Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris)

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Abstract
Using comparative genetics, genes, repetitive DNA sequences and chromosomes were studied in the Oryzeae in order to more fully exploit the rice genome sequence data. Of particular focus was Zizania palustris L., n = 15, commonly known as American wildrice. Previous work has shown that rice chromosomes 1, 4 and 9 are duplicated in wildrice. The Adh1 and Adh2 genes were sequenced and, based on phylogenetic analyses, found to be duplicated in wildrice. The majority of the sequence diversity in the Adh sequences was in intron 3, in which were found several MITE insertions. Cytological and molecular approaches were used to analyze the evolution of rDNA and centromeric repetitive sequences in the Oryzeae. In wildrice, copies of the 5S rDNA monomer were found at two loci on two different chromosomes near the centromeres, as in rice. One nucleolar organizer region (NOR) locus was found adjacent to the telomere, as in rice. RCS1, a middle repetitive sequence in rice, was present in all of the centromeres of wildrice. RCS2/CentO, the highly repetitive component of Oryza sativa L. centromeres, was conserved in eight of the Oryza species examined, but was not found in wildrice. Three other middle repetitive centromeric sequences (RCH1, RCH2/CentO and RCH3) were also examined and found to have variable evolutionary patterns between species of Oryza and Zizania.