All Hot Topics

  • Released: Triticum turgidum Durum Wheat Svevo Rel. 2.0 pseudomolecules

    The Triticum turgidum Durum Wheat Svevo Rel. 2.0 pseudomolecules (2024) is made available under the prepublication data sharing principle of the Toronto agreement (Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009) https://doi.org/10.1038/461168a).

    If you want to have access to data, please send an email to taner.sen@usda.gov for access (in the email, please include your full name, email, and institution). Please do not share the datasets or the login/password information with others. Thank you for your understanding.

    By using this data, you agree to:
    • respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
    • not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.
    • contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.
    • fully cite the prepublication data along with any applicable versioning details.
    • understand that this data as accessed is precompetitive and is not patentable in its present state.

    The Triticum turgidum Durum Wheat Svevo Rel. 2.0 pseudomolecules (2024)
    The reference genome durum wheat cultivar Svevo (Maccaferri et al., 2019), defined as Triticum turgidum Durum Wheat Svevo Rel. 1.0 pseudomolecules (2019), has been updated to a Platinum-quality level (RefSeq2.0), fulfilling with the ultimate requirements of contiguity, completeness, correctness. PACBIO HiFi long read 35X sequencing was coupled with Bionano Optical Mapping, producing 259 Hybrid scaffolds (N50 = 112.3 Mb) that were ordered by Hi-C data into 14 contiguous pseudomolecules spanning 10.4 Gb (Svevo v2). A complete and accurate gene annotation was generated by coupling Illumina RNA-seq and Nanopore Isoseq sequencing of 58 samples representative of a range of tissues and developmental stages from plants grown under optimal conditions or exposed to biotic, abiotic, and nutrient stresses (drought, heat, salinity, nitrogen, Fusarium graminearum infection). A total of 68,154 high-confidence and 93,888 low-confidence protein-coding genes, 3,241 ncRNAs and 7,959 pseudogenes and low-confidence predictions have been displayed on the Genome Browser.

    For any questions or suggestions about of this dataset, please contact: Marco Maccaferri (marco.maccaferri@unibo.it), Cristian Forestan (cristian.forestan@unibo.it); Elisabetta Mazzucotelli (elisabetta.mazzucotelli@ucrea.gov.it); Anthony Hall (anthony.hall@earlham.ac.uk), Manuel Spannagl (manuel.spannagl@helmholtz-munich.de), Curtis Pozniak (curtis.pozniak@usask.ca), Roberto Tuberosa (roberto.tuberosa@unibo.it), Luigi Cattivelli (luigi.cattivelli@crea.gov.it).

    Acknowledgements
    Institutions participating in the “Svevo Platinum” collaborative project
    • CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
    • Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
    • Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
    • Canadian Grain Commission, Winnipeg, Manitoba, Canada
    • Department of plant science, University of Manitoba, Winnipeg, MB, Canada
    • Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
    • Corteva Agriscience, Johnston, IA, USA
    • Earlham Institute, Norwich, United Kingdom
    • Helmholtz Munich, German Research Center for Environmental Health, Plant Genome and Systems Biology, Neuherberg, Germany
    • Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
    • Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
    • Institute of Experimental Botany, Šlechtitelů 31, Olomouc, Czech Republic
    • CREA Research Centre for Forestry and Wood, Arezzo, Italy
    • CREA Research Centre for Cereal and Industrial Crops, Foggia, Italy
    • CNR Institute for Biosciences and Bioresources, Bari, Italy
    • CNR Institute of Agricultural Biology and Biotechnology, Milano, Italy
    • ENEA, Casaccia Research Center, Rome, Italy
    • University of Bari, Bari, Italy
    • Scuola superiore Sant'Anna Pisa, Pisa, Italy
    • Barilla, Parma, Italy
    • USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND USA
    • USDA-ARS Western Regional Research Center, Albany, CA, USA
    • Technical University of Madrid, Madrid, Spain
    • ICARDA, Rabat, Morocco
    • Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
    • Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
    • Earlham Institute, Norwich, Norfolk, United Kingdom
    • University of Tuscia, Viterbo, Italy
    • University of Udine, Udine, Italy

    Funding
    This work has been funded by the following projects/funding organizations PanWheatGrain, AGRITECH (part of PNRR Next Generation EU), Canadian Tetraploid Pan Genomics, Horizon EU PRO-GRACE (contract n. 101094738‬), German Ministry of Education and Research (de.NBI 031A536), PlantaSyst, E-crops PON Agrifood Program, Contract ARS01_01136).

  • Community Notice – Some applications will not be available in GrainGenes for security updates

    Dear GrainGenes Users,

    When we were performing regular testing of GrainGenes IT systems, we identified an IT security issue that needed to be addressed immediately. The issue affected the following applications in GrainGenes:
    1. GSP: Genome Specific Primers,
    2. RJPrimers,
    3. BatchPrimer3
    4. PIECE2

    Until further notice, these applications won’t be available publicly. We have been working on identifying the origin of the issue and fully resolving it. We have also started a much-needed containerization of these applications, which will enhance the IT security further. Unfortunately, we do not currently have an estimated time of delivery, but we expect the conversion will take several weeks.

    We apologize for the inconvenience. For inquiries, please contact Taner Sen at taner.sen@usda.gov.

    Thank you for your understanding and continuing support of GrainGenes.

  • CASA-Bio: Call to all Bioeconomy Researchers and Developers

    Calling all Bioeconomy Researchers and Developers,

    If you think your research is not relevant to the bioeconomy – think again! We are seeking input from researchers interested in climate change, food and agriculture, supply chain resilience, human health, or any number of cross-cutting advances like data science; artificial intelligence; workforce development; biomanufacturing scale-up; or multiple areas of social, behavioral, and economic sciences; and security. Your ideas will impact future directions for the bioeconomy. Please check out www.casa-bio.net to learn how you can participate through interactive Town Halls, sharing individual research ideas, and more.

    In a nutshell, CASA-Bio (Catalyzing Across Sectors to Advance the Bioeconomy) was designed to be a collaborative, facilitated activity with stakeholders that include federal funding agencies, industries, non-profits, and the public sector research community. Come help us define the R&D approaches that will advance the future of the bioeconomy.

    What’s on your mind? Let us know what you and your community are thinking. Participate to ensure your ideas are part of the future conversations. Act now! Two options at www.casa-bio-net.

    Option 1
    If you can attend, register for a Town Hall to collaborate with others on developing research ideas, and share your individual ideas ahead of the Town Hall.

    1) Select Your Best Date

    February 21, 2024 from 12-1:30 PM ET

    February 22, 2024 from 5-6:30 PM ET

    2) Share Your Exciting Research Idea About Your Favorite Theme!

    Option 2
    If you are unable to attend a Town Hall, we would still love to hear our research ideas, so please share online.

  • Updated guidelines for gene nomenclature in oat

    [January 2, 2024]
    The journal article “A uniform gene and chromosome nomenclature system for oat (Avena spp.)” was published (Jellen et al, Crop and Pasture Science, 2024).

    Please promote the journal article to facilitate the adoption of common gene nomenclature for oat research.

    *

    Open access article: https://doi.org/10.1071/CP23247

    Context: Several high-quality reference genomes for oat (Avena sativa L. and relatives) have been published, with the prospect of many additional whole-genome assemblies emerging in the near future.

    Aims: This has necessitated an effort by the International Oat Nomenclature Committee (IONC; all co-authors on this paper) to devise a universal system for naming oat genomes and subgenomes, chromosomes, genes, gene models and quantitative trait loci.

    Methods: We evaluated existing naming practices, recent data from oat whole-genome sequencing, and the newly published convention for wheat nomenclature.

    Key results: A framework for these rules has been posted on the GrainGenes database website (https://wheat.pw.usda.gov/GG3/oatnomenclature). The gene naming convention requires adoption of a numerical identifier for each genotype; we propose that these identifiers be assigned by contacting the GrainGenes curators, the curator of the Oat Newsletter, or a member of the IONC (as listed at the GrainGenes link above).

    Conclusions: We encourage oat researchers to refer to these resources, policies, procedures and conventions, adopting them as an international nomenclature standard.

    Implications: Adoption of these standards will facilitate communication and dissemination of oat research and allow programmatic access and data sharing across platforms, and will contribute to oat breeding and research worldwide.

    *
    Full Citation:
    Jellen Eric N., Wight Charlene P., Spannagl Manuel, Blake Victoria C., Chong James, Herrmann Matthias H., Howarth Catherine J., Huang Yung-Fen, Juqing Jia, Katsiotis Andreas, Langdon Tim, Li Chengdao, Park Robert, Tinker Nicholas A., Sen Taner Z. (2024) A uniform gene and chromosome nomenclature system for oat (Avena spp.). Crop & Pasture Science 75, CP23247.
    *

    Link to the Oat Nomenclature page in GrainGenes.

  • The Wheat Genome book is out

    [Posted on November 20, 2023]

    Dear IWGSC Members and Friends,

    We are very pleased to announce that the first comprehensive book about the Wheat Genome is now out and available in open access.

    You can read or download The Wheat Genome book here: https://link.springer.com/book/10.1007/978-3-031-38294-9

    Edited by Rudy Appels, Kellye Eversole, Catherine Feuillet and Dusti Gallagher, the Wheat Genome book highlights the groundbreaking research ongoing for wheat – a critical food security crop. It illustrates the value and impact of having high-quality reference genomes for overall crop improvements that address the dual challenges of producing a reliable, safe, and sustainable supply of wheat while facing a rapidly changing climate.

    The book includes articles describing the development of the reference sequence, new assemblies of commercial varieties, genome-wide studies, and the accelerated cloning of agronomically important genes and provides valuable resources and literature for fundamental and applied research, crop improvement and teaching.

    A huge thank you to all the IWGSC members who contributed insights and co-authors chapters in the book.

    The IWGSC Team

  • US Federal Register notice: Movement of Organisms Modified or Produced Through Genetic Engineering

    [Note: Five new rules as to the nature, size, and number of mutations in plants are being proposed to reduce regulatory burden. The public is asked to provide comments.]

    AGENCY: Animal and Plant Health Inspection Service, USDA.

    SUMMARY:

    We are advising the public that we are proposing to add five new types of genetic modifications a plant can contain and be exempt from the regulations for the movement of organisms modified or produced through genetic engineering because such modifications could otherwise be achieved through conventional breeding methods.

    First, we propose any diploid or autopolyploid plant with any combination of loss of function modifications (i.e., a modification that eliminates a gene's function) in one to all alleles of a single genetic locus, or any allopolyploid plant with any combination of loss of function modifications in one or both alleles of a single genetic locus on up to four pairs of homoeologous chromosomes, without the insertion of exogenous DNA, would qualify for exemption. Second, we propose that any diploid or autopolyploid plant in which the genetic modification is a single contiguous deletion of any size, resulting from cellular repair of one or two targeted DNA breaks on a single chromosome or at the same location(s) on two or more homologous chromosomes, without insertion of DNA, or with insertion of DNA in the absence of a repair template, would qualify for exemption. Third, we propose to extend the modifications described in certain existing exemptions in the regulations to all alleles of a genetic locus on the homologous chromosomes of an autopolyploid plant. Fourth, we propose that plants with up to four modifications that individually qualify for exemption and are made simultaneously or sequentially would be exempt from regulation, provided that each modification is at a different genetic locus. Fifth, we propose that plants that have previously completed a voluntary review confirming exempt status and that have subsequently been produced, grown, and observed consistent with conventional breeding methods appropriate for the plant species, could be successively modified in accordance with the exemptions. This action would reduce the regulatory burden for developers of certain plants modified using genetic engineering that are not expected to pose plant pest risks greater than the plant pest risks posed by plants modified by conventional breeding methods.

    DATES:

    We will consider all comments that we receive on or before December 15, 2023.

    https://www.federalregister.gov/documents/2023/11/15/2023-25122/movement...

  • Morex V3 mapped barley spike transcriptome in ePlant browser

    [Provided by Ravi Koppolu; edited and posted on Oct 31, 2023]

    Here is an update about the barley spike transcriptome atlas which has been published in 2021 Sci. Adv. 2021 from Prof. Schnurbusch lab at IPK.

    As part of the published paper from 2021 Ravi Koppolu and Thorsten Schnurbusch have integrated the transcriptome data based on Morex v1 transcript reference in barley ePlant browser (BAR, Uni. Toronto, Canada).

    Since Morex V3 reference has been available for a while, we have remapped our spike transcriptome data with Morex V3 reference and integrated the same into barley ePlant browser.

    The barley ePlant now has transcriptome visualizations for both V1 and V3 data sets. These data sets can be accessed under following URLs

    V3 data
    https://bar.utoronto.ca/eplant_barley/
    Legacy version (published V1 data)
    https://bar.utoronto.ca/eplant_barley_legacy/

    GrainGenes barley genome browsers provide links to the ePlant Browsers from the high-confidence gene models:
    Barley Morex v3: https://wheat.pw.usda.gov/jb?data=/ggds/bar-morex3
    Barley Morex v1: https://wheat.pw.usda.gov/jb?data=/ggds/bar-morex

  • Einkorn genomics sheds light on history of the oldest domesticated wheat

    [Posted on September 15, 2023]

    The journal article “Einkorn genomics sheds light on history of the oldest domesticated wheat” was published.

    Key message: This manuscript describes a high quality genome of world oldest cultivated wheat "Einkorn wheat" and its potential in future wheat improvement.

    Open access article: https://www.nature.com/articles/s41586-023-06389-7

    Abstract Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

    Resources:

    https://wheat.pw.usda.gov/GG3/pangenome

    GrainGenes hosts an interactive webpage for the data described in the manuscript. This webpage provides:

    • latest JBrowse2 genome browser
    • chromosome level BLAST
    • synteny viewer between Monococcum and other wheat varieties
    • a search feature for two reference monococcum assembles.

  • Updated guidelines for gene nomenclature in wheat

    [March 23, 2023]
    The journal article “Updated guidelines for gene nomenclature in wheat” was published. Please promote the journal article to facilitate the adoption of common gene nomenclature for wheat research.

    *

    Open access article: https://link.springer.com/article/10.1007/s00122-023-04253-w

    Key message: Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community.

    Abstract

    The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

  • The release of A. sativa (cv Sang), A. longiglumis, and A. insularis

    GrainGenes links
    To reach genome browsers, BLAST, and Data Download for these assemblies and annotations, please follow this link.

    **
    Press Release [May 18, 2022]:

    The oat genome unlocks the unique health benefits of oats

    Researchers have succeeded in sequencing and characterizing the entire genome of oat. Compared to other cereals and humans, the oat genome architecture is very complex. An international research team under the leadership of Lund University, the ScanOats Industrial Research Center and Helmholtz Munich finally elucidated at the genetic level why oats are healthier and cause fewer allergies and intolerances compared to other cereals.

    "Oats are not only an increasingly popular cereal, but also a very complicated one, genetically" says Nick Sirijovski from Lund University and ScanOats, now employed at Oatly. The team of researchers from five different countries spent six years decoding and investigating the oat genome, and identified the entire set of genes contained in this important cereal. The complexity of the oat genome is a result of its size and structure: common oat is what is known as a hexaploid and has six sets of chromosomes with more than 80,000 genes combined, while humans have only two sets of chromosomes with about 20,000 genes. Moreover, the order of genes along the chromosomes is substantially less “sorted” than in other cereals with a considerable amount of genes having been relocated between the chromosomes, resulting in a mosaic-like genome architecture.

    Tracking down the health benefits of oats
    Knowing the genome sequence allows us to better understand which genes are responsible for which traits. In the case of oats, the researchers were particularly interested in finding out why oat products trigger fewer allergies and intolerances compared to other cereals such as wheat or rye. They discovered that oats have fewer of the proteins that correspond to gluten in wheat. Since these proteins are directly related to celiac disease and wheat intolerances, oats lead to fewer intolerances in humans. "This allowed us to confirm on a genomic level that oats are suitable for a gluten-free diet," says Manuel Spannagl from Helmholtz Munich. Compared to other cereals, oats also contain a much higher proportion of so-called beta-glucans. These dietary fibers reduce blood cholesterol levels and have a positive effect on people with metabolic diseases such as type 2 diabetes. Thanks to their sequencing effort, the researchers could identify the genes involved in the synthesis of the health-promoting beta-glucans.

    New potential for breeding
    Oats are not only interesting because of their innate health benefits; their cultivation also requires fewer treatments with insecticides, fungicides and fertilizers compared to other cereals. Thanks to the new insights into the oat genome, breeding and cultivation of more nutritious and sustainable oats can now be accelerated. "We have created freely available resources that increase the potential of targeted breeding in oats, and we are now able to tell which oat varieties are compatible with another," says Nadia Kamal of Helmholtz Munich. ’’We are now able to identify specific genes responsible for specific phenotypes in oat, as we did for an agronomic trait related to water use efficiency,’’ says Nikos Tsardakas Renhuldt of Lund University and ScanOats. The researchers have demonstrated the utility of the genome which further opens the possibility of combining traits for even more favorable health profiles, higher yields, better resistance to disease and drought, and most importantly, in preparation for climate change. Since oats produce high yields even on marginal soils and have an overall smaller environmental footprint than wheat, these aspects are particularly exciting for researchers in light of future challenges in providing nutritious plant-based alternative foods for a growing global population in a sustainable way.

    About the researchers
    Dr. Nick Sirijovski from Lund University and the ScanOats Industrial Research Center in Sweden led the sequencing project. ScanOats is an Industrial Research Center funded by Stiftelsen för Strategisk Forskning (SSF) and the members include Lund University, Research Institute of Sweden (RISE), the Swedish University of Agricultural Sciences (SLU, Alnarp), Lantämmen, Oatly and Swedish Oat Fiber. In his team, Olof Olsson, Nikos Tsardakas Renhuldt (as first author) and Johan Bentzer contributed to the study.
    Dr. Manuel Spannagl is a scientist at the Environmental Health Center at Helmholtz Munich and head of the study on the German side. In his team, Dr. Nadia Kamal collaborated on the study as first author, as well as Georg Haberer, Heidrun Gundlach, Thomas Lux and Daniel Lang.

    About the international collaboration
    Behind the publication are 29 researchers from 20 institutions in five countries. For details see the affiliations section of the paper.
    A companying study about the hidden breeding barriers in oat is published in Communications Biology at the same time:
    Tinker, et al., 2022: Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement. Communications Biology.
    DOI: 10.1038/s42003-022-03256-5.
    https://www.nature.com/articles/s42003-022-03256-5

    Original publication
    Kamal et al., 2022: The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature.
    DOI: 10.1038/s41586-022-04732-y.
    https://www.nature.com/articles/s41586-022-04732-y

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