Genetic Analysis of SSR Markers in F2 Reciprocal Populations of the Rice genotypes, Horkuch and IR29 show high segregation distortion

A total of 58 simple sequence repeat (SSR) markers were tested for genotyping and constructing a genetic linkage map of a reciprocal F2 populations of a salt tolerant rice landrace, Horkuch and high-yielding but sensitive IR29. The IR29♀ (IH) population was 200, while the Horkuch♀ (HI) one, 100. In the F2 population, 24 (~73%) and 39 (78%) markers showed significant segregation distortion (P<0.05) in the IH and HI populations respectively. 14 and 10 markers were skewed for the female, IR29 and male Horkuch, respectively in the IH population. On the other hand, 19 markers each were skewed either toward the female parent Horkuch or male parent IR29 with one for the heterozygote in the HI population. Nuclear and cytoplasmic effects were detected for the 25 common markers used in the 2 populations. The segregation distortion of 16 (64%) and 9 (36%) markers were found to have nuclear and cytoplasmic effects respectively. Gametic and zygotic selections analyzed by allele frequency and F2 genotype frequency distribution showed that the segregation distortion of 8, 5 and 22 markers were influenced by respectively by zygotic, gametic or both selections simultaneously. 15 out of 50 marker loci of the HI population were mapped on 7 linkage group covering a total length of 462.857 cM on the rice genome (average intervals of 30.86 cM between adjacent markers). No linkage group was found on chromosome 2, 4, 6, 8 and 11.