Haplotype frequencies of linked loci in backcross populations derived from inbred lines

Linkage disequilibrium among loci is an important parameter in explaining genotypic means and variances in animal and plant breeding populations. Joint haplotype frequencies and their sampling covariance matrix for any number of linked loci were derived for backcross populations derived from inbred lines. The predicted frequencies can be used to test whether the linkage disequilibrium observed between (marker) loci in backcross populations is as expected