Search

Resistance gene-dependent accumulation of expressed sequence tags (ESTs) was studied in a blast resistant, Oryza sativa ssp. indica cv. Tetep after challenge inoculation with an incompatible race of Magnaporthe oryzae. The nucleotide sequence of 287 randomly selected cDNA clones from the rice cDNA library constructed from the RNA isolated after challenge inoculation of the host was obtained and submitted in NCBI Genbank (Accession Nos. – ). Of these, 184 (63%) ESTs were highly representative of the rice transcriptomes. A set of 178 unique transcripts was identified after assembly of 287 ESTs into unigenes. These unigenes were categorized into 17 functional groups. Analysis of this EST library illustrated a broad functional representation. Twenty-one unigenes were identified as putative homologues of the genes that were up regulated during host–pathogen interaction. Similarity search of 178 unigenes with NCBI database of 14 plants unigenes showed similarity ranging from 29–100%. The unigenes obtained in this study were physically located on the pseudomolecules of rice genome. This information can be used for determining the arrays of genes being expressed during Oryza sativa–M. oryzae interactions, which will be helpful in understanding the molecular basis of disease resistance. [ABSTRACT FROM AUTHOR]

The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2 cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10× redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score ≥ 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome. [ABSTRACT FROM AUTHOR]