Plant Genome III Conference Plant Genome III Conference
cDNA is a blue print of expressed genes. The nucleotide sequence information revealed in cDNA is a prerequisite for elucidating the genome structure. In the Rice Genome Research Program (RGP), the cataloguing of cDNAs is done to capture all the expressed genes. For this, a large scale CDNA analysis with single-run partial sequencing is performed. With the aid of computer software, similarity search against already known sequences could putatively identify the gene names of many randomly cloned cDNAs.
So far, around 20,000 cDNA clones have been analyzed from libraries of several types of calli, root, green shoot, etiolated shoot and developing seed. Redundancy of analyzed clones was estimated by computer analysis using several assumptions, but, for more accurate checking, a hybridization method is now planned. Linkage analysis using about I 100 partially sequenced cDNAs as probes for detecting RFLP has been completed. The cDNA markers have been mapped on identical loci in the 186 progenies of one F2 population, and are being used to pick up different YACs from a library of 7000 clones blotted on a filter. Once a YAC contig is constructed, catalogued cDNAs should be used for identifying their location within the contig. This procedure could facilitate the positional cloning of tagged genes.
Statistical analysis of nucleotide sequences of rice CDNA clones revealed novel characteristics in repeated sequences. Unlike Arabidopsis, GCC repeat is the most abundant, followed by GGA. This characteristics could be taken into account for synthesizing PCR primers for efficient detection of RAPDs.
The cDNA research in rice impacts not only rice genome research, as described above, but also other cereal genome researchers, because the nucleotide sequences are highly homologous within cereals. The results in RGP should be beneficial also for other plant molecular biologists.