Genetic analysis using trans-dominant linked markers in an F2 family

Trans-dominant linked markers pairs (trans referring to the repulsion linkage phase) provide a model for inferring the F₂ progeny genotype based upon both the conditional probabilities of F₂ genotypes, given the F₂ phenotype, and prior information on marker arrangement. Prior information of marker arrangement can be readily obtained from a linkage analysis performed on marker segregation data in a family resulting by crossing the F₁ individual to a tester parent or else can be obtained directly from the gametes of the F₁, or from recombinant inbred lines. We showed that a trans-dominant linked marker (TDLM) pair can be recoded as a co-dominant megalocus when the recombination fraction, r₁, for apair of TDLMs is less than 0.05. We obtained a maximum-likelihood estimator (MLE) of the recombination frequency, r₂, between a TDLM pair and a co-dominant marker in an F₂ family using the EM algorithm. The MLE was biased. Mean bias increased as r₁ and r₂ increased, and decreased as sample size increased. The information content for r₂ was compared to the information content of dominant and co-dominant markers segregating in an F₂ family. It was almost identical with two co-dominant markers when r₁0.01 and r₂0.05. For larger values of r₁, (0.05r₁0.15) a TDLM pair provided 75%–66% of the information content of two co-dominant markers. Although dominant markers can be converted to co-dominant markers by a laborious process of cloning, sequencing, and PCR, TDLM pairs could easily substitute for co-dominant markers in order to detect quantitative trait loci (QTLs) and estimate gene action in an F₂ family.