Iwate Biotechnology Research Center

Kitakami, Japan

Iwate Biotechnology Research Center

Kitakami, Japan
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Varshney R.K.,Indian International Crops Research Institute for the Semi Arid Tropics | Varshney R.K.,University of Western Australia | Terauchi R.,Iwate Biotechnology Research Center | McCouch S.R.,Cornell University
PLoS Biology | Year: 2014

Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population. © 2014 Varshney et al.


Sasaki N.,Iwate Biotechnology Research Center | Nakayama T.,Tohoku University
Plant and Cell Physiology | Year: 2015

Genetic engineering of roses and other plants of floricultural importance to give them a truly blue petal color is arguably one of the holy grails of plant biotechnology. Toward this goal, bluish carnations and roses were previously engineered by establishing an exclusive accumulation of delphinidin (Dp)-type anthocyanins in their petals via the heterologous expression of a flavonoid 3′,5′-hydroxylase gene. Very recently, purple-blue varieties of chrysanthemums were also genetically engineered via a similar biochemical strategy. Although the floral colors of these transgenic plants still lack a true blue color, the basis for the future molecular breeding of truly blue flowers is via the engineering of anthocyanin pathways. Anthocyanins with multiple aromatic acyl groups (often referred to as polyacylated anthocyanins) in the 3′-or 7-position tend to display a more stable blue color than non-acylated anthocyanins. The 7-polyacylation process during the biosynthesis of purple-blue anthocyanins in delphinium (Delphinium grandiflorum) was found to occur in vacuoles using acyl-glucose as both the glucosyl and acyl donor. Glucosyltransferases and acyltransferases involved in anthocyanin 7-polyacylation in delphinium are vacuolar acyl-glucose-dependent enzymes belonging to the glycoside hydrolase family 1 and serine carboxypeptidae-like protein family, respectively. The 7-polyacylation proceeds through the alternate glucosylation and p-hydroxybenzoylation catalyzed by these enzymes. p-Hydroxybenzoyl-glucose serves as the p-hydroxybenzoyl and glucosyl donor to produce anthocyanins modified with a p-hydroxybenzoyl-glucose concatemer at the 7-position. This novel finding has provided a potential breakthrough for the genetic engineering of truly blue flowers, where polyacylated Dp-type anthocyanins are accumulated exclusively in the petals. © 2014 The Author.


Varshney R.K.,Indian International Crops Research Institute for the Semi Arid Tropics | Terauchi R.,Iwate Biotechnology Research Center | McCouch S.R.,Cornell University
PLoS biology | Year: 2014

Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.


Nishihara M.,Iwate Biotechnology Research Center | Nakatsuka T.,Iwate Biotechnology Research Center
Biotechnology Letters | Year: 2011

Recent advances in genetic transformation techniques enable the production of desirable and novel flower colors in some important floricultural plants. Genetic engineering of novel flower colors is now a practical technology as typified by commercialization of a transgenic blue rose and blue carnation. Many researchers exploit knowledge of flavonoid biosynthesis effectively to obtain unique flower colors. So far, the main pigments targeted for flower color modification are anthocyanins that contribute to a variety of colors such as red, pink and blue, but recent studies have also utilized colorless or faint-colored compounds. For example, chalcones and aurones have been successfully engineered to produce yellow flowers, and flavones and flavonols used to change flower color hues. In this review, we summarize examples of successful flower color modification in floricultural plants focusing on recent advances in techniques. © 2010 Springer Science+Business Media B.V.


Yamagishi M.,Hokkaido University | Shimoyamada Y.,Hokkaido University | Nakatsuka T.,Iwate Biotechnology Research Center | Masuda K.,Hokkaido University
Plant and Cell Physiology | Year: 2010

Anthocyanins are secondary metabolites that contribute to colors of flowers, fruits and leaves. Asiatic hybrid lily (Lilium spp.) accumulates cyanidin anthocyanins in flower tepals, tepal spots and leaves of juvenile shoots. To clarify their mechanisms of regulation of anthocyanin pigmentation, two full-length cDNAs of R2R3-MYB (LhMYB6 and LhMYB12) were isolated from the anthocyanin-accumulating tepals of cultivar 'Montreux'. Analysis of the deduced amino acid sequences indicated they have homology with petunia AN2, homologous sequences of which had not been isolated in species of monocots. Yeast two-hybrid analysis showed that LhMYB6 and LhMYB12 interacted with the Lilium hybrid basic helixloophelix 2 (LhbHLH2) protein. Transient expression analysis indicated that co-expression of LhMYB6 and LhbHLH2 or LhMYB12 and LhbHLH2, introduced by a microprojectile, activated the transcription of anthocyanin biosynthesis genes in lily bulbscales. Spatial and temporal transcription of LhMYB6 and LhMYB12 was analyzed. The expression of LhMYB12 corresponded well with anthocyanin pigmentation in tepals, filaments and styles, and that of LhMYB6 correlated with anthocyanin spots in tepals and light-induced pigmentation in leaves. These results indicate that LhMYB6 and LhMYB12 positively regulate anthocyanin biosynthesis and determine organ-and tissue-specific accumulation of anthocyanin.


Nakatsuka T.,Iwate Biotechnology Research Center | Nishihara M.,Iwate Biotechnology Research Center
Planta | Year: 2010

3-Deoxyanthocyanins are rare anthocyanin pigments produced by some mosses, ferns, and higher plants. The enzymes and genes responsible for biosynthesis of 3-deoxyanthocyanins have not been well characterized. We identified a novel gene encoding UDP-glucose:3-deoxyanthocyanidin 5-O-glucosyltransferase (dA5GT) from Sinningia cardinalis, which accumulates abundant 3-deoxyanthocyanins in its petals. Five candidate genes (ScUGT1 to ScUGT5) were isolated from an S. cardinalis flower cDNA by degenerate PCR targeted for the UGT88 clade. ScUGT1, ScUGT3, and ScUGT5 exhibited 45-47% identity with rose anthocyanidin 5,3-O-glucosyltransferase, which catalyzes glucosylation at the 5- and 3-position of 3-hydroxyanthocyanidin. Based on its temporal and spatial gene expression patterns, and enzymatic activity assays of the recombinant protein, ScUGT5 was screened as a dA5GT candidate. Recombinant ScUGT5 protein expressed in Escherichia coli was used to analyze the detailed enzymatic properties. The results demonstrated that ScUGT5 specifically transferred a glucosyl moiety to 3-deoxyanthocyanidins in the presence of UDP-glucose, but not to other flavonoid compounds, such as 3-hydroxyanthocyanidins, flavones, flavonols, or flavanones. © 2010 Springer-Verlag.


Matsumura H.,Iwate Biotechnology Research Center
Methods in molecular biology (Clifton, N.J.) | Year: 2011

SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. Combined with the ultrahigh-throughput sequencing technologies, SuperSAGE enables analysis of millions of transcripts with lower cost and reduced effort and time. In this chapter, we present an updated protocol for this High-throughput SuperSAGE method with a special emphasis on the technique of library multiplexing.


Chanda B.,University of Kentucky | Xia Y.,University of Kentucky | Mandal M.K.,University of Kentucky | Yu K.,University of Kentucky | And 9 more authors.
Nature Genetics | Year: 2011

Glycerol-3-phosphate (G3P) is an important metabolite that contributes to the growth and disease-related physiologies of prokaryotes, plants, animals and humans alike. Here we show that G3P serves as the inducer of an important form of broad-spectrum immunity in plants, termed systemic acquired resistance (SAR). SAR is induced upon primary infection and protects distal tissues from secondary infections. Genetic mutants defective in G3P biosynthesis cannot induce SAR but can be rescued when G3P is supplied exogenously. Radioactive tracer experiments show that a G3P derivative is translocated to distal tissues, and this requires the lipid transfer protein, DIR1. Conversely, G3P is required for the translocation of DIR1 to distal tissues, which occurs through the symplast. These observations, along with the fact that dir1 plants accumulate reduced levels of G3P in their petiole exudates, suggest that the cooperative interaction of DIR1 and G3P orchestrates the induction of SAR in plants. © 2011 Nature America, Inc. All rights reserved.


Konno N.,Iwate Biotechnology Research Center | Sakamoto Y.,Iwate Biotechnology Research Center
Applied Microbiology and Biotechnology | Year: 2011

A β-1,6-glucanase, LePus30A, was purified and cloned from fruiting bodies of the basidiomycete Lentinula edodes. β-1,6-Glucanases degrade β-1,6-glucan polysaccharides, a unique and essential component of fungal cell walls. The complementary DNA of LePus30A includes an open reading frame of 1,575 bp encoding an 18 amino acid signal peptide and the 506 amino acid mature protein. Sequence analysis indicated that LePus30A is a member of glycoside hydrolase family 30, and highly similar genes are broadly conserved among basidiomycetes. The purified LePus30A catalyzed depolymerization of β-1,6-glucan endolytically and was highly specific toward β-1,6-glucan polysaccharide. It is known that the cell walls of fruiting bodies of basidiomycetes are autodegraded after harvesting by means of enzymatic hydrolysis. The transcript level of LePus30A gene (lepus30a) was significantly increased in fruiting bodies after harvesting. Moreover, LePus30A showed hydrolyzing activity against the cell wall components of L. edodes fruiting bodies. These results suggest that LePus30A is responsible for the degradation of the cell wall components during fruiting body autolysis after harvest. © 2011 Springer-Verlag.


Terauchi R.,Iwate Biotechnology Research Center | Yoshida K.,Iwate Biotechnology Research Center
New Phytologist | Year: 2010

Pathogen-plant host coevolutionary interactions exert strong natural selection on both organisms, specifically on the genes coding for effectors (pathogens), as well as on those coding for effector targets and R proteins (plant hosts). Natural selection leaves behind DNA sequence signatures on such genes and on linked genomic regions. These signatures can readily be detected by studying the patterns of intraspecies polymorphisms and interspecies divergence of the DNA sequences. Recent developments in DNA sequencing technology have made whole-genome studies on patterns of DNA polymorphisms: divergence possible. This type of analysis, called 'population genomics', appears to be powerful enough to identify novel effector-effector target genes. Here, we provide an overview of the statistical tools used for population genomics and their applications. This is followed by a brief review of evolutionary studies on plant genes involved in host-pathogen interactions. Finally we provide an example from our study on Magnaporthe oryzae. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

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