Loss-of-function of an a-SNAP gene confers resistance to soybean cyst nematode

Authors: USOVSKY, MARIOLA - University Of Missouri; GAMAGE, VINAVI - University Of Georgia; MEINHARDT, CLINTON - University Of Missouri; DIETZ, NICHOLAS - University Of Missouri; TRILLER, MARISSA - University Of Missouri; BASNET, PAWAN - University Of Missouri; Gillman, Jason; Bilyeu, Kristin; Song, Qijian; DHITAL, BISHNU - University Of Missouri; NGUYEN, ALICE - University Of Missouri; MITCHUM, MELISSA - University Of Georgia; SCABOO, ANDREW - University Of Missouri

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2023
Publication Date: 11/22/2023
Citation: Usovsky, M., Gamage, V.A., Meinhardt, C.G., Dietz, N., Triller, M., Basnet, P., Gillman, J.D., Bilyeu, K.D., Song, Q., Dhital, B., Nguyen, A., Mitchum, M.G., Scaboo, A. 2023. Loss-of-function of an a-SNAP gene confers resistance to soybean cyst nematode. Nature Communications. 14. Article e7629. https://doi.org/10.1038/s41467-023-43295-y.
DOI: https://doi.org/10.1038/s41467-023-43295-y

Interpretive Summary: Plant-parasitic nematodes are costly agricultural pests. In soybean, soybean cyst nematode (SCN) is the most serious pest, which on average costs American farmers an estimated 1.5 billion dollars annually. Finding and deploying new means to improve resistance to SCN continues to be a major breeding target. Here we report identification of a new resistance gene, which we confirmed grants resistance to SCN through independent means. Our results will accelerate and enable novel breeding strategies to enhance soybean resistance to SCN.

Technical Abstract: Plant-parasitic nematodes are one of the most economically impactful pests in agriculture resulting in billions of dollars in realized annual losses worldwide. Soybean cyst nematode (SCN) is the number one biotic constraint on soybean production making it a priority for the discovery, validation and functional characterization of native plant resistance genes and genetic modes of action that can be deployed to improve soybean yield across the globe. Here, we present the discovery and functional characterization of a soybean resistance gene, GmSNAP02. We use unique bi-parental populations to fine-map the precise genomic location, and a combination of whole genome resequencing and gene fragment PCR amplifications to identify and confirm causal haplotypes. Lastly, we validate our candidate gene using CRISPR-Cas9 genome editing and observe a gain of resistance in edited plants. This demonstrates that the GmSNAP02 gene confers a unique mode of resistance to SCN through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target. We highlight the immediate impact of utilizing GmSNAP02 as a genome-editing-amenable target to diversify nematode resistance in commercially available cultivars.