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Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. HI is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high [[pi].sub.non]/[[pi].sub.syn] ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen--host shift from Italian millet to rice.

The expression of nitrogenase genes of Herbaspirillum sp. B501 associated in shoot of wild rice, Oryza officinalis, is explored by means of reverse transcription-PCR (RT-PCR) targeted at the nifH gene. The results indicate that in planta nitrogen fixation by the endophyte shows a daily rhythm determined by the plant's light environment.

The genetic diversity was investigated among and within natural populations of Asian common wild rice, Oryza rufipogon, from three different classes of data that are quantitative traits, allozymes, and Restriction Fragment Length Polymorphisms (RFLPs). The results reflected the occurrence of adaptive differentiation in response to habitat conditions by quantitative trait analysis and the effect of isolation by distance by allozyme and RFLP analyses.

Several recent reports indicate that mobile elements are frequently found in and flanking many wild-type plant genes. To determine the extent of this association, we performed computer-based systematic searches to identify mobile elements in the genes of two 'model' plants, Oryza sativa (domesticated rice) and Arabidopsis thaliana. Whereas 32 common sequences belonging to nine putative mobile element families were found in the noncoding regions of rice genes, none were found in Arabidopsis genes. Five of the nine families (Gaijin, Castaway, Ditto, Wanderer, and Explorer) are first described in this report, while the other four were described previously (Tourist, Stowaway, p-SINE1, and Amy/LTP). Sequence similarity, structural similarity, and documentation of past mobility strongly suggests that many of the rice common sequences are bona fide mobile elements. Members of four of the new rice mobile element families are similar in some respects to members of the previously identified inverted-repeat element families, Tourist and Stowaway. Together these elements are the most prevalent type of transposons found in the rice genes surveyed and form a unique collection of inverted-repeat transposons we refer to as miniature inverted-repeat transposable elements or MITEs. The sequence and structure of MITEs are clearly distinct from short or long interspersed nuclear elements (SINEs or LINEs), the most common transposable elements associated with mammalian nuclear genes. Mobile elements, therefore, are associated with both animal and plant genes, but the identity of these elements is strikingly different.

The rice genus, Oryza (Poaceae), comprises 23 species and nine recognized genome types. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germplasm. By generating and comparing two nuclear genes (Adh1 and Adh2) trees as well as a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event and their maternal parent had the CC genome. The BBCC genome species had different origins and their maternal parents had either a BB or CC genome. A new genome type, HHKK, was recognized for O. schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. Phylogenetic relationship of the AA genome, which contains cultivated rice, is further investigated with additional nuclear gene markers.

The wild species, Oryza rufipogon, a weedy relative of cultivated rice, contains genes that can substantially increase the yield of rice. V/64 is a top yielding rice variety in China, derived from a cross between V20A and Ce64. The wild species O. rufipogon is crossed with V/64, V20B and Ce64 to produce BC(sub 2) test-cross families. The BC(sub 2) test-cross families outperform V/64 with respect to yield, grains per plant and 1,000-grain weight. The O. rufipogon alleles, yld1.1 and yld2.1, at marker loci RM5 on chromosome 1 and RG256 on chromosome 2, respectively are associated with enhanced yield.