Rice Genetics IV - IRRI books - International Rice Research Institute

arthii and O. longistaminata, and to the New World species, O. glumaepatula. Theseresults are in general agreement with studies using various markers (Wang et al 1992,Aggarwal et al 1999, Joshi et al 2000).An important argument in our three gene phylogenies involves the position ofPorteresia coarctata that was once recognized as a species of Oryza (O. coarctataRef.), but treated as a monotypic genus by Tateoka (1965a). It is shown that P. coarctataand O. schlechteri share the same genome type, HHKK, and are closely related toeach other according to the phylogenies of the two Adh genes and the matK gene(Figs. 1, 2). Therefore, Porteresia coarctata should be treated as a member of Oryzarather than as a separate genus. Recent AFLP and ISSR analyses also showed someaffinities of P. coarctata and Oryza species (Aggarwal et al 1999, Joshi et al 2000).Remaining questions and future directionsA robust phylogeny and the taxonomic position of particular speciesOur recent phylogenetic study using Adh and matK genes has led to a better understandingof the phylogeny of Oryza, but relationships among the genomes still remainpartially unresolved or weakly supported (Fig. 1). In the Adh phylogenies, for example,the A and C genomes are sister groups on the Adh1 tree, whereas the A and Bgenomes are sister groups on the Adh2 tree (Fig. 1). The topological incongruencewas statistically significant and the reasons for the incongruence need to be furtherinvestigated (Ge et al 1999).Furthermore, the relationship of the F genome remains unsolved on the overallphylogenetic hypothesis of the genus (Figs. 1, 3). It was grouped strongly with the Hgenome on the Adh2 tree but did not form a strongly supported group with any genometype on the Adh1 tree (Fig. 1). Previous morphological and molecular studiesalso showed conflicting results regarding the taxonomic position of O. brachyanthaof the F genome. It has been associated with the O. ridleyi complex on the basis of itsembryo structure and other morphological traits (Vaughan 1994), but showed someaffinity to the O. sativa complex according to a nuclear RFLP study (Wang et al1992). In contrast, data from recent AFLP and ISSR studies demonstrated that the Fgenome did not align with any species complex in Oryza (Aggarwal et al 1999, Joshiet al 2000). Because O. brachyantha is morphologically, cytologically, and geneticallydistinct from all other Oryza species (Vaughan 1989, Aggarwal et al 1999), Lu(1999) treated it as a separate section. The position of the F genome remains questionableand should be further clarified with additional gene markers (Ge et al 1999).Additionally, we were not able to isolate one homeologous Adh1 locus from O.ridleyi and O. longiglumis and one homeologous Adh2 locus from O. schlechteri andPorteresia coarctata although various PCR strategies have been tried (Ge et al 1999).These results support the hypothesis of gene deletion, that is, deletion of the Adh1gene from the K genome of O. schlechteri and P. coarctata and deletion of the Adh2gene from the J genome of O. ridleyi and O. longiglumis. The deletion of one of thehomeologous loci may be a mechanism of reduction of genetic redundance in theseallotetraploid rice species. On both Adh phylogenies, the sequences of the HJ and HK100 Song Ge et al