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

Allele Survey -Allele Survey -North American OatsNorth American Oats

Nick Tinker et al.Nick Tinker et al.

Agriculture and Agri-Food Agriculture and Agri-Food Canada Canada

Markers Markers are are

boring.boring.

Germplasm is exciting!Germplasm is exciting!

Germplasm is defined by allelesGermplasm is defined by alleles Markers are our best window into the Markers are our best window into the

alleles that define germplasm.alleles that define germplasm.– through linkage analysisthrough linkage analysis– through surveys and diversity analysisthrough surveys and diversity analysis– Through association analysisThrough association analysis

We still need more markers in oatWe still need more markers in oat And we need information about themAnd we need information about them

SOAPSOAP

““SStandard tandard OOat at AAllele llele PPanel”anel”– (for North America)(for North America)

Selected by collaborators following Selected by collaborators following AOWC meeting in Wilmington 2002AOWC meeting in Wilmington 2002

Stay tuned for Global Oat Allele Stay tuned for Global Oat Allele Panel and new DArT markersPanel and new DArT markers

Why ?Why ?

Common point of reference for marker Common point of reference for marker screeningscreening

Share biological materials (seed, DNA) Share biological materials (seed, DNA) Collect orthogonal dataCollect orthogonal data Share common and relevant dataShare common and relevant data

How ?How ?

10 breeders / adaptation regions10 breeders / adaptation regions Nominate Nominate “current germplasm representing “current germplasm representing

packages of alleles giving adaptation to your packages of alleles giving adaptation to your region and/or unique quality”region and/or unique quality”

Used (or will be used) extensively in crossingUsed (or will be used) extensively in crossing 3 to 5 representative genotypes per region3 to 5 representative genotypes per region Narrowed down by avoiding co-ancestryNarrowed down by avoiding co-ancestry Re-increased from single seed of representative Re-increased from single seed of representative

breeders line(s)breeders line(s)

Lines 1-18 (note duplicates)

Lines 18 - 37

Why Common markers?Why Common markers?

So we don’t all report results using different So we don’t all report results using different markers if common markers are available. markers if common markers are available.

Share technology, materials, experienceShare technology, materials, experience Collect orthogonal dataCollect orthogonal data Share common and relevant dataShare common and relevant data Select optimum markers for further workSelect optimum markers for further work Use for predicting MAS feasibilityUse for predicting MAS feasibility

– (is a marker polymorphic in your material?)(is a marker polymorphic in your material?) Potential use in association analysisPotential use in association analysis

Orthogonal is NiceOrthogonal is NiceMarkers

Ger

mpl

asm

M1M1 M2M2 M3M3 M4M4 M5M5 M6M6 P1P1 P2P2 P3P3 P4P4 P5P5

VAVA AA AA BB BB AA BB 2424 4545 5252 2727 2323

VBVB BB AA AA BB BB AA 3232 4343 6565 7676 3232

VCVC CC DD EE FF GG AA 3232 5454 7676 4343 6565

VDVD AA BB AA AA BB AA 4343 6565 7676 7878 6565

VEVE AA AA AA DD FF GG 4343 4343 7676 3232 6565

VFVF BB AA DD CC AA TT 7676 6363 4747 6868 4444

VGVG TT AA RR BB AA BB 4646 7575 7676 3434 6767

Phenotypes

…….This is Not.This is NotMarkers

Ger

mpl

asm

M1M1 M2M2 M3M3 M4M4 M5M5 M6M6 P1P1 P2P2 P3P3 P4P4 P5P5

VAVA ?? ?? ?? BB AA BB 2424 ?? ?? 2727 2323

VBVB ?? ?? ?? BB BB AA 3232 4343 6565 7676 3232

VCVC ?? ?? ?? FF ?? ?? ?? ?? ?? ?? ??

VDVD AA BB AA ?? BB AA 4343 ?? 7676 7878 6565

VEVE AA AA ?? ?? FF GG 4343 4343 ?? ?? ??

VFVF BB AA ?? ?? AA TT 7676 6363 ?? ?? ??

VGVG TT AA ?? ?? AA BB 4646 7575 ?? ?? ??

Phenotypes

Marker screened in SOAPMarker screened in SOAP

SCARs (Molnar and Orr) – 50SCARs (Molnar and Orr) – 50 Other misc. (Wight) - 5Other misc. (Wight) - 5 New SSR markers (Wight) – 12New SSR markers (Wight) – 12 Jannink - SSRs, SCARs – 12Jannink - SSRs, SCARs – 12 Approx 80 Primer pairs Approx 80 Primer pairs

= 200 polymorphic bands = 100 loci ?= 200 polymorphic bands = 100 loci ? To do: To do:

– other SSRs, AFLP? RFLP? other SSRs, AFLP? RFLP? DArT DArT

How to record the data ?How to record the data ?

Some markers defined and mappedSome markers defined and mapped Others new, un-mappedOthers new, un-mapped Anticipate need to share screening results Anticipate need to share screening results

and screening methods . . .and screening methods . . . Future need for others to contribute Future need for others to contribute

directly to online database? directly to online database?

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

GELATOGELATO

Demo: Demo: avena.agr.gc.ca/gelatoavena.agr.gc.ca/gelato Freestyle Freestyle web basedweb based marker scoring marker scoring Record what you see (“Virtual Lite-Brite”)Record what you see (“Virtual Lite-Brite”) Clickable grid – any cell can be a “band”Clickable grid – any cell can be a “band”

– Black (present), white (absent), pink (unknown) Black (present), white (absent), pink (unknown) Optional: Paint bands from same locus Optional: Paint bands from same locus Stored in a relational databaseStored in a relational database Query data in the same format Query data in the same format Generate “virtual gels” Generate “virtual gels”

Simple SCAR markerSimple SCAR marker

Complex, multi-locus (avenin)Complex, multi-locus (avenin)

MicrosatelliteMicrosatellite

The following is more of an The following is more of an inventory than an analysis . . .inventory than an analysis . . .

Extract data from GelatoExtract data from Gelato Each band as a characterEach band as a character 200 polymorphic bands200 polymorphic bands (Locus-based extraction in progress)(Locus-based extraction in progress) Make numerical data set Make numerical data set

1=absent, 2=faint, 3=present1=absent, 2=faint, 3=present

41 entries

250 “bands”PresentFaintAbsent

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

Zoom on varieties

Note: • Paired lines = alternate seed sources• Most lines un-related• Some known relationship:

• Medallion Ronald• Jay Sesqui ?

• Kanota = oddball

Cluster – zoom on markers

Add phenotypic dataAdd phenotypic data

First year of replicated testsFirst year of replicated tests

Ottawa (Yan)Ottawa (Yan)

Saskatoon (Rossnagel)Saskatoon (Rossnagel)

Data Unification and Distillation Engine

Information systems for crop performance data N. A. Tinker and W. Yan    647–662

Biplot analysis of multi-environment trial data: Principles and applications

W. Yan and N. A. Tinker  623–645

Can J. Plant Sci. 86 (July 2006)

ConclusionsConclusions

SOAP Seed and DNA available NOWSOAP Seed and DNA available NOW SOAP survey will be published and sharedSOAP survey will be published and shared Planned repository Planned repository

– GELATO + GrainGenes ? GELATO + GrainGenes ? Also coming (and related):Also coming (and related):

– GELATO GELATO – DUDEDUDE– OatGenesOatGenes– SCAR markers (Molnar)SCAR markers (Molnar)– DArT markers and extended global panelDArT markers and extended global panel

Thanks !Thanks !

Doers:Doers: Charlene WightCharlene Wight Jitka DeylJitka Deyl Shan He Shan He Diane Bergeron Diane Bergeron Hai PhamHai Pham Klaus JakubinekKlaus Jakubinek Winson Orr Winson Orr Julie ChapadosJulie Chapados

DreamersDreamers Steve Molnar (AAFC)Steve Molnar (AAFC) Weikai Yan (AAFC)Weikai Yan (AAFC) Art McElroyArt McElroy Judith Fregeau-ReidJudith Fregeau-Reid Brian RossnagelBrian Rossnagel

SOAP panel Development:SOAP panel Development: Deon Stuthman, Howard Rines, Deon Stuthman, Howard Rines,

Steve Harrison, Ron Barnett, Jennifer Steve Harrison, Ron Barnett, Jennifer Mitchell-Fetch, Herb Ohm, Mike Mitchell-Fetch, Herb Ohm, Mike McMullen, Fred Kolb, Heidi Kaepler, McMullen, Fred Kolb, Heidi Kaepler, and many others who provided and many others who provided seed….seed….