Heterozygosity for genes influencing a quantitative trait

Choosing families to sample for a quantitative trait locus mapping experiment is a critical component of experimental design because only heterozygous families contribute information to the analysis. Additive genetic variance of a paternal half-sib family can be partitioned into two parts: a variance component of maternal source that is constant across different families and a variance component of paternal source that is defined as an index of heterozygosity of a sire. This index is shown to be an upper limit of variance among marker genotypes of a half-sib family and can be used to identify highly heterozygous sires, thus improving the power of detecting QTL in detection studies. Simulated progeny phenotypic data were used to estimate sire's heterozygosity index via an ANOVA method, and accuracy of the estimation was evaluated with the correlation coefficient between the true and estimated index summarized both as the correlation and by the correct ranking of results as measured by the ratio of the true average heterozygosity index of experimentally selected parents to average heterozygosity of all sires. Positive but small correlation can be achieved in the estimation of a sire's heterozygosity when based on the daughters' phenotypic data, and accuracy was improved when progeny-tested sons were used to estimate their grandsire's heterozygosity index, depending on the genetic model of a trait and the size and structure of families.