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GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

Development and Mapping of PCR-Based SCAR and CAPS Markers Linked to Oil QTLs in Oat

Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Central Experimental Farm, 960 Carling Ave., Ottawa, ON, K1A 0C6 Canada. ECORC Publication Number: 03-378

^* Corresponding author (molnarsj{at}agr.gc.ca).

Oat cultivars (Avena sativa L.) are unusually diverse in groat oil content, and breeding for this trait can increase the value of oat in human and livestock diets. Seven random amplified polymorphic DNA (RAPD) fragments closely linked or tentatively linked to quantitative trait loci (QTLs) for oil content in the ‘Terra’ x ‘Marion’ (TM) or the ‘Kanota’ x ‘Ogle’ (KO) hexaploid oat mapping populations were used to develop more robust sequence characterized amplified region (SCAR) or cleaved amplified polymorphic sequence (CAPS) markers. Three SCAR and two CAPS markers mapped on the TM population to the same map locations as the corresponding RAPD markers. One SCAR marker mapped to a homeologous TM linkage group (LG). The last two SCAR markers were mapped to regions that are currently not known to be orthologous to the original RAPD locations. All SCAR and CAPS markers were also tested in two additional high x low oil content populations. These SCAR markers have potential utility for marker-assisted selection (MAS) for high and low oil germplasm in oat breeding programs.

Abbreviations: CAPS, cleaved amplified polymorphic sequence • cM, centimorgan • DE, ‘Dal’ x ‘Exeter’ • FR, ‘Francis’ x ‘Rigodon’ • KM, ‘Kanota’ x ‘Marion’ • KO, ‘Kanota’ x ‘Ogle’ • LG, linkage group • MAS, marker-assisted selection • OM, ‘Ogle’ x ‘MAM17-5’, PCR, polymerase chain reaction • QTLs, quantitative trait loci • RAPD, random amplified polymorphic DNA • RFLP, restriction fragment length polymorphism • RIL, recombinant inbred line • SCAR, sequence characterized amplified region • SSR, simple sequence repeat • TM, ‘Terra’ x ‘Marion’.