Genetic control of phenotypic plasticity in Asian cultivated and wild rice in response to nutrient and density changes.

Phenotypic plasticity is an adaptive mechanism adopted by plants in response to environmental heterogeneity. Cultivated and wild species adapt in contrasting environments; however, it is not well understood how genetic changes responsible for phenotypic plasticity were involved in crop evolution. We investigated the genetic control of phenotypic plasticity in Asian cultivated (Oryza sativa) and wild rice (O. rufipogon) under 5 environmental conditions (2 nutrient and 3 density levels). Quantitative trait locus (QTL) analysis was conducted for traits affecting plant architecture and biomass production. By analysing the phenotypic means, QTLs of large effects were detected as a cluster on chromosome 7 under all the environmental conditions investigated; this might have contributed to transitions of plant architecture during domestication, as reported previously. Multiple QTLs of plasticity were also found within this QTL cluster, demonstrating that allele-specific environmental sensitivity might control plasticity. Furthermore, QTLs controlling plasticity without affecting phenotypic means were also identified. The mode of action and direction of allele effects of plasticity QTLs varied depending on the traits and environmental signals. These findings confirmed that cultivated and wild rice show distinctive genetic differentiation for phenotypic plasticity, which might have contributed to adaptation under contrasting environmental heterogeneity during the domestication of rice.

Diversification in flowering time due to tandem FT-like gene duplication, generating novel Mendelian factors in wild and cultivated rice.

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.