Nakao Kubo

Kyoto Prefectural University, Kioto, Kyōto, Japan

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Publications (38)102.84 Total impact

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    ABSTRACT: The radish displays great morphological variation but the genetic factors underlying this variability are mostly unknown. To identify quantitative trait loci (QTLs) controlling radish morphological traits, we cultivated 94 F4 and F5 recombinant inbred lines derived from a cross between the rat-tail radish and the Japanese radish cultivar 'Harufuku' inbred lines. Eight morphological traits (ovule and seed numbers per silique, plant shape, pubescence and root formation) were measured for investigation. We constructed a map composed of 322 markers with a total length of 673.6 cM. The linkage groups were assigned to the radish chromosomes using disomic rape-radish chromosome-addition lines. On the map, eight and 10 QTLs were identified in 2008 and 2009, respectively. The chromosome-linkage group correspondence, the sequence-specific markers and the QTLs detected here will provide useful information for further genetic studies and for selection during radish breeding programs.
    Breeding Science 06/2013; 63(2):218-26. DOI:10.1270/jsbbs.63.218 · 1.34 Impact Factor
  • Acta horticulturae 01/2013; 1005:89-96.
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    Euphytica 09/2012; 187(1). DOI:10.1007/s10681-012-0768-z · 1.69 Impact Factor
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    ABSTRACT: Plant architecture plays an important role in the yield, product quality, and cultivation practices of many crops. Branching pattern is one of the most important components in the plant architecture of melon (Cucumis melo L.). ‘Melon Chukanbohon Nou 4 Go’ (Nou-4) has a short-lateral-branching trait derived from a weedy melon, LB-1. This trait is reported to be controlled by a single recessive or incompletely dominant major gene called short lateral branching (slb). To find molecular markers for marker-assisted selection of this gene, we first constructed a linkage map using 94 F2 plants derived from a cross between Nou-4 and ‘Earl’s Favourite (Harukei-3)’, a cultivar with normal branching. We then conducted quantitative trait locus (QTL) analysis and identified two loci for short lateral branching. A major QTL in linkage group (LG) XI, at which the Nou-4 allele is associated with short lateral branching, explained 50.9 % of the phenotypic variance, with a LOD score of 12.5. We suggest that this QTL corresponds to slb because of the magnitude of its effect. Another minor QTL in LG III, at which the Harukei-3 allele is associated with short lateral branching, explained 9.9 % of the phenotypic variance, with a LOD score of 4.2. Using an independent population, we demonstrated that an SSR marker linked to the QTL in LG XI (slb) could be used to select for short lateral branching. This is the first report of mapping a gene regulating the plant architecture of melon.
    Euphytica 09/2012; 187(1). DOI:10.1007/s10681-012-0667-3 · 1.69 Impact Factor
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    ABSTRACT: Viola grayi, a coastal violet, is found on sandy seashores in limited regions in Japan, but not on rocky sea cliffs or in inland areas. This stemmed violet is classified in the subsection Rostratae. Because of recent human activity on sandy seashores, this species is now recorded as endangered. The present status of this species was surveyed and its genetic diversity was analyzed using 17 newly developed simple sequence repeat markers. The results are compared with those for two commonly found inland violet species in the same subsection, V. grypoceras and V. kusanoana. The coastal violet populations showed markedly lower genetic diversity than those of the common species, V. grypoceras, whereas V. kusanoana showed intermediate genetic diversity. About a half of the total genetic variation of V. grayi is found among populations in analysis of molecular variance. In contrast, only less than 25% of the total variation is found among populations for the two common violets. These three species showed a remarkably high inbreeding coefficient, which indicates high inbreeding under natural mating conditions, although these species have both chasmogamous and cleistogamous flowers. In a population-based dendrogram, V. grayi was clustered in a single and concise group, whereas V. grypoceras and V. kusanoana were found in somewhat discrete positions. In the Bayesian analysis of genetic structure of the coastal violet, delta K was the highest at K = 7, and the seven clusters almost correspond to seven populations studied here. Implications of the conservation of this endangered coastal violet are presented.
    Conservation Genetics 06/2012; 13(3). DOI:10.1007/s10592-012-0333-2 · 1.85 Impact Factor
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    ABSTRACT: Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar 'California Wonder' and a Malaysian small-fruited cultivar 'LS2341 (JP187992)', which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.
    Breeding Science 03/2012; 62(1):93-8. DOI:10.1270/jsbbs.62.93 · 1.34 Impact Factor
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    ABSTRACT: Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed clear polymorphisms between two radish lines; a rat-tail radish and a Japanese cultivar, 'Harufuku'. As a test case for evaluation of the present SSRs, we conducted two studies. First, we selected 16 SSRs to calculate polymorphism information contents (PICs) using 16 radish cultivars and four other Brassicaceae species. These markers detected 3-15 alleles (average = 9.6). PIC values ranged from 0.54 to 0.92 (average = 0.78). Second, part of the present SSRs were tested for mapping using our previously-examined mapping population. The map spanned 672.7 cM with nine linkage groups (LGs). The 21 radish SSR markers were distributed throughout the LGs. The SSR markers developed here would be informative and useful for genetic analysis in radish and its related species.
    Breeding Science 12/2011; 61(4):413-9. DOI:10.1270/jsbbs.61.413 · 1.34 Impact Factor
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    ABSTRACT: The edible berry species Vaccinium sieboldii, Vaccinium ciliatum, and Vaccinium oldhami are deciduous shrubs found growing at low altitudes in Japan. They are classified in the same section. Of these, the former two species are listed as endangered species. The present status of these two species was surveyed. V. sieboldii was found in a very limited range, 65km wide, in central Japan. Many plants are thought to have been lost because of habitat destruction in the past 50years. Loss of pine forests from pine-wilt disease is thought to be a major threat to this species. In contrast, V. ciliatum was found over a range of more than 300km in western Japan. Habitats of both species were heavily fragmented. The genetic diversity and phylogenetic relationships of the three species were studied using nine simple-sequence repeat loci. V. sieboldii and V. ciliatum have a close genetic relationship, although their present growth ranges are widely separated. Despite its limited growth range and the limited number of remaining plants, the genetic diversity of V. sieboldii is similar to that of another endangered species, V. ciliatum, and that of the widely grown species, V. oldhami. Seven populations of the former two species were used to create population-based dendrograms. They were separated into three groups: three populations of V. sieboldii, two mountainous populations of V. ciliatum, and two coastal populations of V. ciliatum. The separation was supported by high bootstrap values. Isolation factors of the two population groups in V. ciliatum are discussed. KeywordsFragmentation-Genetic diversity-Population differentiation-Simple sequence repeat- Vaccinium
    Plant Systematics and Evolution 06/2010; 287(1):75-84. DOI:10.1007/s00606-010-0291-4 · 1.15 Impact Factor
  • Breeding Science 01/2010; 60(1):76-80. DOI:10.1270/jsbbs.60.76 · 1.34 Impact Factor
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    ABSTRACT: The Brassica species displays great variation with regard to morphology. However, the genetic mechanisms that underlie this variability are mostly unknown. We generated 188 F2 plants derived from a cross between a Chinese cabbage and a vegetable turnip, and scored several morphological traits (head formation, leaf lobe, pubescence, and turnip formation) twice (2005 and 2007) in two subsets of 94 individuals. With the exception of pubescence, we did not find any typical discrete segregation of these traits in F2 plants, suggesting that they are controlled by multiple genes. We constructed a linkage map to conduct quantitative trait locus (QTL) analysis, and detected eight and 14 QTLs in 2007 and 2005, respectively, for head formation, leaf lobe, pubescence, turnip size, and turnip weight. The amplified fragment length polymorphism (AFLP) fragments linked to the QTLs were converted into sequence-tagged site (STS) markers. The QTLs detected here and their linkage markers may provide useful information for the selection of traits during the breeding of Chinese cabbage and turnip cultivars.
    Breeding Science 01/2010; 60(2):164-171. DOI:10.1270/jsbbs.60.164 · 1.34 Impact Factor
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    ABSTRACT: The water lotus, genus Nelumbo, contains two species, the sacred (Nelumbo nucifera) and American lotuses (Nelumbo lutea). Hundreds of flowering lotus cultivars are currently known. However, their classification is unclear. For the classification of Nelumbo cultivars, in addition to 35 simple sequence repeat (SSR) markers recently developed, we have developed 17 and 16 of new Nelumbo SSR markers from SSR-enriched genomic libraries and expressed sequence tag (EST) data, respectively. Out of these 68 SSRs, along with SSRs recently published by others, 52 showed clear polymorphisms in 98 Nelumbo samples. A total of 300 alleles were observed, ranging from 2 to 11 alleles per locus, with an average of 5.77. Alleles specific for the American lotus-derived cultivars and a cluster of the American lotus-derived cultivars on a neighbour-joining tree confirmed genetic differences between N. lutea and N. nucifera. In addition, a possible differentiation between Chinese and Japanese cultivars was also suggested. Parentage analysis using the SSR markers confirmed four known parentages and predicted currently-unknown parentages of six cultivars. The present data have demonstrated that site-specific, co-dominant SSR markers enable more accurate classification, identification and comparison of Nelumbo species.
    Plant Genetic Resources 12/2009; 7(03). DOI:10.1017/S1479262109356580 · 1.06 Impact Factor
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    ABSTRACT: A QTL analysis for clubroot resistance (CR) of radish was performed using an F(2) population derived from a crossing of a CR Japanese radish and a clubroot-susceptible (CS) Chinese radish. F(3) plants obtained by selfing of F(2) plants were used for the CR tests. The potted seedlings were inoculated and the symptom was evaluated 6 weeks thereafter. The mean disease indexes of the F(3) plants were used for the phenotype of the F(2). The results of two CR tests were analyzed for the presence of QTL. A linkage map was constructed using AFLP and SSR markers; it spanned 554 cM and contained 18 linkage groups. A CR locus was observed in the top region of linkage group 1 in two tests. Therefore, the present results suggest that a large part of radish CR is controlled by a single gene or closely linked genes in this radish population, although minor effects of other genomic areas cannot be ruled out. The CR locus was named Crs1. Markers linked to Crs1 showed sequence homology to the genomic region of the top of chromosome 3 of Arabidopsis, as in the case of Crr3, a CR locus in Brassica rapa. These markers should be useful for breeding CR cultivars of radish. As Japanese radishes are known to be highly resistant or immune to clubroot, these markers may also be useful in the introgression of this CR gene to Brassica crops.
    Theoretical and Applied Genetics 12/2009; 120(5):1021-7. DOI:10.1007/s00122-009-1230-z · 3.51 Impact Factor
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    Nakao Kubo · Shin-ichi Arimura
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    ABSTRACT: Mitochondrial genomes of plants are much larger than those of mammals and often contain conserved open reading frames (ORFs) of unknown function. Here, we show that one of these conserved ORFs is actually the gene for ribosomal protein L10 (rpl10) in plant. No rpl10 gene has heretofore been reported in any mitochondrial genome other than the exceptionally gene-rich genome of the protist Reclinomonas americana. Conserved ORFs corresponding to rpl10 are present in a wide diversity of land plant and green algal mitochondrial genomes. The mitochondrial rpl10 genes are transcribed in all nine land plants examined, with five seed plant genes subject to RNA editing. In addition, mitochondrial-rpl10-like cDNAs were identified in EST libraries from numerous land plants. In three lineages of angiosperms, rpl10 is either lost from the mitochondrial genome or a pseudogene. In two of them (Brassicaceae and monocots), no nuclear copy of mitochondrial rpl10 is identifiably present, and instead a second copy of nuclear-encoded chloroplast rpl10 is present. Transient assays using green fluorescent protein indicate that this duplicate gene is dual targeted to mitochondria and chloroplasts. We infer that mitochondrial rpl10 has been functionally replaced by duplicated chloroplast counterparts in Brassicaceae and monocots.
    DNA Research 11/2009; 17(1):1-9. DOI:10.1093/dnares/dsp024 · 4.98 Impact Factor
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    ABSTRACT: Simple sequence repeat (SSR) markers were developed in the water lotus (Nelumbo nucifera Gaertn.) from an SSR-enriched genomic library. Of the SSR markers tested, 11 primer pairs produced clearly distinguishable DNA banding patterns. Forty-three alleles were detected with the 11 markers. The allele number per locus ranged from 2 to 5 with an average of 3.9. Polymorphism values ranged from 0.11 to 0.66 with an average of 0.51. These primers were also applicable to another Nelumbo species, Nelumbo lutea (Willd.) Pers. (American lotus) and hybrids between N. nucifera and N. lutea. These results indicate that the SSR markers developed in this study are informative and will be useful for genetic analysis in Nelumbo species.
    Aquatic Botany 02/2009; 90(2-90):191-194. DOI:10.1016/j.aquabot.2008.06.006 · 1.47 Impact Factor
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    ABSTRACT: The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they must have acquired cis-regulatory elements compatible with eukaryotic gene expression. However, most of such processes remain unknown. The ribosomal protein L6 gene (rpl6) has been lost in presently-known angiosperm mitochondrial genomes. We found that each of the two rice rpl6 genes (OsRpl6-1 and OsRpl6-2) has an intron in an identical position within the 5'-untranslated region (UTR), which suggests a duplication of the rpl6 gene after its transfer to the nucleus. Each of the predicted RPL6 proteins lacks an N-terminal extension as a mitochondrial targeting signal. Transient assays using green fluorescent protein indicated that their mature N-terminal coding regions contain the mitochondrial targeting information. Reverse transcription-PCR analysis showed that OsRpl6-2 expresses considerably fewer transcripts than OsRpl6-1. This might be the result of differences in promoter regions because the 5'-noncoding regions of the two rpl6 genes differ at a point close to the center of the intron. There are several sequences homologous to the region around the 5'-UTR of OsRpl6-1 in the rice genome. These sequences have characteristics similar to those of the transposable elements (TE) belonging to the PIF/Harbinger superfamily. The above evidences suggest a novel mechanism in which the 5'-UTR of the transferred mitochondrial gene was acquired via a TE. Since the 5'-UTRs and introns within the 5'-UTRs often contain transcriptional and posttranscriptional cis-elements, the transferred rice mitochondrial rpl6 gene may have acquired its cis-element from a TE.
    BMC Evolutionary Biology 12/2008; 8:314. DOI:10.1186/1471-2148-8-314 · 3.41 Impact Factor
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    ABSTRACT: Genetic factors controlling root shape and red pigmentation on the surface of the hypocotyl (upper part of root) were investigated using a molecular linkage map based on an F-2 population derived from a cross between two radish cultivars, 'Huang-he hong-wan' and 'Utsugi-gensuke'. One hundred and ninety-eight segregating markers (169 AFLPs, 28 Brassica SSRs and one SLG-CAPS) were located on 14 linkage groups (LGs) at a LOD threshold value of 5.0. The mapping position of Brassica SSRs revealed that frequent genomic rearrangements occurred between the Brassica and Raphanus genomes. Three quantitative trait loci (QTLs) for root shape with LOD values of 2.42, 3.22 and 2.88 were identified on LGs 3, 8 and 9, respectively. These three QTLs accounted for 42.4% of the phenotypic variance when joined together. Analysis of QTL(s) for root diameter revealed the presence of two QTLs on LG4 and LG8. The QTL on LG8 was considered to control root thickening and to affect the root shape. For hypocotyl pigmentation, a QTL which exerted a large genetic effect with a LOD value of 9.58, was recognized on LG 11 and accounted for 43.8% of the phenotypic variance.
    Breeding Science 03/2008; 58(1):55-61. DOI:10.1270/jsbbs.58.55 · 1.34 Impact Factor
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    ABSTRACT: Soybean [Glycine max (L.) Merrill] is the most important leguminous crop in the world due to its high contents of high-quality protein and oil for human and animal consumption as well as for industrial uses. An accurate and saturated genetic linkage map of soybean is an essential tool for studies on modern soybean genomics. In order to update the linkage map of a F2 population derived from a cross between Misuzudaizu and Moshidou Gong 503 and to make it more informative and useful to the soybean genome research community, a total of 318 AFLP, 121 SSR, 108 RFLP, and 126 STS markers were newly developed and integrated into the framework of the previously described linkage map. The updated genetic map is composed of 509 RFLP, 318 SSR, 318 AFLP, 97 AFLP-derived STS, 29 BAC-end or EST-derived STS, 1 RAPD, and five morphological markers, covering a map distance of 3080 cM (Kosambi function) in 20 linkage groups (LGs). To our knowledge, this is presently the densest linkage map developed from a single F2 population in soybean. The average intermarker distance was reduced to 2.41 from 5.78 cM in the earlier version of the linkage map. Most SSR and RFLP markers were relatively evenly distributed among different LGs in contrast to the moderately clustered AFLP markers. The number of gaps of more than 25 cM was reduced to 6 from 19 in the earlier version of the linkage map. The coverage of the linkage map was extended since 17 markers were mapped beyond the distal ends of the previous linkage map. In particular, 17 markers were tagged in a 5.7 cM interval between CE47M5a and Satt100 on LG C2, where several important QTLs were clustered. This newly updated soybean linkage map will enable to streamline positional cloning of agronomically important trait locus genes, and promote the development of physical maps, genome sequencing, and other genomic research activities.
    DNA Research 01/2008; 14(6):257-69. DOI:10.1093/dnares/dsm027 · 4.98 Impact Factor
  • Breeding Science 01/2008; 58(4):475-483. DOI:10.1270/jsbbs.58.475 · 1.34 Impact Factor
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    M Saito · N Kubo · S Matsumoto · K Suwabe · M Tsukada · M Hirai
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    ABSTRACT: A linkage map of Chinese cabbage (Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F(3) population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences in the top arm of Arabidopsis chromosome 3, suggesting a synteny between the two species. For fine mapping of Crr3, a number of STS markers were developed based on genomic information from Arabidopsis. We obtained polymorphisms in 23 Arabidopsis-derived STS markers, 11 of which were closely linked to Crr3. The precise position of Crr3 was determined using a population of 888 F(2) plants. Eighty plants showing recombination around Crr3 locus were selected and used for the mapping. A fine map of 4.74 cM was obtained, in which two markers (BrSTS-41 and BrSTS-44) and three markers (OPC11-2S, BrSTS-54 and BrSTS-61) were cosegregated. Marker genotypes of the 21 selected F(2) families and CR tests of their progenies strongly suggested that the Crr3 gene is located in a 0.35 cM segment between the two markers, BrSTS-33 and BrSTS-78.
    Theoretical and Applied Genetics 01/2007; 114(1):81-91. DOI:10.1007/s00122-006-0412-1 · 3.51 Impact Factor
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    ABSTRACT: Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.
    Genome 11/2006; 49(11):1481-9. DOI:10.1139/g06-105 · 1.56 Impact Factor

Publication Stats

961 Citations
102.84 Total Impact Points

Institutions

  • 2004–2013
    • Kyoto Prefectural University
      • Graduate School of Life and Environmental Sciences
      Kioto, Kyōto, Japan
  • 1996–2008
    • National Institute of Agrobiological Sciences
      Tsukuba, Ibaraki, Japan
  • 1999
    • Chiba University
      • Faculty of Horticulture
      Chiba-shi, Chiba-ken, Japan
  • 1995
    • University of Tsukuba
      Tsukuba, Ibaraki, Japan