Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

Authors: BASNET, PAWAN - University Of Missouri; MEINHARDT, CLINTON - University Of Missouri; USOVSKY, MARIOLA - University Of Missouri; Gillman, Jason; JOSHI, TRUPTI - University Of Missouri; Song, Qijian; DIERS, BRIAN - University Of Illinois; MITCHUM, MELISSA - University Of Georgia; SCABOO, ANDREW - University Of Missouri

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2022
Publication Date: 4/5/2022
Citation: Basnet, P., Meinhardt, C.G., Usovsky, M., Gillman, J.D., Joshi, T., Song, Q., Diers, B., Mitchum, M.G., Scaboo, A. 2022. Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations. Theoretical and Applied Genetics. 135:2025-2039. https://doi.org/10.1007/s00122-022-04091-2.
DOI: https://doi.org/10.1007/s00122-022-04091-2

Interpretive Summary: Soybean Cyst Nematode (SCN) is a soil borne pest and the number one biotic cause for reduced seed yield in soybean. Annually more than $1.5 billion in losses occur in the United States as a result of this pathogen. Identifying and deploying soybean genetic resistance genes is the most efficacious and economical method of controlling the economic cost of SCN infestation of fields. In this study, we evaluated three populations specifically created to identify and test different genetic resistance genes using a number of different SCN virulence races. Soybean cyst nematode resistance loci rhg1-a and Rhg2 in PI 90763 impart vigorous resistance through an epistatic interaction against multiple SCN populations. We were also able to fine-map the Rhg2 gene to a very small genomic interval (~169 kilobasepairs, containing <22 genes) and identified a strong candidate gene for Rhg2. Our results can be employed to accelerate and improving ongoing breeding efforts to diversify SCN resistance in modern soybean resistant cultivars.

Technical Abstract: With more than 95% of the $46.1B soybean market dominated by a single type of genetic resistance, breeding for SCN resistant soybeans that can effectively combat the widespread increase in virulent soybean cyst nematode (SCN) populations is of immense significance. Rhg genes play a key role in resistance to SCN; however, their deployment beyond the use of the rhg1-b allele has been hampered by a lack of understanding of the complex genetic interactions. In this study, quantitative trait loci (QTL) were mapped in two bi-parental F3:4 recombinant inbred line populations against a SCN population with HG type 1.2.5.7. QTL located on chromosome 18 (rhg1-a) and chromosome 11 (Rhg2) were determined to engender SCN resistance in PI 90763. We demonstrated a unique epistatic interaction between rhg1-a and Rhg2 loci critical for conferring resistance to the most prevalent virulent nematode populations. The Rhg2 locus was fine-mapped to 169 Kbp region pinpointing GMSNAP11 as the strongest candidate gene. Further, the SCN phenotyping of RILs with different combinations of homozygous resistant loci against different virulent SCN populations showed that the pyramiding of SCN resistance loci with a conventional mode of resistance i.e., rhg1-b is only effective for SCN HG type 0 (race 3) but extremely ineffective for other virulent SCN populations. This elevates the importance of resistance pyramiding based on rhg1-a and Rhg2 rather than rhg1-b allele to maximize the impact of gene pyramiding strategies towards SCN management. This study presented the first report of QTL mapping in a population segregating for rhg1-a and rhg1-b alleles and established a breeding strategy without a need of testing for copy number variation. Our findings can potentially direct strategic resistance loci pyramiding to limit specific nematode populations. Together, our results lay the foundation for a paradigm shift for the next generation of soybean resistance breeding to combat the number one pathogen on soybeans.