Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 20, 2002
Publication Date: N/A
Resistant cultivars have long been used to control losses resulting from soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Single nucleotide polymorphisms (SNPs) were identified that are closely associated with rhg1 and rhg4, two important loci controlling resistance to SCN. In this study we examine the use of molecular beacons and locked nucleic acids (LNAs) to identify genotypes carrying alleles at rhg1 and rhg4 for resistance or susceptibility. Molecular beacons are hairpin shaped fluorescent oligonucleotide probes that can report the presence of a completely complimentary DNA target. The 5' end of a molecular beacon contains a fluorescent dye and the 3' end a fluorescence-quenching moiety. When the molecular beacon is not annealed to a complementary target the hairpin structure places the fluorophore and the quencher in close proximity preventing fluorescence. When hybridized to the target sequence, the fluorophore and the quencher are separated and fluorescence is observed. The second approach uses LNAs, which are oligonucleotides containing one or more nucleic acids with a methylene bridge that connects the 2'-O position to the 4'-C position. This increases the specificity for the target sequence. For SNP detection, the LNA residue is placed at the 3' end of the allele specific PCR primer. Single base extension and cytometric analysis of fluorescent microspheres was used to confirm the results of these two techniques. The ability of these two approaches to identify genotypes carrying alleles for SCN race 3 resistance or susceptibility at the rhg1 and rhg4 loci will be presented.