Development of a sequence characterized amplified region (SCAR) based indirect selection method for a dominant blast-resistance gene in rice

Abstract

Two randomly amplified polymorphic DNA (RAPD) markers, OPF6₂₇₀₀ and OPH18₂₄₀₀, tightly linked to Pi-10, a dominant blast-resistance gene conferring complete resistance to isolate 106 (international race IB46) of the blast fungus were identified. To derive sequence characterized amplified regions (SCARs) from OPF6₂₇₀₀ and OPH18₂₄₀₀, these amplified RAPD products were cloned and sequenced. Nucleotide sequence information, obtained for each end of the two linked RAPD markers, was used to design 24-mer oligonucleotide primers for PCR amplification of the respective SCARs. Polymorphisms appearing as differences in the length of the SCAR's alternate alleles were considered for the indirect selection of Pi-10. Such polymorphisms converted the linked dominant RAPD loci into codominant SCAR markers and also facilitated the indirect scoring of the blast-resistant and blast-susceptible genotypes. The development of length variant codominant SCAR markers linked to a major gene for blast resistance in rice is described. The codominant SCARs will facilitate marker-assisted selection of the Pi-10 locus in rice breeding programs and will also be useful as genetic markers for high resolution mapping of the Pi-10 region.