Rice Genetics IV - IRRI books - International Rice Research Institute

group with the diploid E genome species, O. australiensis, on both Adh gene trees(Fig. 1). Although there were different opinions on the D genome donors of the CCDDspecies (Wang et al 1992, Fukui et al 1997), strong support of monophyly of the Dgenome sequence and the E genome sequence on both Adh trees suggested the closestrelationship of the E genome to the D genome progenitors, which gave rise to theCCDD species. Thus, the clade containing the diploid E genome and sequences fromthe CCDD genome species could be treated as the D genome clade (Fig. 3).The clade containing O. ridleyi, O. longiglumis, O. schlechteri, and Porteresiacoarctata on each Adh gene tree (Fig. 1) was designated as the H genome clade. Theother clade containing O. ridleyi and O. longiglumis on the Adh1 phylogeny representedthe J genome. The clade containing O. schlechteri and P. coarctata on theAdh2 tree was then given a new genome type, K (Fig. 1). Consequently, all species inthe genus Oryza have the genome type recognized, that is, the A, B, C, BC, CD, E, F,G, HJ, and HK genomes (Table 1).Phylogeny of rice genomes and intrageneric classificationBased on the two Adh data sets, we generated a consensus tree (Fig. 3) in which thecongruent relationships between the two gene trees were maintained and the incongruentrelationships were left unresolved (Swofford 1991). Monophyletic groups revealedby the phylogenetic reconstruction are either concordant or discordant withtaxonomic sections recognized in the most recent classification of the genus (Table1). The A, B, and C genomes are most closely related and together form a sister groupwith the D (E) genome. This monophyletic group, containing the A to E genomes,corresponds to section Oryza (section Sativa sensu Roschevicz 1931) (Fig. 3, Table1). The G genome, which occupies the most basal position of the genus, constitutessection Granulata sensu Roschevicz (1931). The remaining genome types that areincluded in section Ridleyanae, however, form a paraphyletic group in the phylogenetichypothesis (Fig. 3). It is evident that the circumscription of section Oryza isconsistent with those in most taxonomic treatments (Table 1). For other sections,however, the Adh gene phylogenies agree better with Roschevicz’s (1931) classificationthat recognized section Ridleyanae and section Granulata although sectionRidleyanae is paraphyletic (Figs. 1, 2). The section Padia recognized by Sharma andShastry (1965) forms a polyphyletic group on the Adh gene phylogenies (Fig. 3, Table1).In addition to the relationships among genome types, three gene phylogenies providesome implications for interspecific relationships within genomes. The A genome,which is present in cultivated rice, is one of the most recently diverged lineages withinthe rice genus (Fig. 1). It contains only diploid species and has the widest geographicdistribution compared with other genome groups in Oryza. Apparently, the A genomeis a well-adapted group that not only diversified recently but also radiated rapidly.The Adh phylogenies further indicated that the Asian cultivated rice, O. sativa, ismost closely related to two Asian wild species, O. nivara and O. rufipogon, supportingthe hypothesis of an Asian origin of O. sativa (Second 1982, Khush 1997). TheAfrican cultivated O. glaberrima is closely related to two African wild species, O.Phylogeny of the genus Oryza . . . 99