Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat

Sequence databases could be efficiently exploited for development of DNA ma rkers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regio ns of previously sequenced genes from Avena and Zea species. Primers were t argeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simp le-sequence repeat (SSR) polymorphism) for amplification-product polymorphi sm. We also developed primers to target 14 SSRs and 12 introns within 18 Av ena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena spec ies for amplification-product polymorphism. In maize, 67% of promoter marke rs, 58% of intron markers, and 13% of exon markers exhibited amplification- product polymorphisms. Among polymorphic primer pairs in maize, genotype di versity was highest for SSR markers (0.60) followed by intron markers (0.46 ), exon markers (0.42), and promoter markers (0.28). Among all Avena genoty pes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, b ut among the cultivars only, 21% of SSR markers and 50% of intron markers w ere polymorphic. Polymorphic-sequence-tagged sites for plant-breeding appli cations can be created easily by targeting noncoding gene regions.