BackgroundSegregation distortion (SD) is a frequently observed occurrence in mapping populations generated from crosses involving divergent genotypes. In the present study, ten genetic linkage maps constructed from reciprocal F2 and BC1F1 mapping populations derived from the parents Dasanbyeo (indica) and Ilpumbyeo (japonica) were used to identify the distribution, effect, and magnitude of the genetic factors underlying the mechanisms of SD between the two subspecies.ResultsSD loci detected in the present study were affected by male function, female function, and zygotic selection. The most pronounced SD loci were mapped to chromosome 3 (transmitted through male gametes), chromosome 5 (transmitted through male gametes), and chromosome 6 (transmitted through female gametes). The level of SD in BC1F1 populations which defined by chi-square value independence multiple tests was relatively low in comparison to F2 populations. Dasanbyeo alleles were transmitted at a higher frequency in both F2 and BC1F1 populations, suggesting that indic a alleles are strongly favored in inter-subspecific crosses in rice. SD loci in the present study corresponded to previously reported loci for reproductive barriers. In addition, new SD loci were detected on chromosomes 2 and 12.ConclusionThe identification of the distribution of SD and the effect of genetic factors causing SD in genetic mapping populations provides an opportunity to survey the whole genome for new SD loci and their relationships to reproductive barriers. This provides a basis for future research on the elucidation of the genetic mechanisms underlying SD in rice, and will be useful in molecular breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0003-8) contains supplementary material, which is available to authorized users.

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Grain size and panicle architecture are important traits determining yield. Here we report a new allele of DEP2 (dense and erect panicle 2) which has a pleiotropic effect on grain size/shape and panicle architecture. A small round grain and erect panicle mutant was obtained by treating japonica cultivar Hwacheong waxy with MNU (N-methyl-N-nitrosourea). Through fine mapping sequence analysis, we identified the single nucleotide substitution in the mutant, which caused splicing error of the first intron, on previously reported DEP2 locus in rice. Since the dep2-1 and dep2-2 have been reported in previous studies, we named this new allele as dep2-3. The dep2-3 mutant manifested reduced grain size and plant height, dense and erect panicle and erect plant architecture. When we crossed the mutant with wild type, panicle and grain of F1 plant showed intermediate phenotype, indicating that dep2-3 showed incomplete dominance, which was not reported in the previous study. Scanning electron microscopy (SEM) results showed that increase in width of mutant grain was due to the increased width of glume cells. Paraffin section of peduncle revealed that outgrowth in outer layer of peduncle compared to inner layer caused the erectness of the panicle. Our results collectively indicated that the dep2-3 might play a significant role in the regulation of grain size/shape and formation of vascular bundles.