A Set of New Simple Sequence Repeat and Avenin DNA Markers Suitable for Mapping and Fingerprinting Studies in Oat (Avena spp.)

Abstract

This study was conducted to develop and test new markers for use in molecular characterization of oat (Avena spp.). Results are presented for two polymerase chain reaction (PCR)‐based markers targeting multiple avenin protein loci and 16 new microsatellite or simple sequence repeat (SSR) markers. The markers were mapped in two segregating oat (Avena sativa L.) populations, ‘Kanota’ × ‘Ogle’ (K×O) and ‘Terra’ × ‘Marion’ (T×M), and were also tested across a diversity panel consisting of 35 cultivated varieties of oat and representatives of five other Avena species. All markers were robust, multiallelic, and highly polymorphic. The SSR markers, some highlighting multiple loci, mapped throughout the genome, and the avenin markers mapped to their expected locations in K×O and T×M. Also as expected, the avenin markers were shown to be linked to the stem rust resistance gene Pg9 in the population ‘OT328’ × ‘Dumont’ (OT×Du). Practical applications in variety identification and germplasm diagnostic assays were explored. The markers were able to distinguish closely related lines for fingerprinting purposes and were also useful for determining whether variation within a line was the result of residual heterozygosity or contamination. In addition, the markers were found to be useful for forensic purposes and for determining whether crossing and backcrossing had been successful.

Improvement of Oat as a Winter Forage Crop in the Southern United States

“…Until recently, successful genetic map development in oat has been based on restriction fragment length polymorphism markers ( Jin et al, 2000;Kremer et al, 2001), amplified fragment length polymorphism markers ( Jin et al, 2000;Groh et al, 2001), and other polymerase chain reaction-based markers such as simple sequence repeat (SSR) ( Jannink and Gardner, 2005;Oliver et al, 2010;Wight et al, 2010). Until recently, successful genetic map development in oat has been based on restriction fragment length polymorphism markers ( Jin et al, 2000;Kremer et al, 2001), amplified fragment length polymorphism markers ( Jin et al, 2000;Groh et al, 2001), and other polymerase chain reaction-based markers such as simple sequence repeat (SSR) ( Jannink and Gardner, 2005;Oliver et al, 2010;Wight et al, 2010).…”

“…The lack of numerous, easily assayed, and codominant markers is still a major barrier in oat genetic and genomic research. Until recently, successful genetic map development in oat has been based on restriction fragment length polymorphism markers ( Jin et al, 2000;Kremer et al, 2001), amplified fragment length polymorphism markers ( Jin et al, 2000;Groh et al, 2001), and other polymerase chain reaction-based markers such as simple sequence repeat (SSR) ( Jannink and Gardner, 2005;Oliver et al, 2010;Wight et al, 2010). Although these maps have been useful for locating quantitative trait loci (QTL), the heterogeneity of marker types has led to difficulty in comparative mapping and has hindered the development of a single consensus map that would enable better integration of information about adaptive loci and alleles.…”

“…However, it has been demonstrated that SSR sequences in oat are generally less polymorphic than in other species Pal et al, 2002). Efforts to develop SSR markers in oat have met with limited success, and available SSR markers do not provide complete genome coverage Pal et al, 2002;Becher 2007;Wight et al, 2010). Furthermore, assays for SSR markers are still not amenable to large-scale automation.…”

The art of attrition: development of robust oat microsatellites

“…However, Wight et al. () reported a mean of eight alleles per assay which is highly informative. The differences in allele number per assay might be due to larger diversity of studied oat lines.…”

“…, Wight et al. ). In addition, 216 microsatellites with good PIC (0.42) have been mined from available expressed tag sequence (EST) databases in oat (Becher ); however, the availability of this EST‐based resource is restricted.…”