Effectiveness of bulking procedures in measuring population-pairwise similarity with dominant and co-dominant genetic markers

Two bulking procedures (bulking individuals before and after genotyping) are commonly applied in similarity based studies of genetic distance at the population or higher level, but their effectiveness is largely unknown. In this study, expected population-pairwise similarity for both bulking procedures is derived with dominant and co-dominant diallelic markers. Numerical examples for the derived formulae are given with up to ten individuals randomly selected from each population. The procedure of bulking individuals after genotyping with either marker system is generally more informative than the procedure of bulking individuals before genotyping, because the former incorporates the information from marker alleles of intermediate frequency. Both procedures are effective with 5-10 individuals selected randomly from either population, but the procedure of bulking before genotyping requires a genotyping effort several-fold less than the procedure of bulking after genotyping. For either bulking procedure, a co-dominant marker system is generally more informative than a dominant marker system.