**Session VI -- Plant Breeding, Germplasm Utilization and Cereal
Genomics -- Poster VI-26**

**Multiple Alleles with Multiple Applications: A New Set of SSR and
Avenin DNA Markers for Oat**

Charlene P. Wight, Weikai Yan, Jitka K. Deyl, and Nicholas A. Tinker\*

Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food
Canada, Central Experimental Farm, 960 Carling Ave., Ottawa, ON K1A 0C6,
Canada.

\*Corresponding Author: PH: (613) 759-1398; E-mail: tinkerna@agr.gc.ca

**Abstract**

Over the last two decades, a large amount of molecular marker data of
varying types has been collected for oats. Each marker system has its
advantages and disadvantages with respect to cost, reproducibility, and
ease of use (including data interpretation). While systems such as AFLP
(Amplified Fragment Length Polymorphisms) can highlight many loci
throughout the genome quite quickly, the markers are generally dominant
in nature, and the banding patterns are very complex. SSR (Simple
Sequence Repeat) markers, on the other hand, generally highlight very
few loci, but are often multiallelic and much simpler to use.

Many of the SSR markers developed previously for oat are dominant in
nature, but we present a set of fifteen new SSR markers that are
multiallelic (MAMA_1 to 15), as well as one that has been monomorphic
across all lines tested to date but is useful for assessing DNA quantity
and quality (MAMA_0). Two SCAR (Sequence Characterized Amplified Region)
markers for avenin genes are also presented. It was expected that these
markers would also be multiallelic because they represent a multigene
family, with large numbers of avenin bands seen on protein
electropherograms.

Thirteen of the SSR markers and both avenin markers could be mapped in
either or both of the Kanota x Ogle (KO) and Terra x Marion hexaploid
oat mapping populations. The avenin markers map to the locations of the
avenin protein loci (or gene blocks), as expected, and the SSR markers
map throughout the genome. By comparative mapping, it was determined
that all seven *A. atlantica* x *A. hirtula* diploid oat linkage groups
are represented.

All of the markers were tested across a set of 35 lines chosen to
represent the diversity in North American oat germplasm (the Standard
Oat Allele Panel, or SOAP). Twelve of the SSRs represent single loci,
with the number of alleles ranging from one to thirteen. The four other
SSR markers have more complex patterns. One avenin marker (MAvn_1)
identifies all three avenin gene blocks and 31 different alleles, while
the other (MAvn_2) identifies two gene blocks and eleven alleles.

While marker efforts in oats have been focussed on their development for
use in QTL (Quantitative Trait Locus) analysis and MAS (Marker-Assisted
Selection), the simplicity and multiallelic nature of the markers
described here could also make them useful for diagnostic purposes. To
test this, the markers were used to genotype five individuals from field
plots of each of the 19 lines comprising the 2007 Ontario Performance
Trial, which contained many closely related lines. All of the lines
could be separated using either the five best quality SSR markers or the
avenin marker MAvn_1 and the two best quality SSR markers. In the latter
case, fewer markers might have been needed if so many of the lines had
not contained the rust resistance gene *Pc*68, which is linked to the
avenin gene block on KO group 4_12. Variation in genotype could be
detected in some of the lines, and contamination of two lines was also
identified (as were the contaminants).