Inventory of Oat SSRs, SNPs, SCARs, and CAPs and Efforts toward Their Development.


Last updated:  2006-July-14


*This document was compiled by Howard Rines ( to summarize the status of oat markers.  It has been updated to list informal information presented at a meeting described here:   We are not responsible for inaccurate information, but updates and corrections can be sent to Nick Tinker (  This document is archived at the following location until further notice:





Li et al. 2000, Theor. Appl. Genet. 101:1259-1268. Oat-derived SSRs AM1-AM61 (listed in GrainGenes), 26/44 polymorphic among 12 Avena species, 16/44 polymorphic among 20 cultivars, 6 mapped in Kanota/Ogle (Wight et al. 2003, Genome 46:28-47);  56 barley SSRs tested, 14 polymorphic among 12 Avena species, 3 polymorphic among 20 cultivars.


Pal. et al. 2002, Crop Sci. 42:912-918.  Oat-derived SSRs AM81-AM124, 18/44 polymorphic among 13 Avena species, 6/44 polymorphic and mapped in Kanota/Ogle; primer pairs derived from 6 cDNA RFLPs detected polymorphisms among 13 Avena species, STS markers from 2 mapped to two loci each in Kanota/Ogle; all listed in GrainGenes.


Holland et al. 2001, Genome 44:1065-1076.  cDNA-derived SSRs, 9/14 polymorphic in 22 cultivars and two diploid Avena species, 3/14 polymorphic in 22 cultivars; Intron-derived primers, 7/12 polymorphic in 22 cultivars and two diploid Avena species, 6/12 polymorphic in 22 cultivars.


Jannink and Gardner 2005, Crop Sci. 45:2383-2387. SSR-containing amplicons from A. sativa sequences in GenBank, 10/32 polymorphic among 4 cultivars, 7 of these plus 9 AM probes mapped to a restricted Ogle/TAM O-301 population.


Zhu and Kaeppler 2003, Theor. Appl. Genet. 107:26-35. Two oat-derived SSRs (Wisc) developed.  These two, four AMs, and two barley-derived SSRs mapped in Ogle/MAM17-5.


Portyanko et al. 2001, Genome 44:249-265. One cDNA-SSR (Rast1-4) and 4 STS primer pairs developed and amplicons mapped on Ogle/TAM O-301.


Wight et al. 2002, Genome 46:28-47.  Two barley SCARs (pABG20 and pBCD175, Tragoonrung et al. 1992, Theor. Appl. Genet. 84:1002-1008) mapped on Kanota/Ogle.


De Koeyer et al. 2004. Theor. Appl. Genet. 108:1285-1298. One SCAR developed and mapped on Terra/Marion.


Wight et al. 2003, Molec. Breed. 14:349-369. One SCAR (cdo113s, Larson et al. 1996, Theor. Appl. Genet. 93:618-625) associated with Pc38.


Chong et al. 2004, Can J. Plant Path. 26:89-96.  Two SCARs developed and associated with Pc94.


Yu and Wise 2000, Genome 43:736-749.  Two Pca-associated SCARs developed from AFLP fragments in diploid oats.


Eckstein et al. 2002, Oat Newsletter 48 (http://wheat/  SCAR markers for loose smut resistance.


Tanhuanpaa et al. 2006. Genome 49:282-287. Two co-dominant SNP markers developed from a REMAP and a RAPD marker associated with short straw (Dw6) in oat.


Yu and Herrmann 2006. Theor. Appl. Genet. 113:429-437. One SSR marker (AM102) and four developed AFLP-derived PCR-based STS markers linked to a powdery mildew resistance gene introgressed from Avena macrostachya into cultivated oat.


Brautigam et al. 2005 BMC Plant Biology (  Generation and analysis of 9792 EST sequences from cold acclimated oat. About 400 EST-SSR sequences found but not characterized.


Abstracts and Proceedings (primer sequences not published):


Poster Abstract for 1998 American Oat Workers Conference, In: Chong J (ed) Oat Newsletter 44 (1998)

 Orr W, De Koeyer D, Chenier C, Tinker N, Molnar SJ (1998) SCAR markers for rust resistance genes Pc68, Pg3 and Pg9 designed for marker assisted selection in oats.  Pp32


Poster Abstracts from the American Oat Workers Conference, May 5-7, 2002, Wilmington, North Carolina. In: Hoffman D (ed) Oat Newsletter 48 (2002),


Orr W, Molnar SJ  Development and mapping of PCR based SCAR markers linked to oil QTL in oat (Avena sativa L.).

Portyanko et al.  Markers for oat crown rust partial resistance QTLs in MN841801-1

Howarth et al.  Identifying microsatellite markers from related species for use in mapping agronomically important traits in oats.


Proceedings of the 7th Intern Oat Conf, Helsinki, Finland,  Peltonen-Saino P, Topi-Hulmi M (eds)

Howarth et al. Development and use of markers for oil in oat. p.53

Yu et al. AB-QTL analysis for beta-glucan content in oats. p.52

Williams et al. Mapping of quantitative trait loci for yield, quality and disease resistance. p.71

Scoles and Epstein. The applications of biotechnology to disease resistance breeding in oat. p.77-84.

Chen et al. Single nucleotide polymorphisms as next generation markers for high throughput screening for crown rust resistance in oat.  p.86.

Brautigam et al. Development of an oat database. p.144.

Rossnagel et al. Low acid detergent ligninoat hull: molecular marker development and chromosome location. p.153.

Kiviharju et al. DNA marker for oat dwarfing gene. p.171.

Brautigam et al. Analysis of 9703 sequence tags in cold acclimated oat. p.193.                                                                                                                                                                                                                                                         



Personal Communications Etc.:


Reports from:


ESTs:   Currently there are 7640 in Genbank.  Most of these have been submitted by Mark Sorrells from earlier RFLP work, and by Howard Rines (approximately 7103).  Others have indicated that collections of ESTs may be submitted in the near future.


Oat-specific SSRs:

Oat-derived SSRs have been developed by Graham Scoles lab (Li et al 2000) and the Illinois lab (Pal et al 2002) but very low polymorphism rates have been reported and few have been mapped in diploid oat.  Nick Tinker reported some recent success with a new SSR library containing tetramers.


Screening SSRs from other species:

- Stine Tuvesson (Svalof) suggested that those screening public SSRs from other species in oat should coordinate to avoid duplication.  She indicated their lab was conducting some work in this area. 

- Tim Langdon, John Valentine and Catherine Howarth (Oatlink: are screening many public SSR sets for use in oats and welcome coordination with other groups to prevent duplication.

- Stephen Molnar (AAFC Ottawa) has screened many barley SSRs in oat with some success.

- Scoles/Rossnagel/Eckstein (U Sask) are interested in screening SSRs and willing to coordinate with other labs.



A large set of EST SSRs with potential to work across grass species was developed in Mark Sorrells lab.  These and other efforts are summarized on Graingenes:

Mark Sorrels indicated that he is continuing work in this area.  


Other PCR markers:

- Alan Schulman (Finland) indicated that they had mapped approximately 200 retrotransposon-derived  markers.

- Joe Anderson (Purdue) indicated that he is having success with RAPD based markers using modified PCR protocols.  Other marker work is being initiated in this lab.

- Stephen Molnar’s lab (AAFC Ottawa) has converted many RAPD and RFLP markers to “SCAR” markers and is currently publishing some of this work.