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Allele Survey - North American Oats

Allele Survey - North American Oats. Nick Tinker et al. Agriculture and Agri-Food Canada . Markers are boring. Germplasm is exciting!. Germplasm is defined by alleles Markers are our best window into the alleles that define germplasm. through linkage analysis

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Allele Survey - North American Oats

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  1. Allele Survey -North American Oats Nick Tinker et al. Agriculture and Agri-Food Canada

  2. Markers are boring.

  3. Germplasm is exciting! • Germplasm is defined by alleles • Markers are our best window into the alleles that define germplasm. • through linkage analysis • through surveys and diversity analysis • Through association analysis • We still need more markers in oat • And we need information about them

  4. SOAP • “Standard Oat Allele Panel” • (for North America) • Selected by collaborators following AOWC meeting in Wilmington 2002 • Stay tuned for Global Oat Allele Panel and new DArT markers

  5. Why ? • Common point of reference for marker screening • Share biological materials (seed, DNA) • Collect orthogonal data • Share common and relevant data

  6. How ? • 10 breeders / adaptation regions • Nominate “current germplasm representing packages of alleles giving adaptation to your region and/or unique quality” • Used (or will be used) extensively in crossing • 3 to 5 representative genotypes per region • Narrowed down by avoiding co-ancestry • Re-increased from single seed of representative breeders line(s)

  7. Lines 1-18 (note duplicates)

  8. Lines 18 - 37

  9. Why Common markers? • So we don’t all report results using different markers if common markers are available. • Share technology, materials, experience • Collect orthogonal data • Share common and relevant data • Select optimum markers for further work • Use for predicting MAS feasibility • (is a marker polymorphic in your material?) • Potential use in association analysis

  10. Orthogonal is Nice Markers Phenotypes Germplasm

  11. ….This is Not Markers Phenotypes Germplasm

  12. Marker screened in SOAP • SCARs (Molnar and Orr) – 50 • Other misc. (Wight) - 5 • New SSR markers (Wight) – 12 • Jannink - SSRs, SCARs – 12 • Approx 80 Primer pairs = 200 polymorphic bands = 100 loci ? • To do: • other SSRs, AFLP? RFLP? DArT

  13. How to record the data ? • Some markers defined and mapped • Others new, un-mapped • Anticipate need to share screening results and screening methods . . . • Future need for others to contribute directly to online database?

  14. Welcome to GELATO!(Diane Bergeron et al. poster)

  15. GELATO • Demo: avena.agr.gc.ca/gelato • Freestyle web based marker scoring • Record what you see (“Virtual Lite-Brite”) • Clickable grid – any cell can be a “band” • Black (present), white (absent), pink (unknown) • Optional: Paint bands from same locus • Stored in a relational database • Query data in the same format • Generate “virtual gels”

  16. Simple SCAR marker

  17. Complex, multi-locus (avenin)

  18. Microsatellite

  19. The following is more of an inventory than an analysis . . . • Extract data from Gelato • Each band as a character • 200 polymorphic bands • (Locus-based extraction in progress) • Make numerical data set 1=absent, 2=faint, 3=present

  20. Present Faint Absent 41 entries 250 “bands”

  21. Cluster analysis (markers and varieties) – Average linkage – Pearson-r

  22. Zoom on varieties • Note: • Paired lines • = alternate seed sources • Most lines un-related • Some known relationship: • Medallion Ronald • Jay Sesqui ? • Kanota = oddball

  23. Cluster – zoom on markers

  24. Add phenotypic data First year of replicated tests Ottawa (Yan) Saskatoon (Rossnagel)

  25. Data Unification and Distillation Engine

  26. Can J. Plant Sci. 86 (July 2006) Information systems for crop performance dataN. A. Tinker and W. Yan    647–662 Biplot analysis of multi-environment trial data: Principles and applicationsW. Yan and N. A. Tinker  623–645

  27. Conclusions • SOAP Seed and DNA available NOW • SOAP survey will be published and shared • Planned repository • GELATO + GrainGenes ? • Also coming (and related): • GELATO • DUDE • OatGenes • SCAR markers (Molnar) • DArT markers and extended global panel

  28. Doers: Charlene Wight Jitka Deyl Shan He Diane Bergeron Hai Pham Klaus Jakubinek Winson Orr Julie Chapados Dreamers Steve Molnar (AAFC) Weikai Yan (AAFC) Art McElroy Judith Fregeau-Reid Brian Rossnagel Thanks ! SOAP panel Development: • Deon Stuthman, Howard Rines, Steve Harrison, Ron Barnett, Jennifer Mitchell-Fetch, Herb Ohm, Mike McMullen, Fred Kolb, Heidi Kaepler, and many others who provided seed….

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