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The Wheat Gene
Catalogue: 50 Years On
Robert A. McIntosh
Plant Breeding Institute
The University of Sydney
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History
– 1968 – 3rd IWGS, Canberra asked to prepare a Wheat Gene Catalogue. Previously a 7p document in Agron. J. (1946)
– 1973 – Draft Catalogue presented 4th IWGS, Columbia, MO. Reports at each IWGS and annual updates
– Early 2000s – Catalogue placed online at the Komugi website
– 2017 – Web-based version for curator editing
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The People (Acknowledgements)
– ER Sears
– Mike Gale, Gary Hart, Katrien Devos, John Rogers,
Craig Morris, Xianchun Xia, John Raupp, Yukiko Yamazaki
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Milestones (Strengths)
– Homoeologous system of nomenclature, e.g., Glu-D1a
– X and Q for anonymous (DNA) and quantitative trait markers
– Temporary designations for incompletely defined and mapped traits, or for genes in non-publically available germplasm
– Broad acceptance
– Where possible there was an emphasis on germplasm
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Weaknesses
– In need of better structure
– Not user-friendly for searching
– Lacks direct reference access; e.g. in-text hotkeys; DOI is being added to current reference inputs
– Does not meet current requirement for various -omics
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What is a gene catalogue?
– A register (lists) of numbers/designations to prevent duplication
– Other information tied to the list is at the discretion of curators
– The requirements for a stem rust R gene might be different from those for an STB R gene, an Rht (e.g., Rht15 or Rht-D1a) gene or a Gli- gene.
– Different traits may be handled differently
– Criteria for gene entry – trait groups, individuals, literature
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Information fields
– Gene (locus) name
– Synonym; in wheat, related species or others
– Chromosome location
– Bin location; could be extended to scaffold or genome address
– The germplasm subdivided into types and needs of trait workers
– Marker associations
– Gene isolation and protein function
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Users of the wheat catalogue
– Informaticists
– Genomaticists
– Transcriptomacists
– Geneticists
– Biochemists (proteomics, industrial quality)
– Breeders
– Agronomists
– Pathologists
– Farmers
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The future
– A universal vocabulary – sequence, scaffold, locus, allele, isoform, haplotype
• Current recommendation – loci be designated with uppercase italics for distinction from alleles designated with an uppercase first letter; e.g., SR6 vs Sr6; GLU-D1 vs Glu-D1a
– More curators (trait-based)
– Can a wheat catalogue meet the needs of all players?
– Should the wheat catalogue be expanded to a Triticeaecatalogue – or even wider?
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Conclusion
– The current wheat catalogue is very conservative and has never been supported by designated funding
– Wheat, barley and rye will continue to be important, but distinctive, food crops for the foreseeable future
– Further discussion of possibilities for a Triticeae gene catalogue will follow this presentation
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