WhenDPL1-N+was launched into NILs possessingDPL1-K/DPL1-KandDPL2-K+/DPL2-N(Fig. to gene circulation between two species provides insight into molecular mechanisms of reproductive isolation (3) and associations between development of barrier genes and speciation. Despite the importance of such studies, only a handful of genes responsible for genetic incompatibilities in intrinsic postzygotic barriers have been recognized from a few well-characterized model species, including mouse, travel, yeast,Arabidopsis, and rice (3,4), where map-based cloning is possible. Asian cultivated rice,Oryza sativa, is usually one such well-characterized species with a small genome size (400 Mb), and genome sequences available for its two differentiated subspecies,indicaandjaponica(5,6). Bothindicaandjaponicacomprise a large variety of strains showing a wide range of genetic diversity and structured populations, which seem to be in the early stages of speciation (79). In the process of rice breeding, various genetic incompatibilities in intersubspecific hybrids betweenindicaandjaponicahave been reported (ref.7; see also Oryzabase atwww.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). Despite many attempts to isolate the genes LFM-A13 responsible for these hybrid incompatibilities, only a few genes have been isolated (1013), and the associations between genetic LFM-A13 incompatibilities and rice differentiation is usually poorly comprehended. To investigate the molecular mechanisms of reproductive isolation and the status of evolutionary differentiation withinOryza, we developed a method to map reproductive barriers by regression analysis of allele frequencies using anindica-japonicaF2populace, and mapped more than 30 reproductive barriers (14). These LFM-A13 mapped barriers are due to interactions between genetic factors of the parents of the hybrid, and detection of interacting loci is the first step toward isolation of the causal genes. In this study, detection of the two-way conversation and positional cloning of the detected interacting loci pair were carried out using the same cross-combination used previously for mapping reproductive barriers (14). LFM-A13 Evolutionary analysis of the causal genes was performed to investigate the establishment of this genetic incompatibility in rice. == Results and Conversation == == Detection of the Interacting Loci Causing Genetic Incompatibility. == For fine mapping of a reproductive barrier as a single genetic factor, and understanding its molecular mechanisms of hybrid incompatibility, it is essential to know interacting loci and where they take action. In the early stages of speciation, as injaponica-indica, genetic incompatibility caused by simple two-way interactions would be expected to be more common, because two-way interactions represent the smallest number of differences, which could cause an incompatibility between them. To detect two-way interactions between segregating genotypes at different loci, 2independence assessments of all codominant marker combinations were performed for any high-density linkage map that was made using an F2populace from a cross betweenjaponicacultivar Nipponbare andindicacultivar Kasalath (15) and utilized for mapping reproductive barriers (14). Contour plots of 2values are shown in black contours of the upper-left part ofFig. 1. High 2values caused by linkage were observed at diagonals between corresponding chromosomes. There were 14 nonlinked chromosomal pair regions where 2peak values were more than 20 and the highest peak value was 33.6 between chromosome 9 and 12. The probability of a 2peak value of 20 with 4 degrees of freedom in a 2distribution is usually less than 5 KLF1 104for a single test. However, this analysis entails a great degree of multiple screening. A Bonferroni correction for multiple screening cannot be applied in this case, because each test was dependent by linkage. To find true interactions, reproducibility of the independence assessments of marker segregation was tested using 286 different LFM-A13 F2plants from your same cross-combination (reddish contours of upper-left part ofFig. 1). Although allele frequency curves were comparable between different populations (Fig. 1AandB), reproducible peaks.