Plant & Animal Genome IX Conference

Poster: Sequencing & EST
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SEQUENCING RICE CHROMOSOME 9: PLATFORM FOR UNDERSTANDING STRUCTURAL AND FUNCTIONAL GENOMICS

Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology, at Kasetsart University, Kamphangsaen, Nakorn Pathom, 73140, Thailand

Rice has become the largest plant genome to be completely sequenced within the next 2-3 years. Chromosome 9, the second smallest chromosome in rice, has the total map distance approximately 30 cM. We chose the subcentromeric region as the entry point for genome sequencing based on several interesting features for both structural and functional genomics. Nearby its centromere, the major QTL for submergence tolerance was mapped into a region where molecular markers were sparsely located. We reported here the finished sequences of four PAC clones spanning 2.6 cM region near the centromere of the rice chromosome 9 where QTL for submergence tolerance was mapped. The initial sequence-ready map was constructed from the Nipponbare's PAC library by using molecular markers previously mapped proximal to the submergence tolerance QTL. Individual PACs were shot-gun sequenced with 10-15 X coverage and finished with Phred score of 30 or better. Sequences of the four PACs were aligned with previously mapped molecular markers. The average physical to genetic distance of 170 kb per cM was surprisingly high considering the sequencing area is proximal to the centromere. Within the 600 kb, 40 genes were predicted and confirmed by homology search. High gene density with small physical to genetic distance makes this subcentromeric region particularly gene-rich and hotspot for recombination. One feature that might contributed to high recombination hot spot is high number of retrotransposon flanking genes. Of 40 genes predicted, seven genes were retrotransposons, nine genes were hypothetical and two genes coded for unknown proteins. The rest of the predicted genes were coded for regulatory proteins. Of particular interest, two sets of proteins containing zinc-finger domains were annotated where the QTL was predicted. Flanking these genes was a small Ras GTP-binding protein. Differential gene expression under submergence tolerance was investigated in both leave and stem sheath. All regulatory proteins expressed differentially one days after complete submergence and stay on at steady-state for several days.These genes might play roles in plant tolerance to submergence stresses. To clone genes involved in the submergence tolerance, a 10 X coverage BAC library was recently constucted from FR13A, the most submergence tolerance landrace from India. The strategies cloning the QTL utilizing sequence-ready technology will be presented.