Update:
In this period of the project, we focused on Objective 1, Development of a high-quality RenSeq platform for the soybean research community. We have re-annotated all NBS-LRR genes in ~30 high-quality genomes of diverse varieties including elite cultivars, landraces, and wild soybean accessions. We also conducted comparative genomics analysis for the NBS-LRR gene clusters to understand how NBS-LRR genes evolve over time. We found dramatic copy number and structural variations of NBS-LRR genes among different varieties. These analyses enhanced our understanding about the challenges and strategies for typical disease resistance(R) gene discovery, mapping, and isolation, we well as the importance of design of functional R gene-based molecular markers for marker-assisted selection of R genes in breeding. All the NBS-LRR gene sequences from the ~30 genomes have been extracted for design of a comprehensive set of baits for RenSeq.
Although subcontractors have just received funds to work on this project, they have made some progresses on screening and characterization of new sources of disease resistances and development of R gene mapping population as defined in Objective 4. Nevertheless, we anticipate a need for a 6-months no-cost extension. This would help the subcontractors to complete their research components defined in this project in year 1.
Update:
In the FY23 period (i.e., Year 1 of the 3-year project), our team has made satisfactory progresses on the proposed Objectives 1, 2, and 4, which are highlighted below. Objectives 3 and 5 were proposed to start in FY24 and FY25, thus there are no progresses have been made.
Objective 1. Development of a high-quality RenSeq platform for the soybean research community.
Progress made: This objective has been fully achieved. We have re-annotated all NBS-LRR (or NLR) genes from the 26 representative genomes used to establish the soybean pangenomes, as well as the reference genomes of Williams 82, ZH13, and a wild soybean accession. We annotated approximately 30-40 new NBS-LRR genes in each of these genomes, totaling 800-900 new NBS-LRR genes, which were not previously annotated but annotated through this project. Based on the entire set of NLR genes in these genomes, a set of RNA baits, composed of ~80,000 unique RNA sequences have been designed in coordination with Arbor Bioscience. These baits have been mapped back to the pangenomes and show 99,9% coverage of all NLR genes. So this set of baits would be able to enrich all NLRs in any soybean varieties. The NLR gene annotation has been deposited in a spreadsheet. The annotation, together with the bait information, will be available to the research community without any restriction.
Deliverables: Improved NLR gene annotation in the soybean pangenomes; A SoyRenSeq platform for NBS-LRR gene capture and enrichment.
Objective 2. Sequencing and assembly of NBS-LRR gene clusters in major soybean lines carrying resistance to prevalent soybean pathogens in the Midwest region.
Progress made: A subset of resistant soybean lines from the co-PIs and the community have been collected, evaluated, and chosen for RenSeq in FY23. We spent much more time than originally anticipated coordinating with Arbor Bioscience for bait design, resulting in the set of SoyRenSeq baits that can maximally and specifically enrich NLRs from any soybean cultivars with lowest costs. We have signed a contract with Arbor Bioscience for processing 96 soybean varieties, from NLR enrichment and PacBio long-read sequencing. The FY23 budget will cover RenSeq of 48 samples and the FY24 budget will cover RenSeq of other 48 samples. The FY23 project has been extended to 03/31/24 without request for additional funds. All the 96 samples will be Ren-sequenced and assembled by the extended end date of the FY23 project.
Deliverables: a set 96 soybean cultivars carrying resistance to the targeted soybean diseases chosen for Ren-sequencing.
Objective 4. Evaluation of resistance to various pathogens and mapping of major R genes and QTL.
Progress made: Our team has made satisfactory progresses on this objective, ranging from cultivar evaluation for specific resistances, mapping population development, to genetic mapping of genes/QTLs underlying specific resistances. In particular, individual co-PIs have their respective foci on specific pathogens that are predominant in their states. In addition, co-PIs have been independently developing mapping populations for dissecting the genetic basis of the resistances, but will coordinate as a team to use the RenSeq approach to identify and clone major QTLs underlying resistances to specific pathogens.
Deliverables: Biparental populations, inheritance pattern of resistances, and initial mapping results.
Overall the project went well, and the non-cost extension will ensure that all objectives are fully achieved.