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Genomewide association study of immune traits in chicken F2 resource population
In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10−6) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10−5) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10−5) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven su...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: Y. Sun, Q. Li, Y. Hu, Y. Sun, R. Liu, M. Zheng, J. Wen, P. Li, L. Liu, G. Zhao Tags: Original Article Source Type: research

Accounting for genetic architecture in single‐ and multipopulation genomic prediction using weights from genomewide association studies in pigs
Summary We studied the effect of including GWAS results on the accuracy of single‐ and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights...
Source: Journal of Animal Breeding and Genetics - February 1, 2016 Category: Genetics & Stem Cells Authors: R. Veroneze, P.S. Lopes, M.S. Lopes, A.M. Hidalgo, S.E.F. Guimarães, B. Harlizius, E.F. Knol, J.A.M. Arendonk, F.F. Silva, J.W.M. Bastiaansen Tags: Original Article Source Type: research

Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers
Summary There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian ...
Source: Journal of Animal Breeding and Genetics - January 18, 2016 Category: Genetics & Stem Cells Authors: M. Heidaritabar, M.P.L. Calus, H‐J. Megens, A. Vereijken, M.A.M. Groenen, J.W.M. Bastiaansen Tags: Original Article Source Type: research

On genetic canalization, infinitesimal model and whole‐genome sequence data
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - January 14, 2016 Category: Genetics & Stem Cells Authors: J. Ødegård, T. Meuwissen Tags: Editorial Source Type: research

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

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

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

Rates of inbreeding and genetic adaptation for populations managed as herds in zoos with a rotational mating system or with optimized contribution of parents
This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned ...
Source: Journal of Animal Breeding and Genetics - October 1, 2015 Category: Genetics & Stem Cells Authors: S. Mucha, H. Komen Tags: Original Article Source Type: research

Cow‐specific diet digestibility predictions based on near‐infrared reflectance spectroscopy scans of faecal samples
This study was designed to obtain information on prediction of diet digestibility from near‐infrared reflectance spectroscopy (NIRS) scans of faecal spot samples from dairy cows at different stages of lactation and to develop a faecal sampling protocol. NIRS was used to predict diet organic matter digestibility (OMD) and indigestible neutral detergent fibre content (iNDF) from faecal samples, and dry matter digestibility (DMD) using iNDF in feed and faecal samples as an internal marker. Acid‐insoluble ash (AIA) as an internal digestibility marker was used as a reference method to evaluate the reliability of NIRS predic...
Source: Journal of Animal Breeding and Genetics - September 28, 2015 Category: Genetics & Stem Cells Authors: T. Mehtiö, M. Rinne, L. Nyholm, P. Mäntysaari, A. Sairanen, E.A. Mäntysaari, T. Pitkänen, M.H. Lidauer Tags: Original Article Source Type: research

Breeding implications resulting from classification of patellae luxation in dogs
Summary Patellar luxation (PL) is one of the major hereditary orthopaedic abnormalities observed in a variety of dog breeds. When the patellae move sideways out of the trochlear groove, this is called PL. The PL score varies between dogs from normal to very severe. Reducing the prevalence of PL by breeding could prevent surgery, thereby improve welfare. Orthopaedic specialists differentiate between normal and loose patellae, where the patellae can be moved to the edge of the trochlear groove, considering scoring loose patellae as normal in the future. Loose patellae are considered acceptable for breeding so far by the bree...
Source: Journal of Animal Breeding and Genetics - September 25, 2015 Category: Genetics & Stem Cells Authors: E.M. Grevenhof, H.A.W. Hazewinkel, H.C.M. Heuven Tags: Original Article Source Type: research

Will models of genetic evaluation and genomic selection ‘converge’?
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - September 17, 2015 Category: Genetics & Stem Cells Authors: R.J.C. Cantet Tags: Editorial Source Type: research

Lack of haplotype structuring for two candidate genes for trypanotolerance in cattle
Summary Bovine trypanotolerance is a heritable trait associated to the ability of the individuals to control parasitaemia and anaemia. The INHBA (BTA4) and TICAM1 (BTA7) genes are strong candidates for trypanotolerance‐related traits. The coding sequence of both genes (3951 bp in total) were analysed in a panel including 79 Asian, African and European cattle (Bos taurus and B. indicus) to identify naturally occurring polymorphisms on both genes. In general, the genetic diversity was low. Nineteen of the 33 mutations identified were found just one time. Seventeen different haplotypes were defined for the TICAM1 gene, and...
Source: Journal of Animal Breeding and Genetics - August 1, 2015 Category: Genetics & Stem Cells Authors: I. Álvarez, L. Pérez‐Pardal, A. Traoré, I. Fernández, F. Goyache Tags: Original Article Source Type: research

Genetic relationships among American donkey populations: insights into the process of colonization
This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model‐based metho...
Source: Journal of Animal Breeding and Genetics - August 1, 2015 Category: Genetics & Stem Cells Authors: J. Jordana, A. Ferrando, J. Miró, F. Goyache, A. Loarca, O.R. Martínez López, J.L. Canelón, A. Stemmer, L. Aguirre, M.A.C. Lara, L.A. Álvarez, S. Llambí, N. Gómez, L.T. Gama, M.F. Nóvoa, R.D. Martínez, E. Pérez, A. Sierra, M.A. Contreras, A.M. G Tags: Original Article Source Type: research

How many markers are enough? Factors influencing parentage testing in different livestock populations
Summary Reliability of parentage test panels is usually based on its power to exclude wrong parentage assignments based on allele frequencies. We evaluated the rates of false exclusions and inclusions in parentage assignments, and how these results are affected by allele frequencies, panel sizes and the number of allowed mismatches. We also evaluated the reliability of parentage testing by comparing populations with distinct genetic backgrounds using pure and composite families of cattle and sheep. Allowing for 1% genotype mismatches in true parent–offspring relations provided the best compromise between false‐positive...
Source: Journal of Animal Breeding and Genetics - August 1, 2015 Category: Genetics & Stem Cells Authors: E.M. Strucken, S.H. Lee, H.K. Lee, K.D. Song, J.P. Gibson, C. Gondro Tags: Original Article Source Type: research

Optimizing selection with several constraints in poultry breeding
Summary Poultry breeding schemes permanently face the need to control the evolution of coancestry and some critical traits, while selecting for a main breeding objective. The main aims of this article are first to present an efficient selection algorithm adapted to this situation and then to measure how the severity of constraints impacted on the degree of loss for the main trait, compared to BLUP selection on the main trait, without any constraint. Broiler dam and sire line schemes were mimicked by simulation over 10 generations and selection was carried out on the main trait under constraints for coancestry and for anoth...
Source: Journal of Animal Breeding and Genetics - July 30, 2015 Category: Genetics & Stem Cells Authors: H. Chapuis, C. Pincent, J.J. Colleau Tags: Original Article Source Type: research

Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress
In conclusion, specific genetic markers responsible for genetic variation in thermoregulation during heat stress in Holsteins were identified. These markers may prove useful in genetic selection for heat tolerance in Holstein cattle. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 22, 2015 Category: Genetics & Stem Cells Authors: S. Dikmen, X.‐z. Wang, M.S. Ortega, J.B. Cole, D.J. Null, P.J. Hansen Tags: Original Article Source Type: research

Genetic analysis of sow longevity and sow lifetime reproductive traits using censored data
Summary Sow longevity is a key component for efficient and profitable pig farming; however, approximately 50% of sows are removed annually from a breeding herd. There is no consensus in the scientific literature regarding a definition for sow longevity; however, it has been suggested that it can be measured using several methods such as stayability and economic indicators such as lifetime piglets produced. Sow longevity can be improved by genetic selection; however, it is rarely included in genetic evaluations. One reason is elongated time intervals required to collect complete lifetime data. The effect of genetic paramete...
Source: Journal of Animal Breeding and Genetics - July 15, 2015 Category: Genetics & Stem Cells Authors: L. Engblom, J.A. Calderón Díaz, M. Nikkilä, K. Gray, P. Harms, J. Fix, S. Tsuruta, J. Mabry, K. Stalder Tags: Original Article Source Type: research

Genetic control of the environmental variance for birth weight in seven generations of a divergent selection experiment in mice
This study has demonstrated that the genetic control of the birth weight environmental variability is possible in mice. Nevertheless, before the results are applied directly in farm animals, it would be worth confirming any other implications on other important traits, such as robustness, longevity and welfare. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 7, 2015 Category: Genetics & Stem Cells Authors: N. Formoso‐Rafferty, I. Cervantes, N. Ibáñez‐Escriche, J.P. Gutiérrez Tags: Original Article Source Type: research

An important anniversary: 150 years since Mendel's laws of inheritance made their first public appearance
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - July 3, 2015 Category: Genetics & Stem Cells Authors: F.W. Nicholas, A. Mäki‐Tanila Tags: Editorial Source Type: research

Genetic selection for increased mean and reduced variance of twinning rate in Belclare ewes
Summary It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records fro...
Source: Journal of Animal Breeding and Genetics - June 16, 2015 Category: Genetics & Stem Cells Authors: D.J. Cottle, A.R. Gilmour, T. Pabiou, P.R. Amer, A.G. Fahey Tags: Original Article Source Type: research

Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed
Summary The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X‐linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX = 0.46 and 0.22 and FX = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non‐founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effecti...
Source: Journal of Animal Breeding and Genetics - June 8, 2015 Category: Genetics & Stem Cells Authors: L. Silió, C. Barragán, A.I. Fernández, J. García‐Casco, M.C. Rodríguez Tags: Original Article Source Type: research

Two single nucleotide polymorphisms in the promoter of the ovine myostatin gene (MSTN) and their effect on growth and carcass muscle traits in New Zealand Romney sheep
Summary Myostatin is a negative regulator of muscle growth and development in mammals, and variation in ovine myostatin gene (MSTN) has been demonstrated to be associated with variation in the muscularity of sheep. Polymerase chain reaction–single‐stranded conformational polymorphism (PCR–SSCP) was used to look for single nucleotide polymorphisms (SNPs) in a 304‐bp amplicon from the promoter region of ovine MSTN. Sequence analyses revealed two previously identified SNPs (c.−2449G/C and c. −2379T/C) that resulted in three haplotypes (H1 (c.[−2449G; −2379C]), H2 (c.[−2449C; −2379C]) and H3 (c.[−2449G; ...
Source: Journal of Animal Breeding and Genetics - June 1, 2015 Category: Genetics & Stem Cells Authors: J. Wang, H. Zhou, J. Hu, S. Li, Y. Luo, J.G.H. Hickford Tags: Original Article Source Type: research

Breeding for better eye health in Finnish blue fox (Vulpes lagopus)
Summary The frequency of eye infections in the Finnish blue fox population has increased during the past decade. Eye infection may incur economic losses to producers due to reduced selection intensity, but ethical aspects need to be considered as well because eye infection can be quite painful and reduce animal well‐being. The purpose of this study was to determine the potential for genetic selection against susceptibility to eye infection. The data were collected from 2076 blue foxes at the MTT fur animal research station. Genetic parameters were estimated using single‐ and multiple‐trait animal models. The heritabi...
Source: Journal of Animal Breeding and Genetics - June 1, 2015 Category: Genetics & Stem Cells Authors: R. Kempe, I. Strandén Tags: Original Article Source Type: research

Genetic variation of the weaning weight of beef cattle as a function of accumulated heat stress
The objective of this study was to identify the genetic variation in the weaning weight (WW) of beef cattle as a function of heat stress. The WWs were recorded at approximately 205 days of age in three Brazilian beef cattle populations: Nelore (93 616), Brangus (18 906) and Tropical Composite (62 679). In view of the cumulative nature of WW, the effect of heat stress was considered as the accumulation of temperature and humidity index units (ACTHI) from the animal's birth to weaning. A reaction norm model was used to estimate the (co)variance components of WW across the ACTHI scale. The accumulation of THI units from b...
Source: Journal of Animal Breeding and Genetics - June 1, 2015 Category: Genetics & Stem Cells Authors: M.L. Santana, A.B. Bignardi, J.P. Eler, J.B.S. Ferraz Tags: Original Article Source Type: research

Characterization of microRNA profile in mammary tissue of dairy and beef breed heifers
In this study, we performed a microarray analysis to identify miRNAs associated with high mammogenic potential of the bovine mammary gland. We identified 54 significantly differentially expressed miRNAs between the mammary tissue of dairy (Holstein‐Friesian, HF) and beef (Limousin, LM) postpubertal heifers. Fifty‐two miRNAs had higher expression in the mammary tissue of LM heifers. The expression of the top candidate miRNAs (bta‐miR‐10b, bta‐miR‐29b, bta‐miR‐101, bta‐miR‐375, bta‐miR‐2285t, bta‐miR‐146b, bta‐let7b, bta‐miR‐107, bta‐miR‐1434‐3p) identified in the microarray experiment...
Source: Journal of Animal Breeding and Genetics - June 1, 2015 Category: Genetics & Stem Cells Authors: Z. Wicik, M. Gajewska, A. Majewska, D. Walkiewicz, E. Osińska, T. Motyl Tags: Original Article Source Type: research

Effect of specialization on genetic parameters of studbook–entry inspection in Dutch Warmblood horses
Summary Recent studies on data from the Dutch Warmblood Studbook (KWPN) have shown that the ongoing specialization of horses for either dressage (DH) or show jumping (JH) has led to a decreasing genetic relationship between the two subpopulations. The aim of this study was to analyse the effect of the specialization process on the genetic parameters of traits measured in the studbook–entry inspection of KWPN during the last fifteen years. Data from 18 125 DH and 23 800 JH recorded from 1998 until 2013 were used to analyse 13 traits scored in both DH and JH. Analyses were performed in a Bayesian framework. Firstly, vari...
Source: Journal of Animal Breeding and Genetics - May 27, 2015 Category: Genetics & Stem Cells Authors: G. Rovere, P. Madsen, E. Norberg, J.A.M. Arendonk, B.J. Ducro Tags: Original Article Source Type: research

A genomewide association mapping study using ultrasound‐scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle
Summary The aim of this study was to identify candidate genes and genomic regions associated with ultrasound‐derived measurements of the rib‐eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for R...
Source: Journal of Animal Breeding and Genetics - May 27, 2015 Category: Genetics & Stem Cells Authors: M.H.A. Santana, R.V. Ventura, Y.T. Utsunomiya, H.H.R. Neves, P.A. Alexandre, G.A. Oliveira Junior, R.C. Gomes, M.N. Bonin, L.L. Coutinho, J.F. Garcia, S.L. Silva, H. Fukumasu, P.R. Leme, J.B.S. Ferraz Tags: Original Article Source Type: research

Impact of relationships between test and training animals and among training animals on reliability of genomic prediction
This study investigated the reliability of genomic prediction in various scenarios with regard to the relationship between test and training animals, and among animals within the training data set. Different training data sets were generated from EuroGenomics data and a group of Nordic Holstein bulls (born in 2005 and afterwards) as a common test data set. Genomic breeding values were predicted using a genomic best linear unbiased prediction model and a Bayesian mixture model. The results showed that a closer relationship between test and training animals led to a higher reliability of genomic predictions for the test anim...
Source: Journal of Animal Breeding and Genetics - May 23, 2015 Category: Genetics & Stem Cells Authors: X. Wu, M.S. Lund, D. Sun, Q. Zhang, G. Su Tags: Original Article Source Type: research

The Dutch national breeding programmes have developed to major globally operating companies
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - May 6, 2015 Category: Genetics & Stem Cells Authors: J. Napel, R.F. Veerkamp Tags: Editorial Source Type: research

Mitogenome revealed multiple postdomestication genetic mixtures of West African sheep
Summary Notable diversity observed within African ovine breeds makes them of great interests, but limited studies on genetic origins and domestications remain poorly understood. Here, we investigate the evolutionary status of West African native breeds, Djallonke and Sahelian sheep using mitogenome sequencing. Compared with other ovine mitogenome sequences, West African sheep were revealed a Eurasian origin, and the initially tamed sheep breeds in West Africa have been genetically mixed with each other and mixed with European breeds. Worldwide domestic sheep is deemed the Eurasian origin and migrated west to Europe and Afr...
Source: Journal of Animal Breeding and Genetics - April 12, 2015 Category: Genetics & Stem Cells Authors: O.H.D. Brahi, H. Xiang, X. Chen, S. Farougou, X. Zhao Tags: Original Article Source Type: research

Genetic management of Dutch golden retriever dogs with a simulation tool
Summary Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each y...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: J.J. Windig, K. Oldenbroek Tags: Original Article Source Type: research

Estimation of indirect genetic effects in group‐housed mink (Neovison vison) should account for systematic interactions either due to kin or sex
Summary Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non‐family members. Here, we investigate kin‐ and sex‐specific non‐genetic social interactions i...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: S.W. Alemu, P. Berg, L. Janss, P. Bijma Tags: Original Article Source Type: research

The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection
Summary The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north‐western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of variou...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Ćurković, J. Ramljak, S. Ivanković, B. Mioč, A. Ivanković, V. Pavić, M. Brka, C. Veit‐Kensch, I. Medugorac Tags: Original Article Source Type: research

Phenotypic and genetic variation in longevity of Polish Landrace sows
Summary The influence of some production traits on the longevity of Polish Landrace sows was evaluated using survival analysis. Estimates of genetic parameters were obtained from the sire and animal components in linear and survival methodologies. Comparison between survival and linear models was based on heritabilities and ranking of estimated breeding values of sires. The same data set, 13 031 sows, was used for both methodologies, even in the presence of censored observations. The effects of herd*year and year*season of the first farrowing had the largest influence on the risk of culling of sows. Sows born in spring se...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Sobczyńska, T. Blicharski Tags: Original Article Source Type: research

Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium
Summary The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP‐LD). In the three GBLUP‐LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP‐LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation da...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: M. Nishio, M. Satoh Tags: Original Article Source Type: research

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study
Summary The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G−1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, di...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: B.O. Fragomeni, D.A.L. Lourenco, S. Tsuruta, Y. Masuda, I. Aguilar, I. Misztal Tags: Original Article Source Type: research

Relationship between perilipin genes polymorphisms and growth, carcass and meat quality traits in pigs
Summary The perilipins (PLIN) belong to a family of structural proteins that play a role regulating intracellular lipid storage and mobilization. Here, PLIN1 and PLIN2 have been evaluated as candidate genes for growth, carcass and meat quality traits in pigs. A sample of 607 Duroc pigs were genotyped for two single‐nucleotide polymorphisms, one in intron 2 of the PLIN1 gene (JN860199:g.173G>A) and the other at the 3′ untranslated region of the PLIN2 gene (GU461317:g.98G>A). Using a Bayesian approach, we have been able to find evidence of additive, dominant and epistatic associations of the PLIN1 and PLIN2 polymor...
Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: S. Gol, R. Ros‐Freixedes, P. Zambonelli, M. Tor, R.N. Pena, S. Braglia, M. Zappaterra, J. Estany, R. Davoli Tags: Original Article Source Type: research

The biodiversity and genetic structure of Balearic sheep breeds
Summary The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was foun...
Source: Journal of Animal Breeding and Genetics - March 31, 2015 Category: Genetics & Stem Cells Authors: A.L. Pons, V. Landi, A. Martinez, J.V. Delgado Tags: Original Article Source Type: research

Quantitative genetics of disease traits
Summary John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James’ most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this r...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: N.R. Wray, P.M. Visscher Tags: Invited Review Source Type: research

Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits
Summary Linkage disequilibrium (LD) influences the genetic variation in a quantitative trait contributed by two or more loci, with positive LD increasing the variance. The magnitude of LD also affects the relative magnitude of dominance and epistatic variation. We quantify the extent of the non‐additive variance expected within populations, deriving analytical expressions for simple models and using numerical simulation in finite population more generally. As LD generates non‐independence among loci, a simple partition into additive, dominance and epistatic components is not possible, so we merely distinguish between a...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: W.G. Hill, A. Mäki‐Tanila Tags: Original Article Source Type: research