Sustainable broad-spectrum SCN resistance varieties using gene editing, TILLING, regulatory epigenome, and whole-genome sequencing
Sustainable Production
Biotic stressGeneticsNematode
Parent Project:
This is the first year of this project.
Lead Principal Investigator:
Henry Nguyen, University of Missouri
Co-Principal Investigators:
Project Code:
Contributing Organization (Checkoff):
Institution Funded:
Brief Project Summary:
Our objective is to 1) Develop innovative gene-editing and genome engineering strategies to create specific alleles and durable SCN resistance; 2) Explore the landscape of soybean epigenome for SCN resistance; 3) Develop next-generation soybean germplasm for durable SCN resistance using new sources of SCN resistance.
Information And Results
Project Summary

Project Objectives

Project Deliverables

Progress Of Work

Final Project Results

Soybean cyst nematode (SCN) is a major pest of soybean which causes devastating losses to soybean industry every year. SCN management practices rely on the resistant genetic source, majorly the rhg1 and Rhg4 loci. Our goal is to alter rhg1 and Rhg4 alleles in the elite susceptible cultivar through prime editing and enhance its resistance to SCN. CRISPR Prime editing is recently (2019) invented tool also called as search and replace tool, which alters DNA (SNPs/haplotypes) in the host genome without leaving any foreign DNA. This tool has been successfully evaluated and used in the mammalian field. Its application in plants has not been shown so far. Here, we are employing prime editing to alter novel haplotypes in susceptible soybean lines. We cloned prime editing components such as dead-Cas9 (dCas9) fusion with reverse transcriptase gene and prime editing guide RNAs of Rhg4 locus haplotypes. Currently, we are evaluating the prime editing components in Soybean hairy roots. Additionally, we are developing novel germplasm populations combining new sources of SCN resistance genes (independent of rhg1 & Rhg4) into elite breeding lines for durable SCN resistance. Haplotype and structural variation analysis demonstrates that, these new SCN resistant lines shows unique and novel haplotypes compared to other existing SCN resistant soybean lines. Additionally, we are studying the landscape of soybean epigenome for SCN resistance to better understand the epigenetic control of SCN resistance and decipher the methylated regions and/or cis elements at the promoter region of the Rhg4 and rhg1 genes that leads to SCN resistance in soybeans. Through TILLING-by-Seq, we have developed six mutants to access new genes for SCN resistances. The SCN phenotyping of these mutants showed two of them have higher cyst count compared to parent genotype indicating involvement of these mutations in SCN resistant mechanism.

Benefit To Soybean Farmers

We identified that Rgh4 and its copy number variation can be genetically engineered to improve SCN resistance in soybean. The engineered nematode-resistant soybean lines with enhanced expression of Rhg4 will have strong resistance to multiple SCN races. Moreover, our gene editing strategies would help to pin-point the role of specific promoter motifs in SCN resistance and these strategies can also be employed to make other susceptible soybean varieties resistant to SCN for sustainable soybean production in the U.S. Discovery of new genetic resources from obj.3 which are independent of PI88788 and Peking type of SCN resistance, have offered new resistant source to improve SCN resistance and develop next generation soybean varieties for the U.S. soybean industry and farmers.

The United Soybean Research Retention policy will display final reports with the project once completed but working files will be purged after three years. And financial information after seven years. All pertinent information is in the final report or if you want more information, please contact the project lead at your state soybean organization or principal investigator listed on the project.