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Oat Molecular Markers: Status and Opportunities Howard W. Rines

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

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Oat Molecular Markers: Status and Opportunities Howard W. Rines

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  1. Oat Molecular Markers: Status and Opportunities Howard W. Rines USDA-ARS and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN

  2. 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.

  3. 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).

  4. 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 Oat microsatellites (AM) and primer sequences at: http://wheat.pw.usda.gov/GG2/quickquery.shtml#microsats –Updates appreciated.

  5. RAPDs, SCARs STSs, or SNPs Reference Associatedtrait 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

  6. 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

  7. 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)

  8. 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

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

  10. 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://www.diversityarrays.com/

  11. International Consortium – OatDArTs Nick Tinker – Coordinator Andrzej Kilian – Technical Coordinator Web site – http://ca.groups.yahoo.com/group/OatDArTs

  12. 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

  13. 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

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