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.

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. Inventory of markers and efforts at: Oat microsatellites (AM) and primer sequences at: – Updates appreciated.

RAPDs, SCARs STSs, or SNPsReference Associated trait 2 RAPDsPenner et al. 1993crown rust, stem rust 2 RAPDsWight et al. 1994day length insens. RAPDO’Donoughue et al. 1996stem rust RAPDRonald et al. 1997percent hull 2 SCARsYu and Wise 2000crown rust in diploid oat 4 STSsPortyanko et al. 2001storage proteins, amylases 2 SCARsEckstein et al. 2002smut 2 SCARsPal et al. 2002BYDV QTL SCARWight et al. 2004crown rust SCARDeKoeyer et al. 2004lodging QTL 2 SCARsChong et al. 2004crown rust 2 SNPsTanhuanpaa et al. 2006dwarf (Dw6) 4 STSsYu and Herrmann 2006powdery mildew

Oat-derived SSRs (primers published) SSRsReferenceMapped 61Li et al in KxO 44Pal et al in KxO 26Holland et al Portyanko et al in OxT 2Zhu and Kaeppler in OxM 32Jannink and Gardner in OxT

Barley- and wheat-derived SSRs on oat Published: 14 of 56 polymorphic in oat – Li et al 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: , 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 (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:

International Consortium – OatDArTs Nick Tinker – Coordinator Andrzej Kilian – Technical Coordinator Web site –

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