transPLANT Resources for Triticeae Genomic Data

@article{Spannagl2016transPLANTRF,
  title={transPLANT Resources for Triticeae Genomic Data},
  author={Manuel Spannagl and Michael Alaux and Matthias Lange and Dan M. Bolser and Kai Christian Bader and Thomas Letellier and Erik Kimmel and Raphael Flores and Cyril Pommier and Arnaud Kerhornou and Brandon Walts and Thomas Nussbaumer and Christoph Grabmuller and Jinbo Chen and Christian Colmsee and Sebastian Beier and Martin Mascher and Thomas Schmutzer and Daniel Arend and Anil S. Thanki and Ricardo H Ramirez-Gonzalez and Martin Ayling and Sarah C. Ayling and Mario C{\'a}ccamo and Klaus F. X. Mayer and Uwe Scholz and Delphine Steinbach and Hadi Quesneville and Paul Julian Kersey},
  journal={The Plant Genome},
  year={2016},
  volume={9}
}
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… 
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12 Citations
Background Citations
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Methods Citations
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12 Citations

Towards a whole‐genome sequence for rye (Secale cereale L.)
TLDR
This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
RepetDB: a unified resource for transposable element references
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RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences, which facilitates the exploration of specific TE families, superfamilies or orders across a large range of species.
Identification of molecular markers for the Pc39 gene conferring resistance to crown rust in oat
TLDR
Six new PCR-based markers for the Pc39 crown rust resistance gene in Avena sativa L. were developed, which will be useful in marker-assisted selection and could find applications in the fine mapping or positional cloning of this gene.
Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs
TLDR
Here, some relevant concepts in population genomics together with recent advances in quantitative genetics are reviewed in order to discuss how the combination of both disciplines can facilitate the use of genetic diversity in plant (pre) breeding programs.
Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.
Chromosomal distributions of oligo-Am1 and (TTG)6 trinucleotide and their utilization in genome association analysis of sixteen Avena species
TLDR
The oligo-Am1 probe produced signals that were particularly enriched on almost whole C-genome chromosomes, whereas the (TTG)6 probe was located in the pericentromeric (M) and telomeric (T) chromosome regions, but showed low matching to C genome.
Towards an open grapevine information system
TLDR
An open working group is formed, in the framework of the International Grapevine Genome Program, to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools.
Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq
TLDR
An F2:3 population derived from a cross between IR36 and Weiguo was used to identify salt-tolerant QTL interval at the bud burst stage and sequence analysis revealed OsSAP16, a stress-associated protein whose expression is increased under drought stress that is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection.
TGAC Browser: An open-source genome browser for non-model organisms
Genome browsers play a vital role to provide visualisation for genomic data. It is often the case that bespoke genome browser customisations are required between different research groups, with an…
Knowledge representation and data sharing to unlock crop variation for nutritional food security
TLDR
Development of a Crop Dietary Nutrition Ontology (CDNO) is proposed as a robust structured controlled vocabulary for dietary nutritional composition and function, and examples of specific use cases and different end users who would benefit from using CDNO terms in their database searches are provided.
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