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  • 1
    Electronic Resource
    Electronic Resource
    Transfer of the mitochondrial rps10 gene to the nucleus in rice: acquisition of the 5′ untranslated region followed by gene duplication (2000)
    Springer
    Molecular genetics and genomics 263 (2000), S. 733-739 
    Details
    ISSN: 1617-4623
    Keywords: Key words Mitochondria ; Gene transfer ; Ribosomal protein S10 ; Rice ; 5′ Untranslated region (UTR)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mitochondrial ribosomal protein S10 (rps10) is encoded by the mitochondrial genome in potato and pea. Here we show that the rps10 gene is absent from the mitochondrial genome of rice and has been transferred to the nucleus. Cloning and transcriptional analysis show that there are two rps10 genes in the rice nuclear genome and that their transcripts differ in abundance. Western analysis detected the RPS10 protein in the soluble fraction of rice mitochondria, although neither RPS10 has any obvious N-terminal presequence for targeting to mitochondria. This result suggests that targeting information is present in the internal region of rice RPS10. Genomic sequence analysis indicated that each rps10 gene has an intron in the 5′ untranslated region (5′ UTR) and that these intron sequences are homologous to each other. This result strongly suggests that a duplication event occurred after transfer of the rps10 gene to the nucleus. The duplicated rps10 genes have since been translocated to different chromosomes, because the two rps10 genes were mapped on chromosomes 6 and 12 by RFLP analysis. Interestingly, the 5′ UTR and the intron of the rice rps10 genes are homologous to sequences found in several rice genes with various functions, such as osk4, EF-1β2 and RAG1, suggesting a common origin and a functional role for the 5′ UTR. Acquisition of the 5′ flanking region might have accelerated the activation of the mitochondrial rps10 gene which was transferred to the nuclear genome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004380051222
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  • 2
    Electronic Resource
    Electronic Resource
    Sequence-tagged sites (STSs) as standard landmarkers in the rice genome (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 728-734 
    Details
    ISSN: 1432-2242
    Keywords: STS ; RFLP ; Rice ; Genetic map ; Coding region
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 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) landmarkers consisting of rice genomic clones. These markers were evenly distributed over the 12 chromosomes and were shown to be single copy by Southern-blot analysis. With improved PCR protocols, 63 standard STS landmarkers in the rice genome were generated. Similarity searches of all partial sequences of RFLP landmarkers by the FASTA algorithm showed that 2 of the 63 RFLP landmarkers, G357 and G385, contained part of the ORFs of aspartate aminotransferase and protein kinase, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223712
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  • 3
    Electronic Resource
    Electronic Resource
    Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 117-122 
    Details
    ISSN: 1432-2242
    Keywords: Plant disease resistance ; Rice ; Xanthomonas oryzae pv. oryzae ; YAC
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Map-based cloning methods have been applied for isolation of Xa-1, one of the bacterial blight resistance genes in rice.Xa-1 was previously mapped on chromosome 4 using molecular markers. For positional cloning of Xa-1, a high-resolution genetic map was made for theXa-1 region using an F2 population of 402 plants and additional molecular markers. Three restriction fragment length polymorphism (RFLP) markers, XNpb235, XNpb264 and C600 were found to be linked tightly to Xa-1, with no recombinants, and U08 750 was mapped 1.5 cM from Xa-1. The screening of a yeast artificial chromosome (YAC) library using theseXa-1-linked RFLP markers resulted in the identification of ten contiguous YAC clones. Among these, one YAC clone, designated Y5212, with an insert of 340 kb, hybridized with all three tightly linked markers. This YAC was confirmed to possess the Xa-1 allele by mapping the Xa-1 gene between both end clones of this YAC (Y5212R and Y5212L).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225736
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  • 4
    Electronic Resource
    Electronic Resource
    Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map (1997)
    Springer
    Theoretical and applied genetics 95 (1997), S. 1025-1032 
    Details
    ISSN: 1432-2242
    Keywords: Key words RFLP markers ; Days-to-heading ; QTL analysis ; Rice ; Epistatic interaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Quantitative trait locus (QTL) analysis has been carried out to identify genes conferring heading date in rice. One hundred and eighty six F2 plants derived from a cross between a japonica variety, Nipponbare, and an indica variety, Kasalath, were used as a segregating population for QTL mapping and more than 850 markers were employed to identify QTLs. Scan-analysis revealed the existence of two QTLs with large effects, Hd-1 and Hd-2, one in the middle of chromosome 6 and one at the end of chromosome 7, respectively. For both loci, the Kasalath alleles reduced days-to-heading. In addition, three QTLs with minor effects, Hd-3, Hd-4 and Hd-5, were found to be located on chromosomes 6, 7 and 8 based on a secondary scan analysis which was carried out by removing the phenotypic effects of Hd-1 and Hd-2. For the three secondary loci, the Nipponbare alleles reduced days-to-heading. The five QTLs explained 84% of the total phenotypic variation in the F2 population based on a multiple-QTL model. The presence of a digenic interaction between Hd-1 and Hd-2 was clearly suggested.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050658
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  • 5
    Electronic Resource
    Electronic Resource
    Genetic and physical mapping of xa13, a recessive bacterial blight resistance gene in rice (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 1022-1028 
    Details
    ISSN: 1432-2242
    Keywords: Key words Genetic map ; Physical map ; Map-based gene cloning ; Disease resistance ; Rice ; DNA markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The recessive gene, xa13, confers resistance to Philippine race 6 (PXO99) of the bacterial blight pathogen Xanthomonas oryzae pv oryzae. Fine genetic mapping and physical mapping were conducted as initial steps in an effort to isolate the gene. Using nine selected DNA markers and two F2 populations of 132 and 230 plants, xa13 was fine-mapped to a genomic region 〈4 cM on the long arm of rice chromosome 8, flanked by two RFLP markers, RG136 and R2027. Four DNA markers, RG136, R2027, S14003, and G1149, in the target region were used to identify bacterial artificial chromosome (BAC) clones potentially harboring the xa13 locus from a rice BAC library. A total of 11 BACs were identified, forming four separate contigs including a single-clone contig, 29I3, associated with the RG136 STS marker, the S14003 contig consisting of four clones (44F8, 41O2, 12A16, and 12F20), the G1149 contig with two clones, 23D11 and 21H18, and the R2027 contig consisting of four overlapping clones, 42C23, 30B5, 6B7 and 21H14. Genetic mapping indicated that the xa13 locus was contained in the R2027 contig. Chromosomal walking on the R2027 contig resulted in two more clones, 33C7 and 14L3. DNA fingerprinting showed that the six clones of the R2027 contig were overlapping. Clone 44F8 hybridized with a single fragment from the clone 14L3, integrating the R2027 and S14003 contigs into a single contig consisting of ten BAC clones with a total size of approximately 330 kb. The physical presence of the xa13 locus in the contig was determined by mapping the ends of the BAC inserts generated by TAIL-PCR. In an F2 population of 230 plants, the BAC-end markers 42C23R and 6B7F flanked the xa13 locus. The probes 21H14F and 21H14R derived from BAC clone 21H14 were found to flank xa13 at a distance of 0.5 cM on either side, using a second F2 population of 132 plants. Thus, genetic mapping indicated that the contig and the 96-kb clone, 21H14, contained the xa13 locus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051163
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  • 6
    Electronic Resource
    Electronic Resource
    Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map (1996)
    Springer
    Theoretical and applied genetics 92 (1996), S. 145-150 
    Details
    ISSN: 1432-2242
    Keywords: Gametophyte gene ; Genetic map ; Hybrid sterility gene ; Rice ; Segregation distortion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have constructed a high-resolution rice genetic map containing 1383 DNA markers covering 1575 cM on the 12 linkage groups of rice using 186 F2 progeny from a cross between a japonica variety, ‘Nipponbare’, and an indica variety, ‘Kasalath’. Using this high-resolution molecular linkage map, we detected segregation distortion in a single wide cross of rice. The frequencies of genotypes for 1181 markers with more than 176 genotype data were plotted along this map to detect segregation distortion. Several types of distorted segregation were observed on 6 of the chromosomes. We could detect 11 major segregation distortions at ten positions on chromosomes 1, 3, 6, 8, 9, and 10. The strongest segregation distortion was at 107.2 cM on chromosome 3 and may be the gametophyte gene 2 (ga-2). The ‘Kasalath’ genotype at this position was transmitted to the progeny with about a 95% probability through the pollen gamete. At least 8 out of the 11 segregation distortions detected here are new. The use of the high-resolution molecular linkage map for improving our understanding of the genetic nature and cause of these segregation distortions is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223368
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  • 7
    Electronic Resource
    Electronic Resource
    Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L. (1997)
    Springer
    Theoretical and applied genetics 95 (1997), S. 828-833 
    Details
    ISSN: 1432-2242
    Keywords: Key words Regeneration ability ; QTL ; Rice ; Oryza sativa L. ; Seed callus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Quantitative trait loci (QTL) controlling the regeneration ability of rice seed callus were detected using 245 RFLP markers and 98 BC1F5 lines derived from two varieties, ‘Nipponbare’ and ‘Kasalath’. Regeneration ability was evaluated by two indices: average number of regenerated shoots per callus (NRS) and regeneration rate (RR). The BC1F5 lines showed continuous segregation for both indices. Five putative QTL for NRS (tentatively named qRg1, qRg2, qRg4a, qRg4b and qRg4c) located on chromosomes 1, 2 and 4 were detected. Digenic interaction among these detected QTL was not significant (P〈0.01). Among the five QTL detected, four ‘Kasalath’ alleles and one ‘Nipponbare’ allele increased NRS. According to an estimate based on the nearest marker loci, the five QTL accounted for 38.5% of the total phenotypic variation of the BC1F5 lines. For RR, four putative QTL were detected on chromosomes 2 and 4, and all of these were in the same chromosomal regions as the NRS QTL. The four RR QTL accounted for 32.6% of the total phenotypic variation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050632
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  • 8
    Electronic Resource
    Electronic Resource
    Saturation mapping with subclones of YACs: DNA marker production targeting the rice blast disease resistance gene, Pi-b (1997)
    Springer
    Theoretical and applied genetics 94 (1997), S. 170-176 
    Details
    ISSN: 1432-2242
    Keywords: Key words Saturation mapping ; Yeast artificial chromosome (YAC) ; Rice ; Pi-b ; Blast disease resistance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 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, were used to construct a plasmid sub-library. Rice-specific and single-copy clones suitable as probes for RFLP analysis were selected from this sub-library by hybridization to the blots of digested DNAs of rice, YACs, and yeast. As a result, 22 markers were produced within a small chromosomal region including Pi-b. This case study shows that overlapping YACs known to cover the gene of interest are very useful in fine-scale physical mapping leading to map-based cloning of the target gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050396
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