The weed red rice is a major problem in rice producing areas world wide. All of the red rice in commercial rice fields in the United States has traditionally been considered to be the same species as commercial rice, Oryza sativa. However, using DNA markers it was found that most of the red rice with black hulls was sufficiently divergent to be considered a separate species. This includes TX4, a red rice ecotype that has been reported to have considerable natural tolerance to the herbicide glufosinate. TX4 is closely related to samples that have been classified as Oryza rufipogon. However, it was shown that both the TX4-like red rice from commercial fields and most of the Oryza rufipogon accessions in the US National Small Grains Collection are more accurately classified as Oryza nivara. This is significant since Oryza rufipogon is regulated under the Federal Noxious Weed Act, while Oryza nivara is not. Oryza nivara closely related to TX4 was found to be widely distributed across the rice production areas of Texas and was also found in Arkansas, Louisiana, and Mississippi. Of 240 samples from across Texas, 23 samples from six different counties were identical with TX4 with all 18 DNA markers tested. The reported glufosinate tolerance of TX4 is a potential problem since this same herbicide would be used in conjunction with genetically modified (GM) that is being developed as a method of red rice control. Thus, field, greenhouse and tissue culture studies were conducted to evaluate the degree of glufosinate tolerance in TX4. TX4 typically was severely damaged by glufosinate, but not efficiently controlled. Even with the maximum number of herbicide applications at the proposed maximum label rate, TX4 often re-sprouted and produced viable seed. Herbicide tolerance was found to be variable, but appears to be sufficient to present a problem with the use of the GM glufosinate resistant varieties currently under development, particularly when combined with variation in the response of ??sensitive?? varieties.

Centromeres are responsible for sister-chromatid cohesion, kinetochore formation, and accurate transmission of chromosomes. Rice provides an excellent model for organizational and functional studies of centromeres since several of its chromosomes contain limited amounts of satellite and other repetitive sequences in their centromeres. To facilitate molecular characterization of the centromeres, we screened several BIBAC and BAC libraries of japonica and indica rice, using several centromere-specific repeat elements as probes. The positive clones were identified, fingerprinted and integrated into our whole genome physical map databases of the two rice subspecies. BAC/BIBACbased physical maps were constructed for the centromeric regions of the subspecies. To determine whether the genomic organization of the centromeres has changed since the cultivated rice split from its progenitor and to identify the sequences potentially playing an important role in centromere functions, we constructed a large-insert BIBAC library for the wild progenitor of Asian cultivated rice, O. rufipogon. The library contains 24,192 clones, has an average insert size of 163 kb, and covers 5 x haploid genome of wild rice. We screened the wild rice library with two centromere 8-specific overgo probes designed from the sequences flanking centromere 8 of japonica rice. A BIBACbased map was constructed for wild rice centromere 8. Two of the clones, B43P04 and B15E04, were found to span the entire region of the wild rice centromere and thus selected for sequencing the centromere. By sequencing the B43P09 clone, a 95% genomic sequence of the long arm side of wild rice centromere 8 was obtained. Comparative analysis revealed that the centromeric regions of wild rice have a similar gene content to japonica rice, but the centromeric regions of japonica rice have undergone chromosomal rearrangements at both large scale and nucleotide levels. In addition, although the 155-bp satellite repeats showed dramatic changes at the middle region, they are conserved at the 5' and 3' ends of satellite monomers, suggesting that those regions might have important functional roles for centromeres. These results provide not only new insights into genomic organization and evolution, but also a platform for functional analysis of plant centromeres.

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