Mixed model approaches for the identification of QTLs within a maize hybrid breeding program.

Two outlines for mixed model based approaches to quantitative trait locus (QTL) mapping in existing maize hybrid selection programs are presented: a restricted maximum likelihood (REML) and a Bayesian Markov Chain Monte Carlo (MCMC) approach. The methods use the in-silico-mapping procedure developed by Parisseaux and Bernardo (2004) as a starting point. The original single-point approach is extended to a multi-point approach that facilitates interval mapping procedures.

Estimates of genetic parameters for 320-day pelvic measurements of males and females and calving ease of 2-year-old females.

Records from 12 breed groups collected from 1983 to 1991, included in the Germ Plasm Utilization project at the U.S. Meat Animal Research Center, were analyzed separately by breed group and combined to estimate heritabilities and genetic correlations for 320-d male and female pelvic width, height, and area, and for 320-d male pelvic and female 2-yr-old calving ease.

Correlations for genetic expression for growth of calves of Hereford and Angus dams using a multivariate animal model.

The purpose of this study was to estimate the correlation between the expression of genes from sires in purebred and crossbred progeny (rPC) and in Hereford and Angus F1 calves (rHA). Performance traits were weights at birth, 200 d, and 365 d. Progeny from Hereford, Polled Hereford, and Angus bulls mated to Hereford or Angus cows were used to estimate rPC.

Estimates of variances due to direct and maternal effects for growth traits of Romanov sheep.

Records of growth traits of 2,086 Romanov lambs were used to estimate variance components for an animal model and genetic correlations between growth traits. Traits analyzed were birth weight (BWT), weaning weight (WW), 90-d weight (W90), and daily gain for the periods birth to weaning (DG1) and weaning to 90 d (DG2). Weaning was at approximately 40 d.

Sequential transformation for multiple traits for estimation of (co)variance components with a derivative-free algorithm for restricted maximum likelihood.

Transformation of multiple-trait records that undergo sequential selection can be used with derivative-free algorithms to maximize the restricted likelihood in estimation of covariance matrices as with derivative methods. Data transformation with appropriate parts of the Choleski decomposition of the current estimate of the residual covariance matrix results in mixed-model equations that are easily modified from round to round for calculation of the logarithm of the likelihood. The residual sum of squares is the same for transformed and untransformed analyses.

Estimated breeding values for meat characteristics of crossbred cattle with an animal model.

Longissimus muscle area, shear force measure, and sensory panel scores for flavor, juiciness, and tenderness, and marbling score were obtained from 682 steer carcasses, resulting from crosses among five Bos taurus and Bos indicus breeds. The single-trait model used included birth year and as covariates breed fractions, weaning age, and days on feed. The numerator relationship matrix was for 1,350 animals (682 steers, 74 pure breed and 52 F1-cross sires and 542 dams).

Estimates of genetic parameters for direct and maternal effects on embryonic survival in swine.

Survival of 16,838 potential embryos was determined by counting corpora lutea and fetuses at 50 d of gestation for 1,081 litters by 225 sires. These data, coded as 1 or 0 depending on whether an ovulation was represented by a fetus, were used to estimate direct and maternal additive genetic variances and their covariance for embryonic survival. Data were from first-parity gilts of a Large White-Landrace composite population subdivided into two lines, one selected for an index of ovulation rate and embryonic survival for seven generations and a contemporary control line.

Derivative-free restricted maximum likelihood estimation in animal models with a sparse matrix solver.

Estimation of (co)variance components by derivative-free REML requires repeated evaluation of the log-likelihood function of the data. Gaussian elimination of the augmented mixed model coefficient matrix is often used to evaluate the likelihood function, but it can be costly for animal models with large coefficient matrices. This study investigated the use of a direct sparse matrix solver to obtain the log-likelihood function.

Association of sire dystocia transmitting ability with progeny linear type traits in Holsteins.

Data on 13 traits of 11,260 progeny of 775 sires in the Carnation Genetics linear type appraisal program were analyzed to determine the association between sire dystocia transmitting ability and progeny linear type traits. Mean linear type scores ranged from 25.0 to 29.

Genetic trend for milk yield from doe evaluations in the northeast United States.

Milk production records of 306 Alpine, 72 LaMancha, 170 Nubian, 84 Saanen, and 235 Toggenburg does born in the Northeast from 1972 through 1979 were used to estimate trends of additive genetic value. Estimated transmitting abilities were doubled and averaged for all does born in each year to obtain yearly estimates of genetic value. Genetic trends from regression of yearly mean genetic value on year of birth for Alpine, LaMancha, Nubian, Saanen, and Toggenburg averaged 11.