Genome-editing approach for engineering broad and durable soybean cyst nematode resistance via novel promoter alleles

Overview

Soybean cyst nematode (SCN) is the most destructive pathogen of soybean, causing significant yield losses across major growing regions. Current resistance sources derived from PI88788 are used in over 93% of US soybean cultivars but are not effective against the full spectrum of SCN races, creating an urgent need for broad and durable resistance solutions.

This research focuses on a novel allele associated with the promoter of the GmSHMT08 gene that has been shown to confer resistance to multiple SCN races. The project applies cutting-edge CRISPR-Cas genome-editing technology to dissect the functional role of these novel promoter alleles, with the goal of engineering next-generation soybean varieties with enhanced, broad-spectrum nematode resistance.

Technical specifications

Key features:

• Identification of novel promoter alleles at the GmSHMT08 gene locus that confer resistance to multiple SCN races
• Whole-genome haplotype and copy number variation analysis of the rhg-1 and Rhg-4 loci (established SCN resistance loci)
• Discovery that certain resistant lines do not carry known resistant alleles at rhg-1/Rhg-4, indicating additional resistance mechanisms
• Haplotype clustering at the promoter level revealing that promoter-region variation provides an additional layer of SCN resistance
• Application of state-of-the-art CRISPR-Cas technology for precise manipulation of promoter regions
• Use of well-established hairy-roots system for functional validation
• Promoter bashing experiments generating a series of targeted alleles to pinpoint key cis-motifs responsible for broad and durable SCN resistance
• Investigation of mechanisms including changes in transcription factor binding motifs and upregulation of gene expression

Technology readiness level

This research is at an early-to-mid stage of development. The discovery of the novel promoter allele and its association with multi-race SCN resistance has been established through whole-genome haplotype and copy number variation analyses. Future validation will employ CRISPR-Cas-based promoter editing using a hairy-root transformation system to create targeted allelic series and identify the critical cis-regulatory motifs driving resistance. The technology is positioned for further validation and development toward eventual deployment in commercial soybean breeding programs.