INTRODUCTION Estimation of covariance components by Restricted Maximum Likelihood (REML) fitting an animal model is widely carried out using a derivative-free (DF) algorithm to locate the maximum of the likelihood function. While such algorithms have proven robust and easy to use, they are generally slow to converge, often requiring many likelihood evaluations, in particular for multivariate an...

INTRODUCTION Maximising the (log) likelihood (logL) in restricted maximum likelihood (REML) estimation of variance components almost invariably represents a constrained optimisation problem. Iterative algorithms available to solve this problem differ substantially in computational resources needed, ease of implementation, sensitivity to choice of starting values and rates of convergence. One of...

applying an appropriate statistical analysis is complementary for conducting a robust experimental design in plant and animal breeding. in these experiments 33 iranian bread wheat genotypes, cultivated in a randomized complete blocks design with three replications in two normal and saline conditions were evaluated at the field of national salinity research center located in yazd province, iran....

Recently tridiagonalizafion and diagonalization have been proposed as methods to speed the EM algorithm for variance component estimation in restricted maximum likelihood. These methods require approximately the same computing resources, but only if the most efficient strategies are employed. When eigenvectors are explicitly calculated in diagonalization, computing requirements more than double...

The effect of the melatonin receptor 1a (MTNR1A) gene on fertility and litter size in autumn lambing was studied with 373 ewes from a population of sheep selected for 10 yr for fertility in May and June matings. Animals were from a composite line of 50% Dorset, 25% Rambouillet, and 25% Finnsheep. Two restriction fragment length polymorphisms were present in the population, with allelic frequenc...

Difficulties with inference in predictive regressions are generally attributed to strong persistence in the predictor series. We show that the major source of the problem is actually the nuisance intercept parameter and propose basing inference on the Restricted Likelihood, which is free of such nuisance location parameters and also possesses small curvature, making it suitable for inference. T...

A herd of Norwegian dairy goats was subject to selection for high and low antibody response to diphtheria toxoid for 12 yr, or approximately 5.5 generations because sires were used for one mating season, whereas dams were used several years. The herd comprised approximately 100 milking goats. Only sires were tested and selected, five to seven sires were used in each line each year, and the perc...

Genome-wide association studies (GWASs), also called common variant association studies (CVASs), have uncovered thousands of genetic variants associated with hundreds of diseases. However, the variants that reach statistical significance typically explain only a small fraction of the heritability. One explanation for the "missing heritability" is that there are many additional disease-associate...