Takashige Ishii

Publications (11)49 Total impact

• Article: OsLG1 regulates a closed panicle trait in domesticated rice.

  Takashige Ishii, Koji Numaguchi, Kotaro Miura, Kentaro Yoshida, Pham Thien Thanh, Than Myint Htun, Masanori Yamasaki, Norio Komeda, Takashi Matsumoto, Ryohei Terauchi, Ryo Ishikawa, Motoyuki Ashikari
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  ABSTRACT: Reduction in seed shattering was an important phenotypic change during cereal domestication. Here we show that a simple morphological change in rice panicle shape, controlled by the SPR3 locus, has a large impact on seed-shedding and pollinating behaviors. In the wild genetic background of rice, we found that plants with a cultivated-like type of closed panicle had significantly reduced seed shedding through seed retention. In addition, the long awns in closed panicles disturbed the free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. We localized the SPR3 locus to a 9.3-kb genomic region, and our complementation tests suggest that this region regulates the liguleless gene (OsLG1). Sequencing analysis identified reduced nucleotide diversity and a selective sweep at the SPR3 locus in cultivated rice. Our results suggest that a closed panicle was a selected trait during rice domestication.
  Nature Genetics 02/2013; · 35.53 Impact Factor
• Article: Estimation of the outcrossing rate for annual Asian wild rice under field conditions.

  Phuong Dang Thai Phan, Hiroki Kageyama, Ryo Ishikawa, Takashige Ishii
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  ABSTRACT: The Asian wild rice, Oryza rufipogon, has partial outcrossing behavior and shows high levels of genetic variation. To estimate an accurate outcrossing rate of annual form of O. rufipogon, two backcross lines (Lines R1 and R2) between Oryza sativa Nipponbare and O. rufipogon W630 were examined under field conditions. A chromosome survey confirmed that these lines had wild chromosomal segments at more than 92% of marker loci. As for the traits of glume, stamen and pistil, Line R1 showed similar floral morphology as that of O. rufipogon W630, whereas Line R2 had larger glumes. In 2005, 2006 and 2008, a total of 22 backcross plants were planted in the middle of wild rice plots. The successive progenies of each plant were examined using microsatellite markers that could clearly detect self-pollination and outcrossing. The outcrossing rates of Line R1 plants ranged from 4.04% to 25.50% with an average of 10.20%. This indicates that cross-pollination of wild rice is a chance event affected by many environmental factors. The outcrossing rates of Line R2 plants also varied, however, no significant difference was observed between the averages of Lines R1 and R2, suggesting that the glume sizes are not critical for outcrossing ability.
  Breeding Science 09/2012; 62(3):256-62. · 1.25 Impact Factor
• Article: Ultra-simple DNA extraction method for marker-assisted selection using microsatellite markers in rice

  Nobuyuki Ikeda, Nonnatus S. Bautista, Tetsuya Yamada, Osamu Kamijima, Takashige Ishii
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  ABSTRACT: We prevent an ultra-simple DNA extraction method for microsatellite analysis of rice. Each extraction requires only one microtube, one disposable pipette tip, TE buffer and few pieces (about 5 mm) of rice leaf tissue. This is sufficient for 200 PCR reactions. The extract can be kept in the freezer for long-term storage. Also, DNA can be extracted from 200–300 individuals in a few hours. These features enabled us to perform rapid largescale seedling genotyping required for marker-assisted selection. We have also examined the applicability of this method for other PCR-based markers: RAPDs, nuclear STS, chloroplast STS and chloroplast microsatellites.
  Plant Molecular Biology Reporter 04/2012; 19(1):27-32. · 2.45 Impact Factor
• Article: Effects of growth and dietary crude protein level until first insemination on milk production during first lactation in Holstein heifers.

  Takashige Ishii, Kenji Kawashima, Haruo Oribe, Hiromi Ueda, Toshiya Hasunuma, Kiyoshi Akiyama, Hirofumi Nakayama, Mitsunori Kurihara, Fuminori Terada, Shiro Kushibiki
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  ABSTRACT: To decrease the age at first calving in Holsteins, the effects of average daily body weight gain (ADG) and crude protein (CP) level until first insemination on growth performance and milk production were examined. The MM group had a target ADG of 0.75 kg and received a diet with a CP level of 14%. The HM and HH groups had a target ADG of 1 kg; both these groups received a diet with CP levels 14% and 16%, respectively. The ADG in the HM and HH groups was 1.1 kg, whereas in the MM group it was 0.97 kg (P < 0.01). The HM and HH groups showed no differences in withers height at body weight 350 kg. The ages at first calving in MM, HM and HH groups were 23.1, 21.0 and 21.8 months, respectively. The HM and HH groups had lower milk yield at day 305 than the MM group (P < 0.01). These results suggest that growth performance until first insemination should be maintained at an ADG of 0.97 kg or less with a CP level of approximately 14%, to shorten time until first insemination and prevent the decrease of milk yield.
  Animal Science Journal 12/2011; 82(6):741-6. · 0.86 Impact Factor
• Article: Effect of cellooligosaccharide or synbiotic feeding on growth performance, fecal condition and hormone concentrations in Holstein calves.

  Toshiya Hasunuma, Kenji Kawashima, Hirofumi Nakayama, Toshiaki Murakami, Hiroyuki Kanagawa, Takashige Ishii, Kiyoshi Akiyama, Kenji Yasuda, Fuminori Terada, Shiro Kushibiki
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  ABSTRACT: We investigated the effect of cellooligosaccharide (CE) or a combination of dextran and Lactobacillus casei ssp. casei strain JCM1134(T) (synbiotic; SB) feeding on growth performance, fecal condition and hormone concentrations in Holstein calves. Fifty-two female Holstein calves were randomly assigned to three treatment groups: CE feeding group (n = 16), SB feeding group (n = 18), and control group (n = 18). Body weight at 90 days of age, as well as daily body weight gain (DG) and feed efficiency after weaning to 90 days of age were greater (P < 0.05) in the CE feeding group than in the control group. The total fecal score tended to be lower (P < 0.1) in the SB feeding group than in the control group. Plasma insulin concentration was higher (P < 0.05) in the CE feeding group than in the control group at 90 days of age. Our results indicate that CE feeding improved DG and feed efficiency in calves. On the other hand, there was less effect on growth performance and fecal Escherichia coli counts in calves fed SB.
  Animal Science Journal 08/2011; 82(4):543-8. · 0.86 Impact Factor
• Article: Allelic interaction at seed-shattering loci in the genetic backgrounds of wild and cultivated rice species.

  Ryo Ishikawa, Pham Thien Thanh, Naoto Nimura, Than Myint Htun, Masanori Yamasaki, Takashige Ishii
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  ABSTRACT: It is known that the common cultivated rice (Oryza sativa) was domesticated from Asian wild rice, O. rufipogon. Among the morphological differences between them, loss of seed shattering is one of the striking characters specific for the cultivated forms. In order to understand the genetic control on shattering habit, QTL analysis was carried out using BC(2)F(1) backcross population between O. sativa cv. Nipponbare (a recurrent parent) and O. rufipogon acc. W630 (a donor parent). As a result, two strong QTLs were detected on chromosomes 1 and 4, and they were found to be identical to the two major seed-shattering loci, qSH1 and sh4, respectively. The allelic interaction at these loci was further examined using two sets of backcross populations having reciprocal genetic backgrounds, cultivated and wild. In the genetic background of cultivated rice, the wild qSH1 allele has stronger effect on seed shattering than that of sh4. In addition, the wild alleles at both qSH1 and sh4 loci showed semi-dominant effects. On the other hand, in the genetic background of wild rice, non-shattering effects of Nipponbare alleles at both loci were examined to inspect rice domestication from a viewpoint of seed shattering. It was serendipitous that the backcross plants individually having Nipponbare homozygous alleles at either shattering locus (qSH1 or sh4) shed all the seeds. This fact strongly indicates that the non-shattering behavior was not obtained by a single mutation in the genetic background of wild rice. Probably, some other minor genes are still associated with the formation or activation of abscission layer, which enhance the seed shattering.
  Genes & Genetic Systems 01/2010; 85(4):265-71. · 0.95 Impact Factor
• Article: QTL analysis for flowering time using backcross population between Oryza sativa Nipponbare and O. rufipogon.

  Pham Thien Thanh, Phuong Dang Thai Phan, Ryo Ishikawa, Takashige Ishii
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  ABSTRACT: In the near future, global average temperature is expected to increase due to the accumulation of greenhouse gases, and increased temperatures will cause severe sterility in many crop species. In rice, since wild species show high genetic variation, they may have the potential to improve the flowering characters of cultivars. In this study, we investigated flowering characters under natural conditions by comparing an Asian wild rice accession of Oryza rufipogon W630 (originated from Myanmar) with a Japanese rice cultivar, O. sativa Japonica cv. Nipponbare. Further, QTL analysis for days to heading (DH) and spikelet opening time (SOT: the time of day when the spikelet opens) was carried out using BC(2)F(8) backcross population derived from the cross between them. Regarding DH, four QTLs were detected, and two of them were found to have wild alleles with strong effects leading to longer days to heading during the Japanese summer. These wild alleles may be used to produce late-heading cultivars that do not flower during the high summer temperatures anticipated in the future. As for SOT, two parameters of SOTb (beginning time when the first spikelet opens) and SOTm (median time when 50% of the spikelets open) were recorded and the time differences from Nipponbare were investigated. Two QTLs on chromosomes 5 and 10 and two QTLs on chromosomes 4 and 5 were detected for SOTb and SOTm, respectively. The wild alleles were responsible for early spikelet opening time at all loci. If the wild alleles detected in this study have the same effects in the genetic background of other cultivars, they will be very useful in producing early-flowering rice cultivars that complete fertilization in the morning before the temperature rises.
  Genes & Genetic Systems 01/2010; 85(4):273-9. · 0.95 Impact Factor
• Source

  Available from: Hideo Matsumura

  Article: Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice.

  Sujay Rakshit, Arunita Rakshit, Hideo Matsumura, Yoshihiro Takahashi, Yoshitaka Hasegawa, Akiko Ito, Takashige Ishii, Naohiko T Miyashita, Ryohei Terauchi
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  ABSTRACT: Polymorphism over approximately 26 kb of DNA sequence spanning 22 loci and one region distributed on chromosomes 1, 2, 3 and 4 was studied in 30 accessions of cultivated rice, Oryza sativa, and its wild relatives. Phylogenetic analysis using all the DNA sequences suggested that O. sativa ssp. indica and ssp. japonica were independently domesticated from a wild species O. rufipogon. O. sativa ssp. indica contained substantial genetic diversity (pi = 0.0024), whereas ssp. japonica exhibited extremely low nucleotide diversity (pi = 0.0001) suggesting the origin of the latter from a small number of founders. O. sativa ssp. japonica contained a larger number of derived and fixed non-synonymous substitutions as compared to ssp. indica. Nucleotide diversity and genealogical history substantially varied across the 22 loci. A locus, RLD15 on chromosome 2, showed a distinct genealogy with ssp. japonica sequences distantly separated from those of O. rufipogon and O. sativa ssp. indica. Linkage disequilibrium (LD) was analyzed in two different regions. LD in O. rufipogon decays within 5 kb, whereas it extends to approximately 50 kb in O. sativa ssp. indica.
  Theoretical and Applied Genetics 03/2007; 114(4):731-43. · 3.30 Impact Factor
• Article: Mitochondrial microsatellite variability in common wheat and its ancestral species.

  Takashige Ishii, Chisa Takahashi, Nobuyuki Ikeda, Osamu Kamijima, Naoki Mori
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  ABSTRACT: On the basis of the entire mitochondrial DNA sequence of common wheat, Triticum aestivum, 21 mitochondrial microsatellite loci having more than ten mononucleotide repeats were identified. The mitochondrial microsatellite variability at all loci was examined with 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploidy evolution. Polymorphic banding patterns were obtained at 15 out of 21 mitochondrial microsatellite loci. The number of alleles per polymorphic microsatellite ranged from 2 to 5 with an average of 3.07, and the diversity values (H) ranged from 0.09 to 0.50 with an average of 0.29. These values are almost two third of wheat chloroplast microsatellite values, indicating that variability of mitochondrial microsatellite is much less than that of chloroplast microsatellite. Based on the allele variation at all loci, a total of seven mitochondrial haplotypes were identified among common wheat and its ancestral species. Three diploid species showed their own specific haplotypes and timopheevi group (11 accessions) had three types, whereas 29 accessions of emmer and common wheat groups shared the same haplotype. These results indicate that a single mitochondrial haplotype determined by microsatellite analysis has conservatively been maintained in the evolutionary lineage from wild tetraploid to cultivated hexaploid species.
  Genes & Genetic Systems 07/2006; 81(3):211-4. · 0.95 Impact Factor
• Source

  Available from: aseanbiotechnology.info

  Article: DNA variation in the metallothionein genes in wild rice Oryza rufipogon: relationship between DNA sequence polymorphism, codon bias and gene expression.

  Naohiko T Miyashita, Kentaro Yoshida, Takashige Ishii
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  ABSTRACT: This study examines the relationship between DNA sequence variation and level of gene expression in four metallothionein genes from wild rice Oryza rufipogon. The nucleotide diversity was 0.0028 to 0.0117 over the entire coding and non-coding region, and it was negatively correlated with gene expression for three type 2 metallothionein genes. In contrast, codon bias and percent of preferred codons correlated positively with gene expression. These results indicate that the intensity of natural selection depends on the level of gene expression, which in turn shapes the level of nucleotide polymorphism. In addition, significant linkage disequilibria were frequent between the metallothionein genes, although significance was not confirmed after multiple test correction. This result suggests that metallothionein genes expressed at different levels are epistatic with respect to fitness, and that gene expression is an important factor determining level of DNA polymorphism.
  Genes & Genetic Systems 07/2005; 80(3):173-83. · 0.95 Impact Factor
• Article: Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat.

  Shujiro Hirosawa, Shigeo Takumi, Takashige Ishii, Taihachi Kawahara, Chiharu Nakamura, Naoki Mori
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  ABSTRACT: To understand the origin and evolution of common wheat, chloroplast (ct) and nuclear DNA variations were studied in five hexaploid and three tetraploid wheat subspecies. Based on chloroplast simple sequence repeats at 24 loci, they were classified into two major plastogroups. Plastogroup I consisted of 11 plastotypes, including the major plastotype H10 that occurred at the highest frequency (59%) in common wheat. Plastogroup II consisted of five plastotypes and occurred in eight out of 27 accessions of T. aestivum ssp. spelta and one accession of ssp. aestivum. As for nuclear DNA variations, AFLP data using 10 primer sets revealed two major clades of a phylogenetic tree constructed by UPGMA (unweighted pair-group method with arithmetic mean), one consisting of common wheat and the other of emmer wheat. The clade of common wheat was further divided into two major and six minor subclades. One of the major subclades consisted only of non-free-threshing ssp. spelta accessions, which were grouped into two clusters, one consisting only of accessions with plastogroup I ctDNA and the other with both plastogroups I and II. T. aestivum ssp. macha, another non-free-threshing common wheat, formed the other cluster. Taken together, our data indicate the existence of at least two maternal lineages in common wheat and support the hypothesis that European spela wheat originated in Europe separately from other groups of common wheat.
  Genes & Genetic Systems 11/2004; 79(5):271-82. · 0.95 Impact Factor