Gibbsthur: Software for estimating variance components and predicting breeding values for ranking traits based on a thurstonian model

(1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming these limitations is to assume an underlying Gaussian liability that represents a horse’s performance and dictates the observed classification in a competition event. That approach can be implemented using Montecarlo Markov Chain (McMC) techniques with a procedure known as the Thurstonian model. (2) Methods: We have developed software (GIBBSTHUR) that analyses ranking traits along with other continuous or threshold traits. The software implements a Gibbs Sampler scheme with a data-augmentation step for the liability of the ranking traits and provides estimates of the variance and covariance components and predictions of the breeding values and the average performance of the competitors in competition events. (3) Results: The results of a simple example are presented, in which it is shown that the procedure can recover the simulated variance and covariance components. In addition, the correlation between the simulated and predicted breeding values and between the estimates of the event effects and the average additive genetic effect of the competitors demonstrates the ability of the software to produce useful predictions for breeding purposes. (4) Conclusions: the GIBBSTHUR software provides a useful tool for the breeding evaluation of ranking traits in horses and is freely available in a public repository (https://github.com/lvaronaunizar/Gibbsthur)

Linear models for joint association and linkage QTL mapping

<p>Abstract</p> <p>Background</p> <p>Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure.</p> <p>Results</p> <p>We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission) average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component) model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided.</p> <p>Conclusion</p> <p>The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.</p

A note on the rationale for estimating genealogical coancestry from molecular markers

BACKGROUND: Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature. METHODS: We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators. RESULTS: The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation. CONCLUSIONS: Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift

Crystal structure of K0.75[FeII 3.75FeIII 1.25(HPO3)6]- 0.5H2O, an open-framework iron phosphite with mixed-valent FeII/FeIII ions

Single crystals of the title compound, potassium hexaphosphitopentaferrate( II,III) hemihydrate, K0.75[FeII 3.75FeIII 1.25(HPO3)6] 0.5H2O, were grown under mild hydrothermal conditions. The crystal structure is isotypic with Li1.43[FeII 4.43FeIII 0.57(HPO3)6] 1.5H2O and (NH4)2[FeII 5(HPO3)6] and exhibits a [FeII 3.75FeIII 1.25(HPO3)6]0.75 open framework with disordered K+ (occupancy 3/4) as counter-cations. The anionic framework is based on (001) sheets of two [FeO6] octahedra (one with point group symmetry 3.. and one with point group symmetry .2.) linked along [001] through [HPO3]2 oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octahedra, giving rise to channels with a radius of ca 3.1 A ˚ where the K+ cations and likewise disordered water molecules (occupancy 1/4) are located. O O contacts between the water molecule and framework O atoms of 2.864 (5) A ˚ indicate hydrogen-bonding interactions of medium strength. The infrared spectrum of the compound shows vibrational bands typical for phosphite and water groups. The Mössbauer spectrum is in accordance with the presence of FeII and FeIII ions.Ministerio de Economía y Competitividad, MAT2013–42092-R // Gobierno Vasco, IT-630–13 y SAI12/82 // Universidad del País Vasco, UPV/EHU, UFI-11/1

Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?

peer reviewe

Variance and covariance of actual relationship between relatives at one locus.

The relationship between pairs of individuals is an important topic in many areas of population and quantitative genetics. It is usually measured as the proportion of thegenome identical by descent shared by the pair and it can be inferred from pedigree information. But there is a variance in actual relationships as a consequence of Mendelian sampling, whose general formula has not been developed. The goal of this work is to develop this general formula for the one-locus situation,. We provide simple expressions for the variances and covariances of all actual relationships in an arbitrary complex pedigree. The proposed method relies on the use of the nine identity coefficients and the generalized relationship coefficients; formulas have been checked by computer simulation. Finally two examples for a short pedigree of dogs and a long pedigree of sheep are given

El microrrelato como material didáctico en la adquisición de la gramática en ELE

[EN] In the present article we intend to make a reflection on the introduction of target language literature in foreign language classrooms. We will analyze the use of short-short stories as a didactic resource in Spanish as Foreign Language classrooms. To this end, we will research different teaching methodologies that have been implemented and investigate the validity of this genre as a suitable material for teaching grammar. We will make an approximation to Focus on Form as an effective approach, which integrates grammar teaching within a communicative context.[ES] En el presente artículo, se pretende realizar una reflexión sobre la introducción de la literatura de la lengua meta en el aula de lenguas extranjeras. Analizaremos el uso del microrrelato en el aula de español como lengua extranjera (ELE) como material didáctico. Para ello, investigaremos las diferentes metodologías de enseñanza que se han puesto en práctica e indagaremos sobre la validez de este género como material idóneo para la enseñanza de la gramática. Realizaremos un acercamiento a la atención a la forma (AF) como un enfoque efectivo en el que se integre la enseñanza de la gramática dentro de un contexto comunicativo.Rodríguez Rodríguez, MN.; García-Perera, D. (2016). El microrrelato como material didáctico en la adquisición de la gramática en ELE. Revista de Lingüística y Lenguas Aplicadas. 11:61-70. doi:10.4995/rlyla.2016.3936.SWORD617011Andrés-Suárez, I. (2012). Antología del microrrelato espa-ol (1906-2011). El cuarto género narrativo. Madrid: Cátedra.Bamidele Oyewo, D. (2009). Competencia Literaria, Literatura Hipertextual y Microrrelatos en el Aula de ELE. Memoria de Máster MEELE. Madrid: Universidad Antonio de Nebrija.Consejo de Europa. (2002). 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