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Kazuo Shinozaki - One of the best experts on this subject based on the ideXlab platform.
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Unlocking Triticeae genomics to sustainably feed the future.
Plant & cell physiology, 2013Co-Authors: Keiichi Mochida, Kazuo ShinozakiAbstract:The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species—barley, wheat, Tausch’s goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)—have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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trifldb a database of clustered full length coding sequences from Triticeae with applications to comparative grass genomics
Plant Physiology, 2009Co-Authors: Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Yasunari Ogihara, Kazuo ShinozakiAbstract:The Triticeae Full-Length CDS Database (TriFLDB) contains available information regarding full-length coding sequences (CDSs) of the Triticeae crops wheat (Triticum aestivum) and barley (Hordeum vulgare) and includes functional annotations and comparative genomics features. TriFLDB provides a search interface using keywords for gene function and related Gene Ontology terms and a similarity search for DNA and deduced translated amino acid sequences to access annotations of Triticeae full-length CDS (TriFLCDS) entries. Annotations consist of similarity search results against several sequence databases and domain structure predictions by InterProScan. The deduced amino acid sequences in TriFLDB are grouped with the proteome datasets for Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and sorghum (Sorghum bicolor) by hierarchical clustering in stepwise thresholds of sequence identity, providing hierarchical clustering results based on full-length protein sequences. The database also provides sequence similarity results based on comparative mapping of TriFLCDSs onto the rice and sorghum genome sequences, which together with current annotations can be used to predict gene structures for TriFLCDS entries. To provide the possible genetic locations of full-length CDSs, TriFLCDS entries are also assigned to the genetically mapped cDNA sequences of barley and diploid wheat, which are currently accommodated in the Triticeae Mapped EST Database. These relational data are searchable from the search interfaces of both databases. The current TriFLDB contains 15,871 full-length CDSs from barley and wheat and includes putative full-length cDNAs for barley and wheat, which are publicly accessible. This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/.
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TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
BMC plant biology, 2008Co-Authors: Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Daisuke Saisho, Kazuo ShinozakiAbstract:Background The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species.
Frank R. Blattner - One of the best experts on this subject based on the ideXlab platform.
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Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.
BMC evolutionary biology, 2017Co-Authors: Nadine Bernhardt, Jonathan Brassac, Benjamin Kilian, Frank R. BlattnerAbstract:Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.
Nadine Bernhardt - One of the best experts on this subject based on the ideXlab platform.
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Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.
BMC evolutionary biology, 2017Co-Authors: Nadine Bernhardt, Jonathan Brassac, Benjamin Kilian, Frank R. BlattnerAbstract:Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.
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Analysis of phylogenetic relationships among diploid Triticeae grasses
2016Co-Authors: Nadine BernhardtAbstract:The grass tribe Triticeae consists of about 360 species and several subspecies in approximately 20-30 genera. The tribe harbours the important cereals bread wheat (Triticum aestivum), barley (Hordeum vulgare), rye (Secale cereale), and their wild relatives. In this thesis a hybridization-based enrichment approach coupled with Illumina sequencing was developed that retrieves phylogenetic sequence information from 451 putative single-copy loci from all taxa of the tribe. The nuclear loci were studied individually and in multilocus datasets and different phylogenetic methods (e.g. network and coalescent-based) were applied. The results identify distinctions among Triticeae genomes. Moreover, they improve our understanding of the relationships among these taxa and of the sequence of speciation events.
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Taxonomic Treatments of Triticeae and the Wheat Genus Triticum
Alien Introgression in Wheat, 2015Co-Authors: Nadine BernhardtAbstract:The taxonomic treatment of the grass tribe Triticeae Dumort. as well as the treatment of its most prominent member, the wheat genus Triticum, is under long-standing debate. Even after decades of research, published studies are largely contradictory and incompatible. The reasons are multifaceted and include the complex mode of evolution of genera and species, due to recurrent hybridization among species resulting in many allopolyploids, and the taxonomic representation of such relationships. The high number of existing species and genera, their worldwide distribution in temperate regions, and their economic importance made them of interest to many taxonomists around the globe. Finally, conceptual and methodological achievements in taxonomy and different opinions of taxonomists resulted in the existence of various different treatments and several correct scientific names for many taxa of Triticeae. The classificatory systems that were proposed for Triticum exhibit a striking example for how different opinions of taxonomist influence the naming of plants. This chapter reviews important historical and current taxonomic treatments of the tribe Triticeae, the wheat genus Triticum, and their underlying methods and perceptions. Current challenges in Triticeae taxonomy are discussed.
Arnaud Kerhornou - One of the best experts on this subject based on the ideXlab platform.
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TransPLANT resources for Triticeae genomic data
PLANT GENOME, 2016Co-Authors: Manuel Spannagl, Michael Alaux, Matthias Lange, Dan M. Bolser, Kai Christian Bader, Thomas Letellier, Erik Kimmel, Raphaël-gauthier Flores, Cyril Pommier, Arnaud KerhornouAbstract:The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.
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transPLANT Resources for Triticeae Genomic Data
The plant genome, 2016Co-Authors: Manuel Spannagl, Michael Alaux, Matthias Lange, Dan M. Bolser, Kai Christian Bader, Thomas Letellier, Erik Kimmel, Cyril Pommier, Raphael Flores, Arnaud KerhornouAbstract:The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT () is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.
Jun Liang Yang - One of the best experts on this subject based on the ideXlab platform.
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Historical review and prospect of taxonomy of tribe Triticeae Dumortier (Poaceae)
Breeding Science, 2009Co-Authors: Chi Yen, Jun Liang YangAbstract:The tribe Triticeae is a taxon in the Poaceae that includes several important cereal crops and forage grasses. All its species, including those that are not used for cereals or forage, are potential sources of genes for crop and forage improvement so they all have high economic value. Taxonomic treatments, including those of the Triticeae, are the basis for identification. They are often designed to reflect phylogenetic relationships and provide a guide for germplasm utilization. Traditional taxonomic treatments of the Triticeae were based on comparative morphology and geography. Morphological characters are phenotypes of an organism, resulting from interactions between or among dominant genes and environmental factors. Morphology cannot reflect recessive inheritance. Similar environmental conditions may result in morphological convergence in distantly related taxa and different environmental conditions in morphological divergence of closely related taxa. Consequently, traditional morphological taxonomy may result in misclassification. Cytogenetic and/or molecular genomic analysis may reveal such mistakes. On the basis of recent genomic investigations of the Triticeae, we have recognized 30 genera in this tribe. The taxonomic changes and genomic constitution of these genera are presented in this paper.
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The diversity of head-scab resistance in Triticeae and their relation to ecological conditions.
Euphytica, 1997Co-Authors: Yong-fang Wan, Chi Yen, Jun Liang YangAbstract:1507 accessions from 93 species of 18 genera in Triticeae were screened for resistance to initial infection and resistance to pathogen spread with multi-floret and single-floret injection inoculation methods respectively. The accessions with high resistance were mainly found in perennial genera: Roegneria, Hystrix, Agropyron, Kengyilia and Elymus. Based on differences in resistance, 18 genera screened in Triticeae could be classified into five groups. The species with high resistance were mainly distributed in humid ecological environments.
