9. Oryza schlechteri Pilger has a distinct genome based on molecular analysis R.K. aogarwai., D.S. brar, G.S. khush and M.T. jackson

Division of Plant Breeding, Genetics and Biochemistry IRRI, P.O. Box 933, 1099 Manila, Philippines

 The genus Oryza to which the cultivated rice belongs has 22 species (2n = 24 or 48), which represent seven genomes (AA, BB, CC, BBCC, CCDD, EE and FF). The genomic constitution of two tetraploid species of the 0. ridleyi complex, three diploid species of the 0. meyeriana complex, and 0. schlechteri is unknown. 0. schlechteri is also the least studied in the genus. Information on its taxonomic status, genomic relationships and crossability with other species is lacking. This species, originally described in 1907, was recently collected as living plants below the Jamu Gorge in the Finisterre Mountains of Papua New Guinea (Vaughan and Sitch 1991). It is a tetraploid species having 2n=48 chromosomes (Naredo and Vaughan 1992). It is distributed along the Beaufort River, Irian Jaya, Indonesia, and in Papua New Guinea. It grows in complete or partial shade in undisturbed forests and is not closely related to any species in the genus Oryza (Vaughan 1994)

Various methods can be used to ascertain the genomic constitution of species, of which chromosome pairing in interspecific hybrids is the most widely used. However, the single accession of this species in the International Rice Genebank Collection (IRGC 82047) was collected as a vegetative sample, and it has not been possible yet to induce flowering. Since this approach was not possible, we chose to make a molecular analysis to determine its genomic constitution.

A Southern blot having Dral digested genomic DNA from all the Oryza species, representing known as well as unknown genomes, 6 related grasses and 3 outgroup taxa, was hybridized with the total genomic DNA of 0. schlechteri and other species as a probe at different stringencies of DNA hybridization. Strikingly, the genomic DNA of 0. schlechteri when used as probe did not show detectable hybridization with DNA of any other species of Oryza (except for its own lane on the blot) even under low stringecy of hybridization and washing permissible to detect 10-15% (homology) related sequences (Fig. 1). Similarly, when genomic DNA from other Oryza species were used as probe, no hybridization signal were observed for 0. schlechteri. These observations demonstrate that the genome of 0. schlechteri is highly (>30%) diverged from rest of the genomes of Oryza at the molecular level.

Restriction fragment length polymorphism (RFLP) analysis involving 46 single locus probes from the rice genomic library covering all the 12 chromosomes of rice and one conserved probe of rDNA, also showed distinct divergence of 0. schlechteri from the rest of the species. The dendrogram (not shown) constructed from the RFLP data, using the distance matrix (Nei and Li 1979) and UPGMA algorithm of clustering (Sokal and Michener 1958) revealed it to be one of the most diverged species in the genus Oryza. which does not align with any other species complex, in a way that is comparable to the related grasses in the tribe Oryzae.

Research Notes 59
Fig. 1. Dra1 -Southern profiles of some of the representative Oryza species and other taxa obtained after hybridization with 32^P-labeled total genomic DNA of 0. schlechteri (6 h exposure after low-stringency wash of 2 x SSC at 60°C). Note the absence of hybridization signal across tracks 1-29 in comparison with the lane 30 which has DNA from 0. schlechteri. Tracks: 1-5: 0. ridleyi complex (Ace. 106028, 105973, 105146, 105148, 105562): 6-9: 0. australiensis(Acc. 100882, 103318, 105269, 105272): 10-11: 0. brachyantha (Ace. 101232, 94-10482); 12-20: 0. meyeriana complex (Ace. 100879, 102118, 104503, 106449, 104986, wsp-90-5, 106473, 106474, 105694); 21-26: Related grasses (2l-Porteresia coarctata, 22-Leersia tisseranti; 23-L. perrieri; 24-Rhynchoryza subulata; 25-Hygroryza aristata; 26-Chi-kusichloa aquatica)', 27-29 Outgroup taxa (local cultivars of maize; sugarcane; and soybean); 30- 0. schlechteri (IRGC 82047). These results suggest that this tetraploid species has distinct genome(s) which are

highly diverged from the other Oryza genomes at the molecular level.

 References 

Naredo, E. and D.A. Vaughan, 1992. The chromosome number of Oryza schlechteri Pilger. Int. Rice Res.

Newsl. 17:5. Nei, M. and W.H. Li, 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci., USA 76: 5269-5273. Sokal, R.R. and C.D. Michener, 1958. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 28: 1409-1438. Vaughan, D.A., 1994. The wild relatives of rice. Intl. Rice Res. Inst., Los Banos, Philippines 137 pp.

Vaughan, D.A. and L.A. Sitch, 1991. Gene flow from the jungle to farmers: wild-rice genetic resources and

their uses. Bioscience 44: 22-28.