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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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