GENETIC-ANALYSIS USING TRANSDOMINANT LINKED MARKERS IN AN F2 FAMILY

Trans-dominant linked markers pairs (trans referring to the repulsion linkage phase) provide a model for inferring the F-2 progeny genotype based upon both the conditional probabilities of F-2 genotypes, given the F-2 phenotype, and prior information on marker arrangement. Prior information of marker arrangement can be readily obtained from a linka ge analysis performed on marker segregation data in a family resulting by crossing the F-1 individual to a ''tester'' parent or else can be obtained directly from the gametes of the F-1, or from recombinant inb red lines. We showed that a trans-dominant linked marker (TDLM) pair c an be recoded as a ''co-dominant megalocus'' when the recombination fr action, r(1), for a pair of TDLMs is less than 0.05. We obtained a max imum-likelihood estimator (MLE) of the recombination frequency, r(2), between a TDLM pair and a co-dominant marker in an F-2 family using th e EM algorithm. The MLE was biased. Mean bias increased as r(1) and r( 2) increased, and decreased as sample size increased. The information content for r(2) was compared to the information content of dominant a nd co-dominant markers segregating in an F-2 family. It was almost ide ntical with two co-dominant markers when r(1) less than or equal to 0. 01 and r(2) greater than or equal to 0.05. For larger values of r(1), (0.05 less than or equal to r(1) less than or equal to 0.15) a TDLM pa ir provided 75%-66% of the information content of two co-dominant mark ers. Although dominant markers can be converted to co-dominant markers by a laborious process of cloning, sequencing, and PCR, TDLM pairs co uld easily substitute for co-dominant markers in order to detect quant itative trait loci (QTLs) and estimate gene action in an F-2 family.