Estimation of milk protein gene frequencies in crossbred cattle by maximum likelihood

A maximum likelihood method is presented to estimate the fraction of animals misclassified and breed effects for milk protein gene frequencies based on crossbred data. A simulation study indicates that the method provides estimates of gene frequencies that agree closely with the true values. Gene frequencies in the Dutch Black and White and the Dutch Red and White crossbred populations, based on data on 10,151 and 580 animals respectively, were estimated. Dutch Friesian and Holstein-Friesian breeds differ in gene frequencies for beta-casein and beta-lactoglobulin. Estimates for fractions misclassified are zero for alpha s1-casein, .09 for beta-casein and beta-lactoglobulin, and .12 for kappa-casein. Differences between Dutch Red and Whites and Red Holstein-Friesian breeds are small, and estimates for fractions misclassified are high but have high approximate standard errors. Compared with the Black and White breeds, the Red and Whites have a high kappa-casein B gene frequency.