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United States Department of Agriculture

Agricultural Research Service

Title: Polymorphism of Pcr-Based Markers Targeting Exon, Intron, Promoter, and Ssrgene Regions in Maize and Introns and Repeat Sequences in Oat.

Authors
item Holland, Jim
item Helland, Sara - UNIVERSITY OF IOWA
item Sharopova, Natalya - UNIVERSITY OF MISSOURI
item Rhyne, David

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 16, 2001
Publication Date: N/A

Interpretive Summary: We developed a new type of genetic marker that can identify differences between copies of the same gene in different lines or hybrids of corn and oats. We found that these markers identified differences among genotypes frequently enough to be of use for genetic mapping and DNA marker-assisted breeding. The markers identify variation within specific regions of the target genes. Gene regions that do not affect the final protein product o the gene tend to be most variable among lines.

Technical Abstract: Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 4maize genes. We surveyed 48 maize inbred lines (previously assayed for SS polymorphism) for amplification product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and two diploid Avena species for amplification product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60), followed by intron markers (0.46), exon nmarkers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of the intron markers were polymorphic. Polymorphic sequence-tagged sites for plant breeding applications can be created easily by targeting non-coding gene regions.

Last Modified: 8/30/2014
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