24 values in ham homogenates and loin (0.14 and 0.16 pH units, respectively) compared to 199V homozygous ones. Meat of 199I homozygous pigs exudates 42.6% less fluid and is d...
Source: Journal of Animal Breeding and Genetics - June 1, 2013 Category: Genetics & Stem Cells Authors: A. Galve, C. Burgos, L. Varona, J.A. Carrodeguas, Á. Cánovas, P. López‐Buesa Tags: Original Article Source Type: research

An insight into population structure and gene flow within pure‐bred cats
Summary Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, F...
Source: Journal of Animal Breeding and Genetics - June 1, 2013 Category: Genetics & Stem Cells Authors: G. Leroy, E. Vernet, M.B. Pautet, X. Rognon Tags: Original Article Source Type: research