The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se-pat gene. Fine mapping in two of these near-isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly-observed recessive gene (se-pat). Molecular dissection suggested that the tandemly duplicated FT-like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype x environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se-pat(+) alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.

It has been theoretically proposed that multiple linked quantitative trait loci (QTLs) play a role in the accumulation of hidden variation within and between populations. In this study, the genetic bases for grain characteristics were examined by comparing two accessions representing the two rice subspecies by QTL analysis. Grain dimensions are known to be quantitative traits and to be diagnostic between these two subspecies. To enhance the power to detect QTL with small effects, after transferring a segment of chromosome 6 from an Indica type into a Japonica type of rice by repeated backcrosses, the introgressed segment was dissected by making recombinant inbred lines (RILs) which were expected to have different sizes of the introgressed segment in the same genetic background. The resulting RILs showed distinct transgression of the grain characteristics examined. Multiple QTLs controlling each of the length and breadth of seeds were detected on the introgressed segment, and showed positive and negative additive effects as well as epistatic interactions. The present study confirmed that transgressive segregation resulted from a breakdown of linkage and that the detection of QTLs was highly dependent upon the genetic effects of the neighboring QTLs, indicating the need for caution in interpreting QTL effects.