A statistical method for genetic mapping of sterility genes that exhibit epistasis in remote hybridization of plants using molecular markers in an F2 population

ShangQian Xie,JianGuo Chen

doi:10.1007/s11434-012-5227-7

Abstract

Estimation of the position and effect of sterility genes is an important problem to be solved to understand the sterility mechanism in remote hybridization in plants. In this study, a maximum likelihood (ML) method was used for estimation of the position and effect of sterility genes that exhibit epistasis in an F2 population using the distorted segregation of markers. The ML solutions for recombination fraction and viability were obtained via an expectation-maximization algorithm. The results of Monte Carlo simulations showed that the estimates of recombination fraction and viability were consistent with their true values. The bias and standard deviation of parameters indicated that a larger sample size, closer linkage and lower viability of sterile genes led to better estimates of the parameters involved. A subset of marker data of the F2 population derived from a single cross between the rice japonica cultivar Nipponbare and the indica cultivar Kasalath was analyzed using this method. Eight sterility genes were identified on chromosomes 1, 3, 6, 8 and 10, and significant epistasis was detected among four pairs of sterility genes.

Highlights

Distorted segregation of molecular markers is a phenomenon in which the genotypic frequency of a marker deviates from the expected Mendelian ratio, which is very common in mapping populations derived from remote hybridization in plants
The parameter estimates for the sterility genes located near the markers 1 chromosome marker 6 (1M6) and 2 chromosome marker 4 (2M4) were almost equal to their true values, and the farther the sterility loci were located from the markers, the greater the estimated values deviated from their true values
The maximum likelihood ratio (LR) value was obtained at the site of 100 and 60 cM on chromosome 1 and 2, respectively, i.e., the marker combination 1M6-2M4, in which the putative sterility genes are located

Summary

Introduction

Distorted segregation of molecular markers is a phenomenon in which the genotypic frequency of a marker deviates from the expected Mendelian ratio, which is very common in mapping populations derived from remote hybridization in plants. The presence of only a small number of SDL can cause the entire chromosome to distort from Mendelian segregation [6] These loci are subject to gametic selection, zygotic selection or both [7,8,9], and most studies show that gametic selection is strongly related to segregation distortion. Zhu et al [17,18] estimated the selection coefficient of viability loci and simultaneously reconstructed the genetic linkage map from the adjusted recombination rate in backcross and F2 populations. Those methods did not consider the possibility of epistasis between vitality loci or sterility genes. We propose a new method that can be used to map sterility genes with epistasis in remote hybridization of plants by using cosegregation data for markers in an F2 population

Methods

Results

Conclusion