New statistical methods for estimation of recombination fractions in F2 population

Abstract

BackgroundDominant markers in an F2 population or a hybrid population have much less linkage information in repulsion phase than in coupling phase. Linkage analysis produces two separate complementary marker linkage maps that have little use in disease association analysis and breeding. There is a need to develop efficient statistical methods and computational algorithms to construct or merge a complete linkage dominant marker maps. The key for doing so is to efficiently estimate recombination fractions between dominant markers in repulsion phases.ResultWe proposed an expectation least square (ELS) algorithm and binomial analysis of three-point gametes (BAT) for estimating gamete frequencies from F2 dominant and codominant marker data, respectively. The results obtained from simulated and real genotype datasets showed that the ELS algorithm was able to accurately estimate frequencies of gametes and outperformed the EM algorithm in estimating recombination fractions between dominant loci and recovering true linkage maps of 6 dominant loci in coupling and unknown linkage phases. Our BAT method also had smaller variances in estimation of two-point recombination fractions than the EM algorithm.ConclusionELS is a powerful method for accurate estimation of gamete frequencies in dominant three-locus system in an F2 population and BAT is a computationally efficient and fast method for estimating frequencies of three-point codominant gametes.Electronic supplementary materialThe online version of this article (10.1186/s12859-017-1804-8) contains supplementary material, which is available to authorized users.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools

“…In the next paper, Tan et al [7] proposed an expectation least squares (ELS) algorithm and binomial analysis of three-point gametes (BAT) for estimating gamete frequencies from F 2 dominant and codominant genotype data, respectively. Using simulated and real datasets, ELS algorithm was able to accurately estimate frequencies of gametes and outperformed the EM algorithm in recovering true linkage maps in coupling and repulsive linkage phases.…”