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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

Some aspects of design and analysis of selection programmes in aquaculture species
In this study, we focus on a few aspects of aquaculture genetics to which Professor James made substantial contributions. His outstanding ability to comprehend, clarify and simplify complex problems with easy‐to‐understand mathematical derivations is clearly demonstrated in the areas of large‐scale strain comparisons, genotype‐by‐environment interactions (GxE), transformations and interpretation of selection response, as well as in the treatment of economic aspects of designing breeding programmes. (Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: Y. Li, R.W. Ponzoni Tags: Invited Review Source Type: research

Community‐based livestock breeding programmes: essentials and examples
Summary Breeding programmes described as community‐based (CBBP) typically relate to low‐input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low‐input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin‐America, Africa and Asia hi...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.P. Mueller, B. Rischkowsky, A. Haile, J. Philipsson, O. Mwai, B. Besbes, A. Valle Zárate, M. Tibbo, T. Mirkena, G. Duguma, J. Sölkner, M. Wurzinger Tags: Invited Review Source Type: research

Comparison of breeding objectives across countries with application to sheep indexes in New Zealand and Ireland
The objective of this study was to describe the methodology to calculate correlations between national selection indexes and gain a deeper understanding of the factors influencing responses in economically important traits in both the New Zealand and Irish sheep industries. Moderate to strong correlations were calculated among indexes within and between countries, with the strongest correlation (0.86) between the New Zealand and Irish maternal indexes. In both countries, responses to selection in the maternal indexes are largely driven by growth traits; each index, however, has a different balance of traits. Ewe mature wei...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: B.F.S. Santos, N. McHugh, T.J. Byrne, D.P. Berry, P.R. Amer Tags: Original Article Source Type: research

How old are quantitative trait loci and how widely do they segregate?
Summary The mutations that cause genetic variation in quantitative traits could be old and segregate across many breeds or they could be young and segregate only within one breed. This has implications for our understanding of the evolution of quantitative traits and for genomic prediction to improve livestock. We investigated the age of quantitative trait loci (QTL) for milk production traits identified as segregating in Holstein dairy cattle. We use a multitrait method and found that six of 11 QTL also segregate in Jerseys. Variants identified as Holstein‐only QTL were fixed or rare [minor allele frequency (MAF) <...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: K.E. Kemper, B.J. Hayes, H.D. Daetwyler, M.E. Goddard Tags: Original Article Source Type: research

Managing the rate of increase in average co‐ancestry in a rolling front tree breeding strategy
Summary In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long‐ and short‐term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by ...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R.J. Kerr, T.A. McRae, G.W. Dutkowski, B. Tier Tags: Invited Review Source Type: research

grain: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach
Summary GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the ‘classical’ inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC), defined here for the first time. AHC is defined as the numbe...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: R. Baumung, J. Farkas, D. Boichard, G. Mészáros, J. Sölkner, I. Curik Tags: Original Article Source Type: research

Genetic contributions and their optimization
Summary Genetic contributions were first formalized in 1958 by James and McBride (Journal of Genetics, 56, 55–62) and have since been shown to provide a unifying framework for theories of gain and inbreeding. As such they have underpinned the development of methods that provide the most effective combination of maximizing gain whilst managing inbreeding and loss of genetic variation. It is shown how this optimum contribution technology can be developed from theory and adapted to provide practical selection protocols for a wide variety of situations including overlapping generations and multistage selection. The natural d...
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: J.A. Woolliams, P. Berg, B.S. Dagnachew, T.H.E. Meuwissen Tags: Invited Review Source Type: research

Quantitative genetics, spread of genes and genetic improvement: papers in honour of John James
(Source: Journal of Animal Breeding and Genetics)
Source: Journal of Animal Breeding and Genetics - March 30, 2015 Category: Genetics & Stem Cells Authors: F.W. Nicholas, C.M. Wade, L. Ollivier, J. Sölkner Tags: Introduction Source Type: research

A 57‐bp deletion in the ovine KAP6‐1 gene affects wool fibre diameter
In this study, we used polymerase chain reaction – single‐strand conformational polymorphism (PCR‐SSCP) analysis to screen for variation in a gene encoding the ovine HGT‐KAP6‐1 protein. We identified three gene variants (A, B and C). Variants A and B were similar to each other, with only three nucleotide differences occurring downstream of the coding sequence. However, variant C had a 57‐bp deletion that would notionally result in a loss of 19 amino acids in the protein. The presence of C was found to be associated with an increase in mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), coeffici...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: H. Zhou, H. Gong, S. Li, Y. Luo, J.G.H. Hickford Tags: Original Article Source Type: research

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs
Summary The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotype...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: T. Aasmundstad, I. Andersen‐Ranberg, Ø. Nordbø, T. Meuwissen, O. Vangen, E. Grindflek Tags: Original Article Source Type: research

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds
In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out‐of‐bag (OOB) error rate for both ranking met...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: F. Bertolini, G. Galimberti, D.G. Calò, G. Schiavo, D. Matassino, L. Fontanesi Tags: Original Article Source Type: research

Y‐chromosomal variation of local goat breeds of Turkey close to the domestication centre
In this study, the male‐specific region markers, sex‐determining region‐Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honamlı, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illus...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: B. Cinar Kul, N. Bilgen, J.A. Lenstra, O. Korkmaz Agaoglu, B. Akyuz, O. Ertugrul Tags: Original Article Source Type: research

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls
The objectives of this study were to characterize the genetic variability of village chickens from three agro‐ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of F...
Source: Journal of Animal Breeding and Genetics - March 17, 2015 Category: Genetics & Stem Cells Authors: F. Z. Mahammi, S. B. S. Gaouar, D. Laloë, R. Faugeras, N. Tabet‐Aoul, X. Rognon, M. Tixier‐Boichard, N. Saidi‐Mehtar Tags: Original Article Source Type: research

Genetic parameters for different growth scales in GIFT strain of Nile tilapia (Oreochromis niloticus)
Summary Body weight, length, width and depth at two growth stages were observed for a total of 5015 individuals of GIFT strain, along with a pedigree including 5588 individuals from 104 sires and 162 dams was collected. Multivariate animal models and a random regression model were used to genetically analyse absolute and relative growth scales of these growth traits. In absolute growth scale, the observed growth traits had moderate heritabilities ranging from 0.321 to 0.576, while pairwise ratios between body length, width and depth were lowly inherited and maximum heritability was only 0.146 for length/depth. All genetic ...
Source: Journal of Animal Breeding and Genetics - March 6, 2015 Category: Genetics & Stem Cells Authors: J. He, H. Gao, P. Xu, R. Yang Tags: Original Article Source Type: research

Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes
Summary Heritabilities and genetic correlations for milk production traits were estimated from first‐parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Legm) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and ...
Source: Journal of Animal Breeding and Genetics - March 2, 2015 Category: Genetics & Stem Cells Authors: E.B. Flores, J. Werf Tags: Original Article Source Type: research

A retrospective analysis of allele frequency changes of major genes during 20 years of selection in the Italian Large White pig breed
In this study, we investigated whether a selection programme based on boar genetic evaluation obtained with a classical BLUP animal model can change allele frequencies in a pig population. All Italian Large White boars born from 1992 to 2012 with estimated breeding value reliability >0.85 (n = 200) were selected among all boars of this breed. Boars were genotyped with markers in major genes (IGF2 intron3‐g.3072G>A, MC4R p.D298N, VRTN PRE1 insertion, PRKAG3 p.I199V and FTO g.276T>G). Genotyping data were analysed grouping boars in eight classes according to their year of birth. To evaluate the influence of time...
Source: Journal of Animal Breeding and Genetics - March 1, 2015 Category: Genetics & Stem Cells Authors: L. Fontanesi, G. Schiavo, E. Scotti, G. Galimberti, D.G. Calò, A.B. Samorè, M. Gallo, V. Russo, L. Buttazzoni Tags: Original Article Source Type: research

Assessment of bagging GBLUP for whole‐genome prediction of broiler chicken traits
Summary Bootstrap aggregation (bagging) is a resampling method known to produce more accurate predictions when predictors are unstable or when the number of markers is much larger than sample size, because of variance reduction capabilities. The purpose of this study was to compare genomic best linear unbiased prediction (GBLUP) with bootstrap aggregated sampling GBLUP (Bagged GBLUP, or BGBLUP) in terms of prediction accuracy. We used a 600 K Affymetrix platform with 1351 birds genotyped and phenotyped for three traits in broiler chickens; body weight, ultrasound measurement of breast muscle and hen house egg production. ...
Source: Journal of Animal Breeding and Genetics - March 1, 2015 Category: Genetics & Stem Cells Authors: R. Abdollahi‐Arpanahi, G. Morota, B.D. Valente, A. Kranis, G.J.M. Rosa, D. Gianola Tags: Original Article Source Type: research

Genetic heteroscedasticity of teat count in pigs
Summary The genetic improvement in pig litter size has been substantial. The number of teats on the sow must thus increase as well to meet the needs of the piglets, because each piglet needs access to its own teat. We applied a genetic heterogeneity model to teat counts in pigs, and estimated a medium heritability for teat counts (0.35), but found a low heritability for residual variance (0.06), indicating that selection for reduced residual variance might have a limited effect. A numerically positive correlation (0.8) was estimated between the breeding values for the mean and the residual variance. However, because of the...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: M. Felleki, N. Lundeheim Tags: Original Article Source Type: research

Genetic analysis of river, swamp and hybrid buffaloes of north‐east India throw new light on phylogeography of water buffalo (Bubalus bubalis)
This study analysed buffaloes from north‐east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South‐East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north‐east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp‐type buffaloes of north‐east India with Lower Assamese (significantly hybrid type) buffaloes in one plane...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: B.P. Mishra, P.K. Dubey, B. Prakash, P. Kathiravan, S. Goyal, D.K. Sadana, G.C. Das, R.N. Goswami, V. Bhasin, B.K. Joshi, R.S. Kataria Tags: Original Article Source Type: research

Additive and epistatic genome‐wide association for growth and ultrasound scan measures of carcass‐related traits in Brahman cattle
This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three‐stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome‐wide epistasis analysis. We fitted these three‐stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits ...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: A.A. Ali, M.S. Khatkar, H.N. Kadarmideen, P.C. Thomson Tags: Invited Review Source Type: research

Sustainable dairy cattle selection in the genomic era
Summary Genomic selection offers considerable flexibility to increase genetic trends in dairy cattle breeding. It is also an opportunity for more sustainable breeding, in terms of breeding goal and genetic variability. With a shorter generation interval, there is a big risk of increasing inbreeding if semen dissemination policy of elite bulls is not changed. However, using a large number of young bulls as service bulls and bull sires is a solution for both maximizing genetic trend while reducing inbreeding trend. Female genotyping is a key challenge for within‐herd selection but, more importantly, for selection of new tr...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: D. Boichard, V. Ducrocq, S. Fritz Tags: Invited Review Source Type: research

Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits
We examined a range of traits in six populations amounting to 173 population‐trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree‐based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as ...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: A. Loberg, J. W. Dürr, W.F. Fikse, H. Jorjani, L. Crooks Tags: Original Article Source Type: research

Genetic conditions of joint Nordic genetic evaluations of lifetime competition performance in warmblood sport horses
Summary Breeding programmes for warmblood sport horses are similar in the Nordic countries Sweden, Denmark, Finland and Norway, and stallions of same origin are used. The aim was to investigate whether a joint Nordic genetic evaluation based on lifetime competition performance is feasible and beneficial for breeding competitive sport horses in the Nordic countries. Results for almost 45 000 horses in show jumping and 30 000 horses in dressage were available. The larger populations in Sweden and Denmark contributed with 85% of the results. Heritabilities and genetic correlations between performances in the different count...
Source: Journal of Animal Breeding and Genetics - February 1, 2015 Category: Genetics & Stem Cells Authors: Å. Viklund, S. Furre, S. Eriksson, O. Vangen, J. Philipsson Tags: Original Article Source Type: research