Comparative genomics in the Oryzeae

American wild rice (Zizania palustris) is a close relative of rice (Oryza sativa), with both belonging to the tribe Oryzeae. To delineate the position of wild rice within the Oryzeae, genes Adh1, Adh2, and matK were sequenced and compared with DNA sequences from other members of the Oryzeae. Both Adh1 and Adh2 appear to be duplicated in the Zizania species, although not because of polyploidy as in the case of many wild rice species. Unlike the rest of the Oryzeae, the Zizania species have chromosome numbers that differ from the basic number of 12. Three chromosomes in Zizania sp. appear to be duplicates of rice chromosomes based on comparative genetic mapping. There is, however, extensive genetic colinearity between wild rice and rice. More than 80% of the RFLP loci are colinear between those two species. We have undertaken a phsyical mapping approach to complement comparative genetic mapping. Although ribosomal DNA loci do not appear to be conserved in number or location within the Oryza species, wild rice has two 5S rDNA loci and one NOR locus. As in other Oryza species, the two 5S rDNA loci are intimately associated with the centromeres and the NOR is telomerically located. Several rice centromeric sequences have been used for FISH and Southern analysis. Only RCS1, a conserved cereal centromeric sequence, appears to be conserved. Bacterial artificial chromosomes, which are part of the rice physical map being sequenced, are being mapped first in rice and subsequently in wild rice to physically compare large genomic regions between these two species, examine chromosome evolution, and evaluate the conservation of gene order and spacing in the Oryzeae. Thus far, there appears to be an accumulation of intergenic sequences that are not conserved between wild rice and rice. Therefore, the accumulation of intergenic DNA in the evolution of cereal plant species appears to occur at a high rate even within closely related species in which genic sequences are closely conserved.