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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Publications at this Location » Publication #417693
Research Project: Redesigning Soybeans for a Resilient Future of Food, Feeds, and Bio-Industry

Location: Plant Genetics Research

Title: Allele-tagged TaqMan® PCR genotyping assays for high-throughput detection of soybean cyst nematode resistance

Author
item USOVSKY, MARIOLA - University Of Missouri
item Bilyeu, Kristin
item BENT, ANDREW - University Of Wisconsin
item SCABOO, ANDREW - University Of Missouri

Submitted to: Molecular Biology Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2024
Publication Date: 12/2/2024
Citation: Usovsky, M., Bilyeu, K.D., Bent, A., Scaboo, A. 2024. Allele-tagged TaqMan® PCR genotyping assays for high-throughput detection of soybean cyst nematode resistance. Molecular Biology Reports. 52. https://doi.org/10.1007/s11033-024-10114-6.
DOI: https://doi.org/10.1007/s11033-024-10114-6

Interpretive Summary: Soybean breeding for resistance to soybean cyst nematode (SCN) is now possible for newly discovered and characterized alleles of multiple genes that interact to condition plant defense against this economically devastating pest. In the past, molecular marker assays were not comprehensive in generating a complete set of results to allow breeders to efficiently make the best breeding decisions. The objective of this work was to fill the gap for a complete high throughput SCN molecular marker panel. New molecular marker assays were designed with a consistent platform for all of the necessary components to comprehensively genotype for SCN resistance, and the markers were validated with different samples sets to ensure effectiveness. The impact of this work is the ability to perform high throughput genotyping for SCN resistance during soybean variety development that should enable valuable enduring genetic resistance in new soybean varieties.

Technical Abstract: Background Whole genome resequencing (WGRS) platforms provide exceptional fingerprinting of the entire genome but are expensive and less flexible to use as a routine genotyping tool for targeting causal polymorphisms within a germplasm collection or breeding program. Therefore, there has been a continuous effort to develop small-scale genotyping platforms that facilitate robust and quick assessments of the allelic status of causal variants for important traits within soybean breeding programs. The objective was to develop a comprehensive panel of soybean cyst nematode (SCN) resistance TaqMan® assays via selecting the causative genes and analyzing their associated alleles. Methods The Soybean Allele Catalog was utilized to investigate WGRS-derived variants which are predicted to cause a change in the amino acid sequence of a gene product. This panel of TaqMan® assays reflects current knowledge about known SCN resistance-causing genes and their associated alleles: GmSNAP18-a and -b, GmSNAP11, GmSHMT08, GmSNAP15, GmNSFRAN07, and GmSNAP02-ins and -del. Developed assays were tested using elite breeding lines and segregating populations. TaqMan assays were compared to other currently available KASP and CAPS assays. Conclusion All assays showed excellent allele determination efficiencies. This SCN genotyping assay panel can be utilized as a simplified, accurate and reliable genotyping platform further equipping the updated soybean breeding toolbox.