# Presentation: 037629

## Oat Molecular Markers:

**Status and Opportunities**
**Howard W. Rines**
**USDA-ARS and Department of Agronomy**
**and Plant Genetics, University of Minnesota,**
**St. Paul, MN**
**	****	**

## Need:	A large number of molecular markers that can be affordably applied in oat germplasm for gene (QTL) identification, mapping, cloning, and marker-assisted selection.

**Need:****	****A large number of molecular markers that can be affordably applied in oat germplasm for gene (QTL) identification, mapping, cloning, and marker-assisted selection.**

## Currently there are several oat maps, notably Kanota x Ogle, based on RFLPs and AFLPs, but these markers are cumbersome, expensive, and not adapted to high throughput.

**Currently there are several oat maps, notably Kanota x Ogle, based on RFLPs and AFLPs, but these markers are cumbersome, expensive, and not adapted to high throughput.**
**– ****Reviewed in chapter by Rines, Molnar, Tinker, and Phillips in *****Genome Mapping and Molecular Breeding in Plants*****, *****Vol.1 Cereals and Millets*****.  C. Kole (ed.), Springer (in press).**

## Desired:	RAPD, SCAR, STS, SSR, or SNP markers analyzed by PCR or other high throughput technologies, but currently only limited number available.

**Desired:****	****RAPD, SCAR, STS, SSR, or SNP markers analyzed by PCR or other high throughput technologies, but currently only limited number available.**
**Inventory of markers and efforts at:**
**	****	****	**_[http://oatnog.com/oatmarkerstatus.htm](http://oatnog.com/oatmarkerstatus.htm)_
**Oat microsatellites (AM) and primer sequences at: **_[http://wheat.pw.usda.gov/GG2/quickquery.shtml#microsats](http://wheat.pw.usda.gov/GG2/quickquery.shtml#microsats)_
**–**  **Updates appreciated.**

## RAPDs, SCARs		

**STSs, or SNPs****	****Reference****	**** Associated** **trait**
**2 RAPDs****	****Penner et al. 1993****	****crown rust, stem rust**
**2 RAPDs****	****Wight et al. 1994****	****day length insens.**
**RAPD****	****O’Donoughue et al. 1996****	****stem rust**
**RAPD****	****Ronald et al. 1997****	****percent hull**
**2 SCARs****	****Yu and Wise 2000****	****crown rust in diploid oat**
**4 STSs****	****Portyanko et al. 2001****	****storage proteins, amylases**
**2 SCARs****	****Eckstein et al. 2002****	****smut**
**2 SCARs****	****Pal et al. 2002****	****BYDV QTL**
**SCAR****	****Wight et al. 2004****	****crown rust**
**SCAR****	****DeKoeyer et al. 2004****	****lodging QTL**
**2 SCARs****	****Chong et al. 2004****	****crown rust**
**2 SNPs****	****Tanhuanpaa et al. 2006****	****dwarf (*****Dw6*****)**
**4 STSs****	****Yu and Herrmann 2006****	****powdery mildew**

## Oat-derived SSRs (primers published)

**Oat-derived SSRs (primers published)**
**	****SSRs****	****Reference****	****Mapped**
**	****61****	****Li et al. 2000****	****6 in KxO**
**	****44****	****Pal et al. 2002****	****6 in KxO**
**	****26****	****Holland et al. 2001****	****--**
**	****1****	****Portyanko et al. 2001****	****1 in OxT**
**	****2****	****Zhu and Kaeppler 2003****	****2 in OxM**
**	****32****	****Jannink and Gardner 2005****	****7 in OxT**

## Barley- and wheat-derived SSRs on oat

**	****Published:  14 of 56 polymorphic in oat ****–**** Li et al. 2000**
**	****Other efforts:  Molnar (Ottawa), Tuvesson (Svalof), Howarth (IGER), Herrmann (Germany), Hu (Aberdeen-this meeting)**
**Retrotransposon markers in oat**
**	****Schulman and Kiviharju (Finland) – about 200 on a DH-population**
**EST-SSRs from other grasses**
**	****Wheat – Sorrells (Cornell), Kantety (Alabama A&M), Gupta et al. MGG 270:315-323, 2003.**
**	****Barley – Varshney (Germany)**
**	****Fescue/Lolium – Saha (Noble Foundation)**

## EST-SSRs from oat – Rayko Becker (BAZ-Federal Centre for Breeding Research, Germany; now at Martin-Luther University, Halle)

**From 7,031 oat EST sequences placed in GenBank by Rines et al. 2004, 216 primer pairs flanking *****Avena***** microsatellite-EST loci (AME) developed.**
**	****	*********	****107 of 195 functional primer sets assayed as ****	****	****	****polymorphic on a set of 12 oat lines**
**	****	*********	****Marker variability average of 3 alleles per locus with ****	****	****a PIC content of 0.42**
**	****	*********	****51 AMEs placed on KxO map on 22 of the 28 ****	****	****	****described linkage groups with 3 unlinked**
**	****	*********	****Forward primers M-13 sequence-tailed on 5’-end; ****	****	****	****PCR at one set of conditions**
**	****	*********	****Primers will be available upon publication, under ****	****	****	****MTA**

## Other ESTs in oat – Brautigm et al. 2005 (Sweden)

**Other ESTs in oat – Brautigm et al. 2005 (Sweden)**
**	****9,792 EST sequences from cold-acclimated oat.**
**	****~ 400 potential SSR sequences found.**

## Display Array Technology (DArT) system

**-****	****Genome-wide marker finger-printing system**
**-****	****Based on hybridization to microarrays**
**-****	****Screening for a few hundred target sequences following specific digestion and amplification enrichment**
**-****	****Low per-marker cost**
**-****	****Ideal for map construction, QTL identification, germplasm fingerprinting, diversity evaluation, associative mapping**
**-****	****Need marker conversion for marker-assisted selection**
**-****	****High initial cost to develop appropriate set of probes**
**Described at:  **_[http://](http://www.diversityarrays.com/)__[www.diversityarrays.com](http://www.diversityarrays.com/)__[/](http://www.diversityarrays.com/)_

## International Consortium – OatDArTs

**	****Nick Tinker – Coordinator**
**	****Andrzej Kilian – Technical Coordinator**
**	****Web site –**
**	****      **_[http://ca.groups.yahoo.com/group/OatDArTs](http://ca.groups.yahoo.com/group/OatDArTs)_

## Opportunities

**Coordinate screening on oat of genomic SSRs from other species**
**Assess polymorphism in an oat panel of genomic and EST-SSRs from other grasses shown to amplify in oat**
**	**** –** **	****map polymorphic sequences on KxO**
**Compare polymorphism revealed by oat and other genomic- and EST-SSRs on the OatDArTs polymorphism panel**
**Generate new genomic SSR libraries and markers from oat**
**Generate oat EST libraries from other oat tissues (e.g., developing seed) as sources of new oat-derived EST-SSRs and for other genome and expression studies**
**Establish a plan and system for collecting and integrating phenotypic data with marker genotypic data in germplasm collections and mapping populations**
**Effective sharing of efforts and results**
**	**** –** **	****Web sites**
**	**** –** **	****Yahoo OatDArTs group; Greengenes group - Oatmail**

## Opportunities – OatDArT system

**Increase hexaploid oat map coverage**
**Identify new QTLs and marker-gene linkages**
**Characterize new mapping populations**
**Characterize breeding populations and germplasm**
- 	 **–** **	****Associative mapping**
**Assess germplasm diversity and relationships**
**Facilitate backcross introgression**