Multi-trait Approach Research Articles

Analysis of censored survival data using random regression models

AbstractCensoring of records is a problem in the prediction of breeding values for longevity, because breeding values are required before actual lifespan is known. In this study we investigated the use of random regression models to analyse survival data, because this method combines some of the advantages of a multitrait approach and the more sophisticated proportional hazards models. A model was derived for the binary representation of survival data and links with proportional hazards models and generalized linear models are shown. Variance components and breeding values were predicted using a linear approximation, including time-dependent fixed effects and random regression coefficients. Production records in lactations 1 to 5 were available on 24741 cows in the UK, all having had the opportunity to survive five lactations. The random regression model contained a linear regression on milk yield within herd (no. = 1417) by lactation number (no. = 4), Holstein percentage and year-month of calving effect (no. = 72). The additive animal genetic effects were modelled using orthogonal polynomials of order 1 to 4 with random coefficients and the error terms were fitted for each lactation separately, either correlated or not. Variance components from the full (i.e. uncensored) data set, were used to predict breeding values for survival in each lactation from both uncensored and randomly censored data. In the uncensored data, estimates of heritabilities for culling probability in each lactation ranged from 0·02 to 0·04. Breeding values for lifespan (calculated from the survival breeding values) had a range of 2·4 to 3·6 lactations and a standard deviation of 0·25. Correlations between predicted breeding values for 129 bulls, each with more than 30 daughters, from the various data sets ranged from 0·81 to 0·99 and were insensitive to the model used. It is concluded that random regression analysis models used for test-day records analysis of milk yield, might also be of use in the analysis of censored survival data.

Estimation of genetic parameters for daily milk yield of primiparous Ayrshire cows by random regression test-day models

Test-day data comprising of 63,331 test-day milk records of 6310 primiparous Finnish Ayrshire cows were used to estimate genetic parameters for daily milk production. Two alternative random regression (RR) sub-models were used to describe breeding values for the shape of lactation curves of individual cows: a five parameter logarithmic polynomial (ASM) or a normalised third order orthogonal polynomial. Permanent environment (PE) of a cow was described by either a common PE effect (ASM and OPM PE1) or a normalised third order orthogonal polynomial (OPM PE4). Variance components were estimated with an animal model using EM-REML. A multitrait (MT) approach together with continuous covariance function (CF) was used to derive reference for RR estimates. Heritability estimates obtained by ASM (0.41–0.60) and OPM PE1 (0.28–0.53) were higher than those derived from CF analysis (0.20–0.28). Fitting the RR sub-model for PE effects strongly influenced the magnitude of heritability estimates (0.23–0.36). Estimates of heritability were found to be highest during early and late lactation when estimated by ASM and OPM PE1 models, while the converse was true for those derived by CF. Estimates obtained by the OPM PE4 model were highest at the beginning of lactation and between 183 and 256 days in milk. Genetic correlations were high between consecutive test days, but decreased when intervals between test days increased. Where models ASM and OPM PE1 indicated a negative correlation between distant test days, OPM PE4 estimates were consistent with those of CF. Due to the statistical complexity of RR test-day models use of MT is a more feasible approach for the estimation of (co)variance components for CF coefficients.

Use of test day yields for the genetic evaluation of production traits in Holstein-Friesian cattle

Bayesian methods and Gibbs sampling techniques have been applied to estimate genetic parameters for test-day (TD) yields in the Spanish Holstein-Friesian population. Three models were analyzed: (a) multitrait model on successive TD yields within the first lactation; (b) multitrait model on the first three lactations considering TD yields as repeated measures within lactations; (c) random regression model (RRM) on first lactation TD yield. Two alternative RRM were adjusted, RRM1 considered random regression on the genetic effects only, RRM2 included random regressions for the genetic and permanent environmental effects and allowed for heterogeneous residual variances. In model (a), heritabilities tended to be larger in middle lactation and genetic correlations among TD measures were large (>0.80). Large genetic correlations among lactations (>0.89) and heterogeneous variances for first vs. other lactations were found for model (b). RRM1 was found to be superior to the simple repeatability model (b) in terms of reducing residual variance. However, RRM1 produced very large estimates of the genetic variance at the beginning and end of the lactation. Genetic and environmental variances estimated under RRM2 tended to be close to the multitrait model (a). Large discrepancies in the genetic correlations among daily yields with respect to the one observed from the multitrait approach were found for RRM1 and, to a lesser extent, for RRM2.

International study onArtemia LVIII. Morphologic differentiation and reproductive isolation ofArtemia populations from South America

SixArtemia populations from coastal and inland sites in Chile, ranging from 20 to 50 degrees latitude south, were compared morphologically. The study included reference samples ofA. franciscana (San Francisco Bay, California-USA) andA. persimilis (Buenos Aires, Argentina). These species are likely to be found in Chile. Samples from Peru (Piura) and Brazil (Macau, Rio Grande do Norte) are two known examples of deliberate introduction ofA. franciscana. The hypothesis ofA. franciscana being the dominant species in South America was tested by multivariate morphological analysis based on ten body measurements. In addition, laboratory cross-fertility tests were performed in order to evaluate levels of reproductive isolation among these widely distributed populations. The analysis showed thatA. franciscana andA. persimilis are morphologically divergent. A number of populations overlap with the San Francisco Bay sample, two are morphologically close to Buenos Aires, whilst others lie morphologically in between. Interpopulation morphological differences along with geographical and, probably, ecological divergence do not reflect reproductive isolation, at least of the pre-mating type. The morphological similarity of two Chilean samples withA. persimilis suggests that the distribution ofA. persimilis should be further investigated. A multi-trait approach forArtemia characterization is stressed as a way to obtain better descriptions and interpretations of the biological diversity in the genus.

A multitrait approach for data involving genotype x environment interaction

A multitrait approach for data involving genotype x environment interaction

Assessment of perennial ryegrass (Lolium perenne L.) for breeding. II. Components of winter hardiness

When breeding for good winter hardiness a broad range of adaptations must be considered. Such a multitrait approach requires some understanding of physiological and genetical relationships between relevant traits. Fourteen winter related characters were measured on field grown plants from 86 perennial ryegrass accessions originating from a wide range of climates. Genetic components of variance and covariance were extracted from the data and a principal components analysis carried out. The first three independent components accounted for 80% of the variance represented by the genetic correlations and were broadly identified as winter growth, winter hardiness and early spring activity factors. None of the accessions exhibited a combination of extreme winter growth and winter hardiness although several with excellent winter hardiness showed better than average winter growth. Amounts of water soluble carbohydrate maintained through the winter appeared important for good survival. It was concluded that a selection index approach may prove useful in future breeding programmes as further information concerning physiological relationships becomes available.

Convergent and Discriminant Validity of the Barclay Classroom Climate Inventory

The purpose of this study was to investigate the convergent and discriminant validity of a multimethod multitrait inventory used for assessing the climate of the elementary classroom. Using self-report, peer judgments, and teacher ratings, the inventory employs the multimethod multitrait factor analysis approach to determine the quality of social interaction and affective variables in the classroom. A computer processing procedure utilizing criteria developed in this approach scores, analyzes, and develops a written report on the pupil. These reports can be cumulated to result in descriptions of the social interaction and affective environment in the elementary classroom. A questionnaire comprised of short paragraphs defining the major factors from the inventory was administered with the inventory to nine elementary classrooms. Each student rated himself for each of the factors (for males, Affiliation, Dominance, Seclusiveness, Physical Skills, and Intellectuality; for females, Dominance, Aggression, Seclusiveness, Affiliation, and Intellectuality) and was in turn rated by a randomly selected peer and the teacher. These three rating sources combined with the inventory's factor scores to form a five trait four method matrix for the assessment of convergent and discriminant validity. Considerable evidence for these aspects of validity was found.