bluuebunny/crossref_metadata_2025 huggingface dataset:
Between Contumacy and Obsequiousness
Authors: Kapust Daniel
Published: June 2009

This article explores Tacitus’ negotiation of the dilemmas of writing due to the emergence of the Principate and the displacement of Republican politics. These developments constrained the orator and the historian, and required a distinctive approach to the writing of history. I argue that Tacitus develops a conception of the historian’s task that centers on the historian’s moral freedom and educative role in the Principate. This freedom is evident in Tacitus’ depiction of good and bad principes, as well as his discussion of how one ought to behave under the Principate. The historian’s task and moral freedom are important given Tacitus’ desire to avoid the twin dangers of writing under autocratic rulers: contumacy and obsequiousness.
The ‘Republican Dilemma’ and the Changing Social Context of Republicanism in the Early Modern Period
Authors: Kennedy Geoff
Published: June 2009

This article relates the evolving relationship between republicanism and the problem of ‘empire’ to the changing social contexts within which republican political theory emerges in the early modern period. It is argued that the initial antagonism between republicanism and empire was a politically constituted dilemma that related to the specific configuration of economic and political power characteristic of pre-capitalist societies. With the development of capitalism in England in the early modern period, the problem of empire becomes partially resolved due to the way in which the separation of economic and political power under capitalism reconstitutes the nature of empire itself. This new social context — characterized by new social, economic and political relationships specific to an emerging capitalist context — laid the foundations for the resolution of the ‘republican dilemma’ of empire and the ideological establishment of the first ‘Republican Empire’ in 18th century America.
Development and Implementation of a Women’s Health Promotion Program
Authors: Durham Danielle , Nichols Tracy R.
Published: June 2009

The Moms for Moms (M4M) program provides mothers the arena necessary to explore new ideas and definitions about mothering as well as skills and strategies concerning parenting, family management, and healthy habits. A participatory approach has been used to understand the development and implementation of the program from the perspective of the participants and community agency staff in an urban city. This approach provides detailed descriptions and interpretations of the shared beliefs, behaviors, and values of the participants as well as how these attributes are shaped by involvement in M4M. The findings from a needs assessment and program feasibility study conducted from August 2006 to June 2008 are used to inform a recently launched Healthy Lifestyles Initiative at a community-based agency for women, to determine if M4M fits within the culture of the organization and to determine the relevance of participatory methods to engage mothers and community agencies in creating health promotion programming.
A Consistent Weighted Ranking Scheme With an Application to NCAA College Football Rankings
Authors: Fainmesser Itay , Fershtman Chaim , Gandal Neil
Published: June 2009

The National Collegiate Athletic Association (NCAA) college football ranking, in which the so-called national champion is determined, has been plagued by controversies the last few years. The difficulty arises because there is a need to make a complete ranking of teams even though each team has a different schedule of games with a different set of opponents. A similar problem arises whenever one wants to establish a ranking of patents or academic journals, etc. This article develops a simple consistent weighted ranking (CWR) scheme in which the importance of (weights on) every success and failure are endogenously determined by the ranking procedure. This consistency requirement does not uniquely determine the ranking, as the ranking also depends on a set of parameters relevant for each problem. For sports rankings, the parameters reflect the importance of winning vs. losing, the strength of schedule, and the relative importance of home vs. away games. Rather than assign exogenous values to these parameters, we estimate them as part of the ranking procedure. The NCAA college football has a special structure that enables the evaluation of each ranking scheme and hence, the estimation of the parameters. Each season is essentially divided into two parts: the regular season and the postseason bowl games. If a ranking scheme is accurate, it should correctly predict a relatively large number of the bowl game outcomes. We use this structure to estimate the four parameters of our ranking function using ‘‘historical’’ data from the 1999-2003 seasons. Finally, we use the parameters that were estimated and the outcome of the 2004-2006 regular seasons to rank the teams each year for 2004-2006. We then calculate the number of bowl games whose outcomes were correctly predicted following the 2004-2006 season. None of the six ranking schemes used by the Bowl Championship Series (BCS) predicted more bowl games correctly over the 2004-2006 period than our CWR scheme.
(Re)Mediatizing HIV/AIDS in South Africa
Authors: Tomaselli Keyan G.
Published: June 2009

Written from a partly autoethnographic perspective, this article investigates current and past South African government stances on HIV/AIDS, grounding them in their larger political and ideological contexts, and examining the broader repercussions. A comparative analysis of South Africa's loveLife and STEPS interventions problematizes the self-branding used by loveLife in favor of the uplifting and humanizing message of STEPS. The author highlights the dangers of favoring AIDS solutions seeped in racial and cultural discourse over scientific ones and calls for the country's current HIV/AIDS strategy to be (re)mediatized in terms of its local and global representations. The idea of sham reasoning is discussed in relation to the generation of pseudoscientific discourses.
Surface modification of polypropylene by radiation grafting of hydrophilic monomers: Physicochemical properties
Authors: Riquet A M , Rohman G , Guinault A , Demilly M
Published: June 2009

The surface of polypropylene was modified by the post-irradiation grafting of acrylic acid (AAc), N,N-dimethylacrylamide (DMA) and mixtures of AAc (DMA) and a quaternary ammonium salt (QAS). The polypropylene sheets were activated by electron beam radiation before the grafting reaction. The degree of grafting was determined by weighing and the surface hydrophilicity was measured by measuring the water contact angles. The presence of oxygen and nitrogen was demonstrated by XPS. The surface charge and the isoelectric point were determined by the streaming potential method. The grafting of DMA, like that of AAc, depended on monomer availability, but the monomer did not permeate into the polypropylene bulk. For the same surface hydrophilicity, depending on the nature of the monomer or comonomer grafted, it is possible to modulate the physicochemical characteristics which determine the phenomena governing adhesion, and probably to adapt them to a given application.
Analytical–experimental approach for accurate depth profile evaluation of diffusion zone in plasma nitrided iron
Authors: Hosseini S R , Ashrafizadeh F , Kermanpur A
Published: June 2009

Nitrogen depth profile of diffusion zone in plasma nitrided pure iron was analytically calculated and experimentally measured. Nitrogen concentration equation was obtained versus nitriding temperature, time and diffusion distance. Plasma nitriding was carried out on pure iron substrate at 550°C in an atmosphere of 75H2–25N2. Nitrogen concentration depth profile in compound layer was characterised by glow discharge optical emission spectroscopy (GDOES) and for detection of nitrogen within the diffusion zone, secondary ion mass spectroscopy (SIMS) technique was employed. Nitrogen diffusion depths were measured accurately by optical and scanning electron microscopy as well as SIMS technique at different nitriding times. Experimental results indicated good agreement with calculated diffusion depths for various nitriding cycles. The extent of nitrogen diffusion depth in alpha zone, detected in this work for 10 h plasma nitriding at 550°C, was in excess of 2000 μm; such values have not been reported in previous investigations that conventionally used EDS, GDS, XPS or EPMA technique.
Activation of Wnt5A signaling is required for CXC chemokine ligand 12–mediated T-cell migration
Authors: Ghosh Manik C. , Collins Gary D. , Vandanmagsar Bolormaa , Patel Kalpesh , Brill Margaret , Carter Arnell , Lustig Ana , Becker Kevin G. , Wood William W. , Emeche Chineye D. , French Amanda D. , O'Connell Michael P. , Xu Mai , Weeraratna Ashani T. , Taub Dennis D.
Published: June 2009

Chemokines mediate the signaling and migration of T cells, but little is known about the transcriptional events involved therein. Microarray analysis of CXC chemokine ligand (CXCL) 12−treated T cells revealed that Wnt ligands are significantly up-regulated during CXCL12 treatment. Real-time polymerase chain reaction and Western blot analysis confirmed that the expression of noncanonical Wnt pathway members (eg, Wnt5A) was specifically up-regulated during CXCL12 stimulation, whereas β-catenin and canonical Wnt family members were selectively down-regulated. Wnt5A augmented signaling through the CXCL12-CXCR4 axis via the activation of protein kinase C. Moreover, Wnt5A expression was required for CXCL12–mediated T-cell migration, and rWnt5A sensitized human T cells to CXCL12-induced migration. Furthermore, Wnt5A expression was also required for the sustained expression of CXCR4. These results were further supported in vivo using EL4 thymoma metastasis as a model of T-cell migration. Together, these data demonstrate that Wnt5A is a critical mediator of CXCL12-CXCR4 signaling and migration in human and murine T cells.
Src homology 2 domain–containing inositol-5-phosphatase and CCAAT enhancer-binding protein β are targeted by miR-155 in B cells of Eμ-MiR-155 transgenic mice
Authors: Costinean Stefan , Sandhu Sukhinder K. , Pedersen Irene M. , Tili Esmerina , Trotta Rossana , Perrotti Danilo , Ciarlariello David , Neviani Paolo , Harb Jason , Kauffman Lauren Rachel , Shidham Aaditya , Croce Carlo Maria
Published: June 2009

We showed that Eμ-MiR-155 transgenic mice develop acute lymphoblastic leukemia/high-grade lymphoma. Most of these leukemias start at approximately 9 months irrespective of the mouse strain. They are preceded by a polyclonal pre–B-cell proliferation, have variable clinical presentation, are transplantable, and develop oligo/monoclonal expansion. In this study, we show that in these transgenic mice the B-cell precursors have the highest MiR-155 transgene expression and are at the origin of the leukemias. We determine that Src homology 2 domain–containing inositol-5-phosphatase (SHIP) and CCAAT enhancer-binding protein β (C/EBPβ), 2 important regulators of the interleukin-6 signaling pathway, are direct targets of MiR-155 and become gradually more down-regulated in the leukemic than in the preleukemic mice. We hypothesize that miR-155, by down-modulating Ship and C/EBPβ, initiates a chain of events that leads to the accumulation of large pre-B cells and acute lymphoblastic leukemia/high-grade lymphoma.
An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree
Authors: Lee Sang Hong , van der Werf Julius H.J.
Published: June 2009

Variance component (VC) approaches based on restricted maximum likelihood (REML) have been used as an attractive method for positioning of quantitative trait loci (QTL). Linkage disequilibrium (LD) information can be easily implemented in the covariance structure among QTL effects (e.g. genotype relationship matrix) and mapping resolution appears to be high. Because of the use of LD information, the covariance structure becomes much richer and denser compared to the use of linkage information alone. This makes an average information (AI) REML algorithm based on mixed model equations and sparse matrix techniques less useful. In addition, (near-) singularity problems often occur with high marker densities, which is common in fine-mapping, causing numerical problems in AIREML based on mixed model equations. The present study investigates the direct use of the variance covariance matrix of all observations in AIREML for LD mapping with a general complex pedigree. The method presented is more efficient than the usual approach based on mixed model equations and robust to numerical problems caused by near-singularity due to closely linked markers. It is also feasible to fit multiple QTL simultaneously in the proposed method whereas this would drastically increase computing time when using mixed model equation-based methods.
The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations
Authors: De Kovel Carolien Gerda Franciska
Published: June 2009

Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1) to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2) to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.
Validation of an approximate approach to compute genetic correlations between longevity and linear traits
Authors: Tarrés Joaquim , Piedrafita Jesús , Ducrocq Vincent
Published: June 2009

The estimation of genetic correlations between a nonlinear trait such as longevity and linear traits is computationally difficult on large datasets. A two-step approach was proposed and was checked via simulation. First, univariate analyses were performed to get genetic variance estimates and to compute pseudo-records and their associated weights. These pseudo-records were virtual performances free of all environmental effects that can be used in a BLUP animal model, leading to the same breeding values as in the (possibly nonlinear) initial analyses. By combining these pseudo-records in a multiple trait model and fixing the genetic and residual variances to their values computed during the first step, we obtained correlation estimates by AI-REML and approximate MT-BLUP predicted breeding values that blend direct and indirect information on longevity. Mean genetic correlations and reliabilities obtained on simulated data confirmed the suitability of this approach in a wide range of situations. When nonzero residual correlations exist between traits, a sire model gave nearly unbiased estimates of genetic correlations, while the animal model estimates were biased upwards. Finally, when an incorrect genetic trend was simulated to lead to biased pseudo-records, a joint analysis including a time effect could adequately correct for this bias.
Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness
Authors: Lagarrigue Sandrine , Pitel Frédérique , Carré Wilfrid , Abasht Behnam , Le Roy Pascale , Neau André , Amigues Yves , Sourdioux Michel , Simon Jean , Cogburn Larry , Aggrey Sammy , Leclercq Bernard , Vignal Alain , Douaire Madeleine
Published: June 2009

Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.
Prediction of genetic gain from quadratic optimisation with constrained rates of inbreeding
Authors: Villanueva Beatriz , Avendaño Santiago , Woolliams John A
Published: June 2009

There are selection methods available that allow the optimisation of genetic contributions of selection candidates for maximising the rate of genetic gain while restricting the rate of inbreeding. These methods imply selection on quadratic indices as the selection merit of a particular individual is a quadratic function of its estimated breeding value. This study provides deterministic predictions of genetic gain from selection on quadratic indices for a given set of resources (the number of candidates), heritability, and target rate of inbreeding. The rate of gain was obtained as a function of the accuracy of the Mendelian sampling term at the time of convergence of long-term contributions of selected candidates and the theoretical ideal rate of gain for a given rate of inbreeding after an exact allocation of long-term contributions to Mendelian sampling terms. The expected benefits from quadratic indices over traditional linear indices (i.e. truncation selection), both using BLUP breeding values, were quantified. The results clearly indicate higher gains from quadratic optimisation than from truncation selection. With constant rate of inbreeding and number of candidates, the benefits were generally largest for intermediate heritabilities but evident over the entire range. The advantage of quadratic indices was not highly sensitive to the rate of inbreeding for the constraints considered.
Optimization of a crossing system using mate selection
Authors: Li Yongjun , Werf Julius HJ van der , Kinghorn Brian P
Published: June 2009

A simple model based on one single identified quantitative trait locus (QTL) in a two-way crossing system was used to demonstrate the power of mate selection algorithms as a natural means of opportunistic line development for optimization of crossbreeding programs over multiple generations. Mate selection automatically invokes divergent selection in two parental lines for an over-dominant QTL and increased frequency of the favorable allele toward fixation in the sire-line for a fully-dominant QTL. It was concluded that an optimal strategy of line development could be found by mate selection algorithms for a given set of parameters such as genetic model of QTL, breeding objective and initial frequency of the favorable allele in the base populations, etc. The same framework could be used in other scenarios, such as programs involving crossing to exploit breed effects and heterosis. In contrast to classical index selection, this approach to mate selection can optimize long-term responses.
Genetic analysis of milking ability in Lacaune dairy ewes
Authors: Marie-Etancelin Christel , Manfredi Eduardo , Aurel Marie-Rose , Pailler François , Arhainx Jean , Ricard Edmond , Lagriffoul Gilles , Guillouet Philippe , Bibé Bernard , Barillet Francis
Published: June 2009

The milking ability of Lacaune ewes was characterised by derived traits of milk flow patterns, in an INRA experimental farm, from a divergent selection experiment in order to estimate the correlated effects of selection for protein and fat yields. The analysis of selected divergent line effects (involving 34 616 data and 1204 ewes) indicated an indirect improvement of milking traits (+17% for maximum milk flow and -10% for latency time) with a 25% increase in milk yield. Genetic parameters were estimated by multi-trait analysis with an animal model, on 751 primiparous ewes. The heritabilities of the traits expressed on an annual basis were high, especially for maximum flow (0.54) and for latency time (0.55). The heritabilities were intermediate for average flow (0.30), time at maximum flow (0.42) and phase of increasing flow (0.43), and low for the phase of decreasing flow (0.16) and the plateau of high flow (0.07). When considering test-day data, the heritabilities of maximum flow and latency time remained intermediate and stable throughout the lactation. Genetic correlations between milk yield and milking traits were all favourable, but latency time was less milk yield dependent (-0.22) than maximum flow (+0.46). It is concluded that the current dairy ewe selection based on milk solid yield is not antagonistic to milking ability.
A note on QTL detecting for censored traits
Authors: Fang Yixin
Published: June 2009

Most existing statistical methods for mapping quantitative trait loci (QTL) assume that the phenotype follows a normal distribution and that it is fully observed. However, some phenotypes have skewed distributions and may be censored. This note proposes a simple and efficient approach to QTL detecting for censored traits with the Cox PH model without estimating the baseline hazard function which is "nuisance".
Variance components for survival of piglets at farrowing using a reduced animal model
Authors: White Ian M.S. , Roehe Rainer , Knap Pieter W. , Brotherstone Sue
Published: June 2009

Farrowing survival is usually analysed as a trait of the sow, but this precludes estimation of any direct genetic effects associated with individual piglets. In order to estimate these effects, which are particularly important for sire lines, it is necessary to fit an animal model. However this can be computationally very demanding. We show how direct and maternal genetic effects can be estimated with a simpler analysis based on the reduced animal model and we illustrate the method using farrowing survival information on 118 193 piglets in 10 314 litters. We achieve a 30% reduction in computing time and a 70% reduction in memory use, with no important loss of accuracy. This use of the reduced animal model is not only of interest for pig breeding but also for poultry and fish breeding where large full-sib families are performance tested.
On the expected relationship between inbreeding, fitness, and extinction
Authors: Theodorou Konstantinos , Couvet Denis
Published: June 2009

We assessed the expected relationship between the level and the cost of inbreeding, measured either in terms of fitness, inbreeding depression or probability of extinction. First, we show that the assumption of frequent, slightly deleterious mutations do agree with observations and experiments, on the contrary to the assumption of few, moderately deleterious mutations. For the same inbreeding coefficient, populations can greatly differ in fitness according to the following: (i) population size; larger populations show higher fitness (ii) the history of population size; in a population that recovers after a bottleneck, higher inbreeding can lead to higher fitness and (iii) population demography; population growth rate and carrying capacity determine the relationship between inbreeding and extinction. With regards to the relationship between inbreeding depression and inbreeding coefficient, the population size that minimizes inbreeding depression depends on the level of inbreeding: inbreeding depression can even decrease when population size increases. It is therefore clear that to infer the costs of inbreeding, one must know both the history of inbreeding (e.g. past bottlenecks) and population demography.
OLA-DRB1 microsatellite variants are associated with ovine growth and reproduction traits
Authors: Geldermann Hermann , Mir Manzoor R. , Kuss Andreas W. , Bartenschlager Heinz
Published: June 2009

The DRB1 intron 2 (GT)n (GA)m microsatellite was genotyped in experimental flocks of seven Merinoland rams and 249 ewes as well as their offspring (381 lambs) from consecutive lambings. A total of 16 DRB1 alleles were detected, ranging between 353 and 857 bp. In comparison with carriers of other alleles, the ewes carrying the predominant 411 bp allele had higher values of all the recorded fertility traits. For ewes carrying the 394 and 857 bp alleles, the birth weight of lambs was about 400 g higher as compared to the residual group of ewes. The observed associations could be due to differences in disease resistance, cell recognition or tissue differentiation between carriers of various MHC haplotypes which can in turn affect individual fertility and growth performance.
Genetic parameters for canalisation analysis of litter size and litter weight traits at birth in mice
Authors: Gutiérrez Juan Pablo , Nieto Blanca , Piqueras Pepa , Ibáñez Noelia , Salgado Concepción
Published: June 2009

The aim of this research was to explore the genetic parameters associated with environmental variability for litter size (LS), litter weight (LW) and mean individual birth weight (IW) in mice before canalisation. The analyses were conducted on an experimental mice population designed to reduce environmental variability for LS. The analysed database included 1976 records for LW and IW and 4129 records for LS. The total number of individuals included in the analysed pedigree was 3997. Heritabilities estimated for the traits under an initial exploratory approach varied from 0.099 to 0.101 for LS, from 0.112 to 0.148 for LW and from 0.028 to 0.033 for IW. The means of the posterior distribution of the heritability under a Bayesian approach were the following: 0.10 (LS), 0.13 (LW) and 0.03 (IW). In general, the heritabilities estimated under the initial exploratory approach for the environmental variability of the analysed traits were low. Genetic correlations estimated between the trait and its variability reached values of -0.929 (LS), -0.815 (LW) and 0.969 (IW). The results presented here for the first time in mice may suggest a genetic basis for variability of the evaluated traits, thus opening the possibility to be implemented in selection schemes.
Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle
Authors: Khatkar Mehar S , Thomson Peter C , Tammen Imke , Cavanagh Julie AL , Nicholas Frank W , Raadsma Herman W
Published: June 2009

We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D'. Estimates of D' from the two approaches were in close agreement (r = 0.91). The mean estimates of D' for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (~37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.
A meta-analytic assessment of a Thyroglobulin marker for marbling in beef cattle
Authors: Wood Ian A. , Moser Gerhard , Burrell Daniel L. , Mengersen Kerrie L. , Hetzel D. Jay S.
Published: June 2009

A meta-analysis was undertaken reporting on the association between a polymorphism in the Thyroglobulin gene (TG5) and marbling in beef cattle. A Bayesian hierarchical model was adopted, with alternative representations assessed through sensitivity analysis. Based on the overall posterior means and posterior probabilities, there is substantial support for an additive association between the TG5 marker and marbling. The marker effect was also assessed across various breed groups, with each group displaying a high probability of positive association between the T allele and marbling. The WinBUGS program code used to simulate the model is included as an Appendix available online at http://www.edpsciences.org/gse.
Genetic relationships among Turkish sheep
Authors: Uzun Metehan , Gutiérrez-Gil Beatriz , Arranz Juan-José , Primitivo Fermín San , Saatci Mustafa , Kaya Mehmet , Bayón Yolanda
Published: June 2009

Genetic relationships among Turkish sheep breeds were analysed on the basis of 30 microsatellite markers. Phylogenetic analyses based on the estimation of genetic distances revealed the closest relationships for the Akkaraman, Morkaraman and Tuj breeds, which were clearly differentiated from the others in the dendrogram. Our pattern was completely confirmed by results from the Factorial Correspondence Analysis. All the results described analysing either population parameters or individuals revealed a clear separation between the fat-tailed group and the others. These results, based on nuclear DNA, are discussed along with those already reported for these breeds through the investigation of mitochondrial DNA, which had revealed the invaluable significance of the genetic background of these Turkish sheep.
A bivariate quantitative genetic model for a threshold trait and a survival trait
Authors: Damgaard Lars Holm , Korsgaard Inge Riis
Published: June 2009

Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.
Multibreed analysis by splitting the breeding values
Authors: García-Cortés Luis Alberto , Toro Miguel Ángel
Published: June 2009

An equivalent model for multibreed variance covariance estimation is presented. It considers the additive case including or not the segregation variances. The model is based on splitting the additive genetic values in several independent parts depending on their genetic origin. For each part, it expresses the covariance between relatives as a partial numerator relationship matrix times the corresponding variance component. Estimation of fixed effects, random effects or variance components provided by the model are as simple as any model including several random factors. We present a small example describing the mixed model equations for genetic evaluations and two simulated examples to illustrate the Bayesian variance component estimation.
Genetic correlations between conformation traits and radiographic findings in the limbs of German Warmblood riding horses
Authors: Stock Kathrin Friederike , Distl Ottmar
Published: June 2009

Studbook inspection (SBI) data of 20 768 German Warmblood mares and radiography results (RR) data of 5102 Hanoverian Warmblood horses were used for genetic correlation analyses. The scores on a scale from 0 to 10 were given for conformation and basic quality of gaits, resulting in 14 SBI traits which were used for the correlation analyses. The radiographic findings considered included osseous fragments in fetlock (OFF) and hock joints (OFH), deforming arthropathy in hock joints (DAH) and distinct radiographic findings in the navicular bones (DNB) which were analyzed as binary traits, and radiographic appearance of the navicular bones (RNB) which was analyzed as a quasi-linear trait. Genetic parameters were estimated multivariately in linear animal models with REML using information on 24 448 horses with SBI and/or RR records. The ranges of heritability estimates were h2 = 0.14–0.34 for the RR traits and h2 = 0.09–0.50 for the SBI traits. Negative additive genetic correlations of rg = -0.19 to -0.56 were estimated between OFF and conformation of front and hind limbs and walk at hand, and between DNB and hind limb conformation. There were indications of negative additive genetic correlations between DAH and all SBI traits, but because of low prevalence and low heritability of DAH, these results require further scrutiny. Positive additive genetic correlations of rg = 0.37–0.52 were estimated between OFF and withers height and between OFH and withers height, indicating that selection for taller horses will increase disposition to develop OFF and OFH. Selection of broodmares with regards to functional conformation will assist, but cannot replace possible selection against radiographic findings in the limbs of young Warmblood riding horses, particularly with regards to OFF.
Improved techniques for sampling complex pedigrees with the Gibbs sampler
Authors: Abraham K. Joseph , Totir Liviu R. , Fernando Rohan L.
Published: June 2009

Markov chain Monte Carlo (MCMC) methods have been widely used to overcome computational problems in linkage and segregation analyses. Many variants of this approach exist and are practiced; among the most popular is the Gibbs sampler. The Gibbs sampler is simple to implement but has (in its simplest form) mixing and reducibility problems; furthermore in order to initiate a Gibbs sampling chain we need a starting genotypic or allelic configuration which is consistent with the marker data in the pedigree and which has suitable weight in the joint distribution. We outline a procedure for finding such a configuration in pedigrees which have too many loci to allow for exact peeling. We also explain how this technique could be used to implement a blocking Gibbs sampler.
Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming (Open Access publication)
Authors: Pong-Wong Ricardo , Woolliams John A.
Published: June 2009

An approach for optimising genetic contributions of candidates to control inbreeding in the offspring generation using semidefinite programming (SDP) was proposed. Formulations were done for maximising genetic gain while restricting inbreeding to a preset value and for minimising inbreeding without regard of gain. Adaptations to account for candidates with fixed contributions were also shown. Using small but traceable numerical examples, the SDP method was compared with an alternative based upon Lagrangian multipliers (RSRO). The SDP method always found the optimum solution that maximises genetic gain at any level of restriction imposed on inbreeding, unlike RSRO which failed to do so in several situations. For these situations, the expected gains from the solution obtained with RSRO were between 1.5–9% lower than those expected from the optimum solution found with SDP with assigned contributions varying widely. In conclusion SDP is a reliable and flexible method for solving contribution problems.
Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle
Authors: Casellas Joaquim , Piedrafita Jesús , Varona Luis
Published: June 2009

The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.
Associations of myostatin gene polymorphisms with performance and mortality traits in broiler chickens
Authors: Ye Xianghai , Brown Stewart R. , Nones Kátia , Coutinho Luiz L. , Dekkers Jack C.M. , Lamont Susan J.
Published: June 2009

Myostatin is a negative regulator of skeletal muscle growth. We evaluated effects of myostatin polymorphisms in three elite commercial broiler chicken lines on mortality, growth, feed conversion efficiency, ultrasound breast depth, breast percentage, eviscerated carcass weight, leg defects, blood oxygen level, and hen antibody titer to infectious bursal disease virus vaccine. Progeny mean data adjusted for fixed and mate effects and DNA from 100 sires per line were used. Single nucleotide polymorphisms (SNPs) of the myostatin gene segregating in these lines were identified by designing specific primers, amplifying individual DNA in each line by polymerase chain reaction, cloning, sequencing and aligning the corresponding products. Individual sires were genotyped for five identified SNPs which contributed to eight haplotypes. Frequencies of SNP alleles and haplotypes differed between lines. Using the allele substitution effect model, the myostatin SNPs were found to have significant (P < 0.031) associations with growth, mortality, blood oxygen and hen antibody titer to infectious bursal disease virus vaccine, although the associations were not often consistent across lines. These results suggest that the myostatin gene has pleiotropic effects on broiler performance.
Influence of priors in Bayesian estimation of genetic parameters for multivariate threshold models using Gibbs sampling
Authors: Stock Kathrin Friederike , Distl Ottmar , Hoeschele Ina
Published: June 2009

Simulated data were used to investigate the influence of the choice of priors on estimation of genetic parameters in multivariate threshold models using Gibbs sampling. We simulated additive values, residuals and fixed effects for one continuous trait and liabilities of four binary traits, and QTL effects for one of the liabilities. Within each of four replicates six different datasets were generated which resembled different practical scenarios in horses with respect to number and distribution of animals with trait records and availability of QTL information. (Co)Variance components were estimated using a Bayesian threshold animal model via Gibbs sampling. The Gibbs sampler was implemented with both a flat and a proper prior for the genetic covariance matrix. Convergence problems were encountered in > 50% of flat prior analyses, with indications of potential or near posterior impropriety between about round 10 000 and 100 000. Terminations due to non-positive definite genetic covariance matrix occurred in flat prior analyses of the smallest datasets. Use of a proper prior resulted in improved mixing and convergence of the Gibbs chain. In order to avoid (near) impropriety of posteriors and extremely poorly mixing Gibbs chains, a proper prior should be used for the genetic covariance matrix when implementing the Gibbs sampler.
Methods for the detection of multiple linked QTL applied to a mixture of full and half sib families
Authors: Gilbert Hélène , Le Roy Pascale
Published: June 2009

A new multiple trait strategy based on discriminant analysis was studied for efficient detection of linked QTL in outbred sib families, in comparison with a multivariate likelihood technique. The discriminant analysis technique describes the segregation of a linear combination of the traits in a univariate likelihood. This combination is calculated for each pair of positions depending on the inheritance of the pairs of QTL haplotypes in the progeny. The gains in power and accuracy for position estimations of multiple trait methods in grid searches were evaluated in reference to single trait detections of linked QTL. The methods were applied to simulated designs with two correlated traits submitted to various effects from the linked QTL. Multiple trait strategies were generally more powerful and accurate than the single trait technique. Linked QTL were distinguished when they were separated enough to identify informative recombinations: at least two genetic markers and 25 cM between the QTL under the simulated conditions. Except in a particular case, discriminant analysis was at least as powerful as the multivariate technique and its implementation was five times faster. Combining the advantages from both methodologies, we finally propose a complete strategy for rapid and efficient systematic multivariate detections in outbred populations.
A periodic analysis of longitudinal binary responses: a case study of clinical mastitis in Norwegian Red cows
Authors: Chang Yu-mei , Gianola Daniel , Heringstad Bjørg , Klemetsdal Gunnar
Published: June 2009

A Bayesian procedure for analyzing longitudinal binary responses using a periodic cosine function was developed. It was assumed that, after adjustment for "seasonal" effects, the oscillation of the underlying latent variables for longitudinal binary responses was a stationary series. Based on this assumption, a single dimension sinusoidal analysis of longitudinal binary responses using the Gibbs sampling and Metropolis algorithms was implemented in a study of clinical mastitis records of Norwegian Red cows taken over five lactations.
Within-family marker-assisted selection for aquaculture species
Authors: Sonesson Anna K.
Published: June 2009

A within-family marker-assisted selection scheme was designed for typical aquaculture breeding schemes, where most traits are recorded on sibs of the candidates. Here, sibs of candidates were tested for the trait and genotyped to establish genetic marker effects on the trait. BLUP breeding values were calculated, including information of the markers (MAS) or not (NONMAS). These breeding values were identical for all family members in the NONMAS schemes, but differed between family members in the MAS schemes, making within-family selection possible. MAS had up to twice the total genetic gain of the corresponding NONMAS scheme. MAS was somewhat less effective when heritability increased from 0.06 to 0.12 or when the frequency of the positive allele was < 0.5. The relative efficiency of MAS was higher for schemes with more candidates, because of larger fullsib family sizes. MAS was also more efficient when male:female mating ratio changed from 1:1 to 1:5 or when the QTL explained more of the total genetic variation. Four instead of two markers linked to the QTL increased genetic gain somewhat. There was no significant difference in polygenic genetic gain between MAS and NONMAS for most schemes. The rates of inbreeding were lower for MAS than NON-MAS schemes, because fewer full-sibs were selected by MAS.
An approximate multitrait model for genetic evaluation in dairy cattle with a robust estimation of genetic trends (Open Access publication)
Authors: Lassen Jan , Sørensen Morten Kargo , Madsen Per , Ducrocq Vincent
Published: June 2009

In a stochastic simulation study of a dairy cattle population three multitrait models for estimation of genetic parameters and prediction of breeding values were compared. The first model was an approximate multitrait model using a two-step procedure. The first step was a single trait model for all traits. The solutions for fixed effects from these analyses were subtracted from the phenotypes. A multitrait model only containing an overall mean, an additive genetic and a residual term was applied on these preadjusted data. The second model was similar to the first model, but the multitrait model also contained a year effect. The third model was a full multitrait model. Genetic trends for total merit and for the individual traits in the breeding goal were compared for the three scenarios to rank the models. The full multitrait model gave the highest genetic response, but was not significantly better than the approximate multitrait model including a year effect. The inclusion of a year effect into the second step of the approximate multitrait model significantly improved the genetic trend for total merit. In this study, estimation of genetic parameters for breeding value estimation using models corresponding to the ones used for prediction of breeding values increased the accuracy on the breeding values and thereby the genetic progress.