Lisa Monna

• CEO at RIZO Inc.

Identification of single nucleotide polymorphisms (SNPs) in a large number of genes will enable estimation of the number of genes having different alleles in a population. In the present study, SNPs between 21 rice cultivars including 17 Japanese cultivars, one upland rice, and three indica cultivars were analyzed by PCR-RF-SSCP. PCR-RF-SSCP analys...

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms ar...

DNA polymorphism of randomly selected genes in rice cultivars was analyzed by the polymerase chain reaction-restriction fragment-single strand conformation polymorphism (PCR-RF-SSCP) technique. Single DNA fragments were amplified from genomic DNA of the Nipponbare cultivar by 671 primer pairs among the 1000 primer pairs tested. PCR-RF-SSCP analysis...

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representat...

Heading date 3a (Hd3a) has been detected as a heading-date-related quantitative trait locus in a cross between rice cultivars Nipponbare and Kasalath. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day (SD) conditions. High-resolution linkage mapping located the Hd3a locus in a approximately 20-kb genomic re...

The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. High-resolution linkage mapping of Hd3 was performed using a large segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasal...

A rice semidwarfing gene, sd-1, known as the "green revolution gene," was isolated by positional cloning and revealed to encode gibberellin 20-oxidase, the key enzyme in the gibberellin biosynthesis pathway. Analysis of 3477 segregants using several PCR-based marker technologies, including cleaved amplified polymorphic sequence, derived-CAPS, and s...

We have constructed a rice function map by collating the results on quantitative trait loci (QTLs) for 23 important physiological and agronomic characters (including 13 newly measured traits) obtained using backcross inbred lines of japonica Nipponbare×indica Kasalath. Using these materials, The Rice Genome project (RGP) has developed a high-densit...

A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1, was identified by means of a map-based cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of approximately 12 kb as a candidate for Hd1. Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolo...

Rice blast, caused by the fungal pathogen Magnaporthe grisea, is one of the most serious diseases of rice. Here we describe the isolation and characterization of Pib, one of the rice blast resistance genes. The Pib gene was isolated by a map-based cloning strategy. The deduced amino acid sequence of the Pib gene product contains a nucleotide bindin...

Saturation mapping of a very small genomic region is indispensable for map-based cloning. We applied a method based on sub-cloning and the Southern-hybridization technique for generating RFLP markers directly from yeast artificial chromosomes (YACs). Two YACs overlapping each other and covering the locus of the rice blast resistance gene, Pi-b, wer...

Polymorphic markers between closely related varieties of rice are necessary for the practical application of molecular markers, such as restriction fragment length polymorphism (RFLP) markers, to rice breeding. In this study, we employed a representational difference analysis (RDA) to develop RFLP markers between closely related japonica varieties,...

We searched partial sequences of over 22,706 rice cDNA and 1220 genomic DNA clones to find and characterize simple sequence repeats (SSRs) in the rice genome. The most frequently found repeated SSR motif in both cDNA and genomic DNA sequences was d(CCG/CGG)n. The second most frequently found SSR was d(AG/CT)n. In contrast with mammalian genomes, in...

Bulked segregant analysis was used to determine randomly amplified polymorphic DNA (RAPD) markers in a specific interval in the middle of chromosome 6 of rice for tagging the photoperiod sensitivity gene. Two pools of F2 individuals (japonica cv. Nipponbare and indica cv. Kasalath) were constructed according to the genotypes of three restriction fr...

Bulked segregant analysis was used to determine randomly amplified polymorphic DNA (RAPD) markers in a specific interval in the middle of chromosome 6 of rice for tagging the photoperiod sensitivitygene. Two pools of F2 individuals (japonica cv. Nipponbare and indica cv. Kasalath) were constructed according to the genotypes of three restriction fra...

We have constructed a high resolution rice genetic map containing 1,383 DNA markers at an average interval of 300 kilobases (kb). The markers, distributed along 1,575 cM on 12 linkage groups, comprise 883 cDNAs, 265 genomic DNAs, 147 randomly amplified polymorphic DNAs (RAPD) and 88 other DNAs. cDNAs were derived from rice root and callus, analysed...

Generating sequence-tagged sites (STSs) is a prerequisite to convert a genetic map to a physical map. With the help of sequence information from these STSs one can also isolate specific genes. For these purposes, we have designed PCR primer sets, of 20 bases each, by reference to sequences of restriction fragment length polymorphism (RFLP) landmark...

The conditions for efficient single-strand conformation polymorphism (SSCP) detection were examined for its application to mapping of DNA regions in the rice genome. Temperature for electrophoresis and glycerol concentrations in gel affected SSCP patterns significantly. The optimal detection conditions for SSCP also depends on the nucleotide sequen...

We produced 102 randomly amplified polymorphic DNA (RAPD) markers mapped on all 12 chromosomes of rice using DNAs of cultivars Nipponbare (japonica) and Kasalath (indica) and of F2 population generated by a single cross of these parents. Sixty random primers 10 nucleotides long were used both singly and in random pairs and about 1,400 primer-pairs...

We produced 102 randomly amplified polymorphic DNA (RAPD) markers mapped on all 12 chromosomes of rice using DNAs of cultivars Nipponbare (japonica) and Kasalath (indica) and of F2 population generated by a single cross of these parents. Sixty random primers 10 nucleotides long were used both singly and in random pairs and about 1,400 primer-pairs...

Staphylococcus auriculans DBF63, which can grow on dibenzofuran (DBF) or fluorene (FN) as the sole source of carbon and energy, was isolated. Salicylic acid and gentisic acid accumulated in the culture broth of this strain when DBF was supplied as a growth substrate. Also, the formation of 9-fluorenol, 9-fluorenone, 4-hydroxy-9-fluorenone, and 1-hy...

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS2, FeS2, and even elemental sulfur. St...