Originally published as Genetics Published Articles Ahead of Print on October 22, 2006.

Genetics, Vol. 175, 923-931, February 2007, Copyright © 2007
doi:10.1534/genetics.106.064030

A New Strategy for Estimating Recombination Fractions Between Dominant Markers From an F2 Population

Yuan-De Tan*,{dagger} and Yun-Xin Fu*,{ddagger},1

* Human Genetics Center, School of Public Health, University of Texas, Houston, Texas 77030, {dagger} College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China and {ddagger} Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming Province, 65091, Yunnan, China

1 Corresponding author: Human Genetics Center, School of Public Health, University of Texas, 1200 Herman Pressler, Houston TX 77030.
E-mail: yunxin.fu{at}uth.tmc.edu

Although most high-density linkage maps have been constructed from codominant markers such as single-nucleotide polymorphisms (SNPs) and microsatellites due to their high linkage information, dominant markers can be expected to be even more significant as proteomic technique becomes widely applicable to generate protein polymorphism data from large samples. However, for dominant markers, two possible linkage phases between a pair of markers complicate the estimation of recombination fractions between markers and consequently the construction of linkage maps. The low linkage information of the repulsion phase and high linkage information of coupling phase have led geneticists to construct two separate but related linkage maps. To circumvent this problem, we proposed a new method for estimating the recombination fraction between markers, which greatly improves the accuracy of estimation through distinction between the coupling phase and the repulsion phase of the linked loci. The results obtained from both real and simulated F2 dominant marker data indicate that the recombination fractions estimated by the new method contain a large amount of linkage information for constructing a complete linkage map. In addition, the new method is also applicable to data with mixed types of markers (dominant and codominant) with unknown linkage phase.