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

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 F-2 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 F-2 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.