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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #139677


item Hofmann, Nicolle
item Arelli, Prakash
item Matthews, Benjamin - Ben
item Quigley, Charles - Chuck
item Cregan, Perry

Submitted to: Biennial Conference on Molecular and Cellular Biology of the Soybean
Publication Type: Abstract Only
Publication Acceptance Date: 12/4/2002
Publication Date: 12/19/2002
Citation: Hofmann, N.E., Arelli, P.R., Matthews, B.F., Quigley, C.V., Cregan, P.B. 2002. Molecular beacons to select for scn resistance at rhg1 and rhg4. Biennial Conference on Molecular and Cellular Biology of the Soybean. P. 211.

Interpretive Summary:

Technical Abstract: Molecular techniques to identify resistant genotypes increase the efficiency of programs focused on developing cultivars resistant to SCN. 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 two approaches for rapid identification of genotypes carrying alleles at rhg1 and rhg4 for resistance or susceptibility. Molecular beacons and locked nucleic acids (LNAs) were used to differentiate genotypes at these loci. Molecular beacons are hairpin shaped fluorescent oligonucleotide probes that can report the presence of a completely complimentary DNA target. Specificity is sufficient to distinguish targets whose nucleotide sequences vary by only a single base. When the molecular beacon hybridizes to the target sequence, the fluorophore and the quencher are separated and fluorescence is observed. The second approach involves LNAs, which are a class of nucleic acid analogues developed to improve hybridization characteristics by increasing specificity and duplex stability with complementary nucleic acid targets. In the application of LNAs for SNP detection, the LNAs residue is placed at the 3' end of the allele specific PCR primer. The increased specificity of the 3' LNA residue decreases the occurrence of amplification in the presence of a 3' mismatch. 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.