Journal of Animal Breeding and Genetics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Genomic prediction of growth in pigs based on a model including additive and dominance effects
Summary Independent of whether prediction is based on pedigree or genomic information, the focus of animal breeders has been on additive genetic effects or ‘breeding values’. However, when predicting phenotypes rather than breeding values of an animal, models that account for both additive and dominance effects might be more accurate. Our aim with this study was to compare the accuracy of predicting phenotypes using a model that accounts for only additive effects (MA) and a model that accounts for both additive and dominance effects simultaneously (MAD). Lifetime daily gain (DG) was evaluated in three pig populations (...
Source: Journal of Animal Breeding and Genetics - December 16, 2015 Category: Genetics & Stem Cells Authors: M.S. Lopes, J.W.M. Bastiaansen, L. Janss, E.F. Knol, H. Bovenhuis Tags: Original Article Source Type: research

Growth traits of four maternal lines of rabbits founded on different criteria: comparisons at foundation and at last periods after selection
The objective was to compare growth traits in four maternal lines of rabbits (A, V, H and LP), with the aim of understanding the consequence of the different foundation and selection processes on the growth performance of the lines. The lines are currently in the 43th, 38th, 22th and 8th generations, respectively. Two comparisons were performed. One compared the values of the lines at their foundation, using the complete data set, the full pedigree and a two‐trait analysis, including data on the selection criteria, litter size. The other comparisons were done during the last period when all the lines were housed together...
Source: Journal of Animal Breeding and Genetics - December 16, 2015 Category: Genetics & Stem Cells Authors: C. Mínguez, J.P. Sanchez, A.G. EL Nagar, M. Ragab, M. Baselga Tags: Original Article Source Type: research

A combined coalescence gene‐dropping tool for evaluating genomic selection in complex scenarios (ms2gs)
We present ms2gs, a combined coalescence – gene dropping (i.e. backward–forward) simulator for complex traits. It therefore aims at combining the advantages of both approaches. It is primarily conceived for very short term, recent scenarios such as those that are of interest in animal and plant breeding. It is very flexible in terms of defining QTL architecture and SNP ascertainment bias, and it allows for easy modelling of alternative markers such as RADs. It can use real sequence or chip data or generate molecular polymorphisms via the coalescence. It can generate QTL conditional on extant molecular information, such...
Source: Journal of Animal Breeding and Genetics - December 1, 2015 Category: Genetics & Stem Cells Authors: M. Pérez‐Enciso, A. Legarra Tags: Original Article Source Type: research

Behavioural linear standardized scoring system of the Lidia cattle breed by testing in herd: estimation of genetic parameters
Summary Docility is very important for cattle production, and many behavioural tests to measure this trait have been developed. However, very few objective behavioural tests to measure the opposite approach ‘aggressive behaviour’ have been described. Therefore, the aim of this work was to validate in the Lidia cattle breed a behavioural linear standardized scoring system that measure the aggressiveness and enable genetic analysis of behavioural traits expressing fearless and fighting ability. Reproducibility and repeatability measures were calculated for the 12 linear traits of this scoring system to assess its accurac...
Source: Journal of Animal Breeding and Genetics - December 1, 2015 Category: Genetics & Stem Cells Authors: R. Pelayo, M. Solé, M.J. Sánchez, A. Molina, M. Valera Tags: Original Article Source Type: research

Identification of genome‐wide selection signatures in the Limousin beef cattle breed
Summary The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection foo...
Source: Journal of Animal Breeding and Genetics - November 27, 2015 Category: Genetics & Stem Cells Authors: A. Gurgul, T. Szmatoła, K. Ropka‐Molik, I. Jasielczuk, K. Pawlina, E. Semik, M. Bugno‐Poniewierska Tags: Original Article Source Type: research

Identification of genome ‐wide selection signatures in the Limousin beef cattle breed
Summary The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection foo...
Source: Journal of Animal Breeding and Genetics - November 25, 2015 Category: Genetics & Stem Cells Authors: A. Gurgul, T. Szmato ła, K. Ropka‐Molik, I. Jasielczuk, K. Pawlina, E. Semik, M. Bugno‐Poniewierska Tags: Original Article Source Type: research

An efficient empirical Bayes method for genomewide association studies
Summary Linear mixed model (LMM) is one of the most popular methods for genomewide association studies (GWAS). Numerous forms of LMM have been developed; however, there are two major issues in GWAS that have not been fully addressed before. The two issues are (i) the genomic background noise and (ii) low statistical power after Bonferroni correction. We proposed an empirical Bayes (EB) method by assigning each marker effect a normal prior distribution, resulting in shrinkage estimates of marker effects. We found that such a shrinkage approach can selectively shrink marker effects and reduce the noise level to zero for majo...
Source: Journal of Animal Breeding and Genetics - November 19, 2015 Category: Genetics & Stem Cells Authors: Q. Wang, J. Wei, Y. Pan, S. Xu Tags: Original Article Source Type: research

Modelling repeated competition records in genetic evaluations of Danish sport horses
Summary Genetic evaluations of sport performance typically consider competition records of ranking points in each competition, accumulated lifetime points or annual earnings. Repeated observations have the advantage of allowing for adjustment of effects associated with each competition such as rider experience, judge and competing horses, but also demands more computer capacity than single‐trait records, which could prohibit multiple‐trait evaluations. The aim of the study was to compare CPU times, estimated breeding values (EBVs), reliabilities and model prediction abilities when modelling repeated competition ranking...
Source: Journal of Animal Breeding and Genetics - November 18, 2015 Category: Genetics & Stem Cells Authors: L. Jönsson, P. Madsen, T. Mark Tags: Original Article Source Type: research

Genome‐wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip
Summary Genome‐wide association study results are presented for intramuscular fat in Italian Large White pig breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome‐wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1...
Source: Journal of Animal Breeding and Genetics - November 17, 2015 Category: Genetics & Stem Cells Authors: R. Davoli, D. Luise, V. Mingazzini, P. Zambonelli, S. Braglia, M. Serra, V. Russo Tags: Original Article Source Type: research

Genetic association between leg conformation in young pigs and sow longevity
Summary Longevity is important in pig production with respect to both economic and ethical aspects. Direct selection for longevity might be ineffective because ‘true’ longevity can only be recorded when a sow has been culled or died. Thus, indirect selection for longevity using information from other traits that can be recorded early in life and are genetically correlated with longevity might be an alternative. Leg conformation has been included in many breeding schemes for a number of years. However, proving that leg conformation traits are good early indicators for longevity still remains. Our aim was to study geneti...
Source: Journal of Animal Breeding and Genetics - November 17, 2015 Category: Genetics & Stem Cells Authors: T.H. Le, P. Madsen, N. Lundeheim, K. Nilsson, E. Norberg Tags: Original Article Source Type: research

Genome ‐wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip
Summary Genome‐wide association study results are presented for intramuscular fat in Italian Large White pig breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome‐wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1...
Source: Journal of Animal Breeding and Genetics - November 16, 2015 Category: Genetics & Stem Cells Authors: R. Davoli, D. Luise, V. Mingazzini, P. Zambonelli, S. Braglia, A. Serra, V. Russo Tags: Original Article Source Type: research

Acknowledgements to referees
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 10, 2015 Category: Genetics & Stem Cells Authors: Asko Mäki‐Tanila, Rodolfo Cantet, Ignacy Misztal, Miguel Pérez‐Enciso, Henner Simianer, Julius Werf Tags: Referee List Source Type: research

Ever‐growing data sets pose (new) challenges to genomic prediction models
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - November 10, 2015 Category: Genetics & Stem Cells Authors: M.P.L. Calus, J. Vandenplas, J. Ten Napel Tags: Editorial Source Type: research

Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle
In this study, fine mapping of this QTL was performed using imputed high‐density SNP chip (HD) genotypes followed by imputed next‐generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p‐value = 2.04 × 10−59 for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450–57 625 355) for associations with direct calving...
Source: Journal of Animal Breeding and Genetics - October 1, 2015 Category: Genetics & Stem Cells Authors: X. Mao, N.K. Kadri, J.R. Thomasen, D.J. De Koning, G. Sahana, B. Guldbrandtsen Tags: Original Article Source Type: research

Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya
Summary Phylogenetic relationships among and genetic variability within 60 goats from two different indigenous breeds in Narok and Isiolo counties in Kenya and 22 published goat samples were analysed using mitochondrial control region sequences. The results showed that there were 54 polymorphic sites in a 481‐bp sequence and 29 haplotypes were determined. The mean haplotype diversity and nucleotide diversity were 0.981 ± 0.006 and 0.019 ± 0.001, respectively. The phylogenetic analysis in combination with goat haplogroup reference sequences from GenBank showed that all goat sequences were clustered into two haplogro...
Source: Journal of Animal Breeding and Genetics - October 1, 2015 Category: Genetics & Stem Cells Authors: F.M. Kibegwa, K.E. Githui, J.O. Jung'a, M.S. Badamana, M.N. Nyamu Tags: Original Article Source Type: research