Soybean diseases continue to be a major limitation to sustainable soybean production in the US. It is estimated that the average annual yield losses due to soybean diseases in the United States are approximately 11%, which translates to more than $4 billion in revenue loss per year. In order to protect soybeans from damages from the destructive pathogens, it is important to identify new sources of disease (R) resistance genes and deploy desirable R genes into elite soybean cultivars. This project uses a technique called Ren-Seq (Resistance Gene Enriched Sequencing), which can specifically capture, enrich, and sequence resistance genes, primarily NBS-LRR genes, to accelerate disease resistance gene discovery. This approach, combined with genetic mapping and gene expression data, allows i) assembling all NBS-LRR genes without a need to sequence the entire genome; ii) finding molecular markers that allow fine mapping of disease resistance genes; iii) pinpointing candidate R genes; iv) designing R gene-based molecular markers for precise R gene selection in breeding – all at affordable costs. We proposed five specific objectives to achoive the overall goal defined in this project.

Objective 1. Development of a high-quality RenSeq platform for the soybean research community. Objective 2. Sequencing and assembly of NBS-LRR gene clusters in major soybean lines carrying resistance to prevalent soybean pathogens in the Midwest region. Objective 3. Analysis of R gene expression and responses to various soybean pathogens. Objective 4. Evaluation of resistance to various pathogens and mapping of major R genes and QTL. Objective 5. Development of candidate R-gene-based molecular markers for precision breeding.

1) Assembled and mapped NBS-LRR gene clusters from 96 (or 48) or soybean cultivars carrying resistance to the targeted soybean diseases; construction of a pan-NLRome.
2) Chromosomal locations and candidate genes for 6 major disease resistance QTLs or qualitative loci. Detailed spectra of resistance of these QTL or qualitative loci
3) Genome-wide NBS-LRR gene expression patterns in 6-12 varieties in response to infection of targeted pathogens in soybean lines carrying major disease resistance QTL or genes.
4) A set of 2-3 candidate R genes of NBS-LRR type underlying specific resistances to different pathogens/strains and DNA markers for precise selection of these R genes.

The utilization of soybean cultivars with durable resistance will reduce the use of harmful chemicals, which will create a higher profit margin for soybean farmers and a healthier environment overall. This project also provide excellent opportunity to train the next-generation researchers whose future endeavors would directly or indirectly contribute to farm profitability.