Physical mapping of duplicated genomic regions of two chromosome ends in rice.

Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated.

Isolation and mapping of a family of putative zinc-finger protein cDNAs from rice.

To understand the functions of rice homologues of the Arabidopsis flowering-time gene CONSTANS (CO) and salt-tolerance gene STO, we performed a similarity search of the single-run sequence data of cDNA clones accumulated by the Rice Genome Research Program, and isolated seven rice cDNA clones (S3574, C60910, S12569, R2931, R1479, R1577, and E10707) coding for proteins containing one of two zinc-finger-like motifs. Comparison of the deduced amino acid sequences between these cDNAs and the CO gene revealed significant similarities (46%-61%) in the region of zinc-finger motifs. A domain having a high content of basic amino acids at the C-terminus of the CO protein was found in the corresponding region of proteins predicted by from cDNAs S3574, C60910, and S12569.

Rice class III chitinase homologues isolated by random cloning of rice cDNAs.

We obtained seven kinds of cDNA clones putatively identified as encoding class III chitinases from cDNA libraries constructed from dichlorophenoxyacetic acid (2,4-D)- and benzyl adenine (BA)- treated rice callus. Putative amino acid sequences encoded in these cDNA clones were compared with those of known chitinases of other plants. Two clones coded for homologues that show high similarity to class III chitinases.

Assignment of YAC clones spanning rice chromosomes 10 and 12.

Yeast artificial chromosome (YAC) clones were assigned on rice (Oryza saliva L. cv. Nipponbare) chromosomes 10 and 12 using DNA markers from our high-density linkage map.

Physical mapping of rice chromosomes 8 and 9 with YAC clones.

First efforts for physical mapping of rice chromosomes 8 and 9 were carried out by ordering YAC clones of a rice genomic DNA library covering six genome equivalents with mapped DNA markers. A total of 79 and 74 markers from chromosomes 8 and 9, respectively, were analyzed by YAC colony and Southern hybridization using RFLP markers of cDNA and genomic clones, and by polymerase chain reaction (PCR) screening using PCR-derived and sequence-tagged site (STS) markers. As a result, 252 YAC clones were confirmed to contain the mapped DNA fragments on both chromosomes.

Genomic organization of 57 ribosomal protein genes in rice (Oryza sativa L.) through RFLP mapping.

Four hundred cDNA clones from rice (Oryza sativa L.) callus and root cDNA libraries, with a high similarity to about 70 kinds of ribosomal proteins (r-protein) in eukaryotic as well as procaryotic organisms, were identified by their deduced amino acid sequences. Southern hybridization of 114 independent cDNA clones with total rice genomic DNA showed 77 distinct and specific hybridization patterns.