Segregation distortion in the BC1F1 population from a cross between indica and japonica rice.

Reproductive barriers are thought to play an important role in the processes of speciation and differentiation. One of the applications of DNA markers in studying reproductive barrier is the analysis of segregation distortions that deviates from expected Mendelian segregation ratios. Therefore, it is necessary to develop high-density molecular linkage maps and to analyze the proportions of genotypes over the whole genome, and moreover, to estimate the locations and effects of segregation distortion loci and the directions of the deviation of genotype frequencies by using model methods. The BC1F1 population consisting of 254 individuals was created from a backcross between an indica variety Taichung Sen10 as recurrent parent and a japonica variety Taikeng2 as donor parent. Genotyping was performed using 133 insertion-deletion (InDel) markers and 14 simple sequence repeat (SSR) markers, yielding a genetic map of 1494.7 cM, with an average interval of 11.072 cM. However, in some regions the map distances between markers showed considerable deviation from the published linkage map. Segregation distortions were found on chromosome 1, 2, 3, 6, 10, 11 and 12 respectively. There were some distorted markers clustered in special regions on chromosome 3, 6 and 11, and they all deviated toward indica homozygote. The positions of regions with serious biased genetic distances and regions where distorted markers clustered were overlapping. This result conforms with other studies which showed that the genetic distances between markers distorted toward the same direction will be underestimated. Chi-square test revealed that there is no interaction between distorted markers on different chromosomes, hence single SDL model method is used. Maximum likelihood method is implemented via an Expectation-Maximum algorithm to estimate the locations and effects of segregation distortion loci. Totally, there are 10 SDLs on all chromosomes in this backcross population from a cross between TCS10 and TK2.