# Presentation: 663693

## 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
-  through surveys and diversity analysis
-  Through association analysis
- We still need more markers in oat
- And we need information about them

## 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

## Why ?

- Common point of reference for marker screening
- Share biological materials (seed, DNA)
- Collect orthogonal data
- Share common and relevant data

## 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)

## Lines 1-18  (note duplicates)

## Lines 18 - 37

## 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

## Orthogonal is Nice

- Markers

- Germplasm

|  | M1 | M2 | M3 | M4 | M5 | M6 | P1 | P2 | P3 | P4 | P5 |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| VA | A | A | B | B | A | B | 24 | 45 | 52 | 27 | 23 |
| VB | B | A | A | B | B | A | 32 | 43 | 65 | 76 | 32 |
| VC | C | D | E | F | G | A | 32 | 54 | 76 | 43 | 65 |
| VD | A | B | A | A | B | A | 43 | 65 | 76 | 78 | 65 |
| VE | A | A | A | D | F | G | 43 | 43 | 76 | 32 | 65 |
| VF | B | A | D | C | A | T | 76 | 63 | 47 | 68 | 44 |
| VG | T | A | R | B | A | B | 46 | 75 | 76 | 34 | 67 |

- Phenotypes

## ....This is Not

- Markers

- Germplasm

|  | M1 | M2 | M3 | M4 | M5 | M6 | P1 | P2 | P3 | P4 | P5 |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| VA | ? | ? | ? | B | A | B | 24 | ? | ? | 27 | 23 |
| VB | ? | ? | ? | B | B | A | 32 | 43 | 65 | 76 | 32 |
| VC | ? | ? | ? | F | ? | ? | ? | ? | ? | ? | ? |
| VD | A | B | A | ? | B | A | 43 | ? | 76 | 78 | 65 |
| VE | A | A | ? | ? | F | G | 43 | 43 | ? | ? | ? |
| VF | B | A | ? | ? | A | T | 76 | 63 | ? | ? | ? |
| VG | T | A | ? | ? | A | B | 46 | 75 | ? | ? | ? |

- Phenotypes

## 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

## 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?

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

## 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”

## Simple SCAR marker

## Complex, multi-locus (avenin)

## Microsatellite

## 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

## 41 

- 41
- entries

- 250 “bands”

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

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

## Zoom on varieties

**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 data

- First year of replicated tests
- Ottawa (Yan)
- Saskatoon (Rossnagel)

## Data Unification and Distillation Engine

- Data Unification and Distillation Engine

## Can J. Plant Sci. 86  (July 2006)

- _[Biplot analysis of multi-environment trial data: ](http://ginkgo.cisti.nrc.ca/ppv/RPViewDoc?_handler_=HandleInitialGet&journal=cjps&volume=86&articleFile=P05-169.pdf)_
- _[Principles and applications](http://ginkgo.cisti.nrc.ca/ppv/RPViewDoc?_handler_=HandleInitialGet&journal=cjps&volume=86&articleFile=P05-169.pdf)_ W. Yan and N. A. Tinker  623–645

- Can J. Plant Sci. 86  (July 2006)

## Slide 27

## Slide 28

## Slide 29

## Slide 30

## 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

## Thanks !

- _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

- _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....