Research Project: Development of Sugar Beet Germplasm Enhanced for Resistance to Important and Emerging Plant Pathogens

Location: Soil Management and Sugarbeet Research

2023 Annual Report

Objectives
Objective 1: Identify novel resistance genes to major sugar beet fungal pathogens and sugar beet cyst nemotode within sugar beet genetic resources, especially its crop wild relatives; introgress the discovered novel sources of resistance into sugar beet germplasm for release; incorporate evaluation and characterization data into the Germplasm Resources Information Network (GRIN) database; and screen sugar beet germplasm and commercial lines for major fungal pathogens. Sub-objective 1A: Introgress novel sources of resistance to major pathogens into sugar enhanced beet germplasm for release. Sub-objective 1B: Screen 64 selected accessions of Beta vulgaris subspecies maritima (B.v. subsp. maritima) using single nucleotide polymorphic (SNP) markers linked to resistance genes. Confirm the resistance to these important diseases and begin to introgress novel sources of resistance into sugar beet germplasm for release. Objective 2: Identify and characterize genetic interactions, biochemical pathways, and metabolic processes that control interactions between sugar beet and fungal pathogens, for more efficacious disease resistance selection and improved germplasm for breeding programs, and to provide practical disease management recommendations for sugar beet producers. Sub-objective 2.A: Screen sugar beet germplasm with the newly discovered pathogen, Fusarium secorum, to identify resistance to the disease caused by this pathogens, Fusarium yellow decline, and to compare resistance in these sugar beet populations to the more traditional disease, Fusarium yellows primarily caused by Fusarium oxysporum f. sp. betae. (Webb) Sub-objective 2.B: Using metabolomic profiling, characterize the biological pathways that are induced during susceptible and resistant interactions with F. oxysporum f. sp. betae and F. secorum.

Approach
The sugar beet research within the Soil Management and Sugar Beet Research Unit contributes to the broader, national sugar beet research effort by USDA-ARS. Our research focuses on sugar beet disease because they remain an important source of pre- and post-harvest crop and sugar losses throughout the United States and internationally. Although advances have been made effective tools for managing important diseases are lacking. The pathogenic fungi Rhizoctonia and Fusarium and the sugar beet cyst nematode have particular economic importance because they are among the major limiting factors for sugar beet production nationwide. As part of a national sugar beet improvement program, we will apply a focused approach to enhance crop improvement methods and produce resistant germplasm through increased understanding of sugar beet genetics, some of its major pathogens, and its wild relatives. This project will exploit increased understanding of sugar beet/pathogen interactions and improve the understanding of pathogen diversity. We will use this knowledge to more quickly and cost effectively select disease resistant germplasm and develop superior disease management strategies. The breeding and pathology components of the project are focused on enhanced sugar beet germplasm through increased understanding of important sugar beet diseases and their epidemiology. This is especially crucial in diseases for which there is no chemical protection or where crop protectants are being phased out.

Progress Report
ARS researchers in Fort Collins, Colorado, continued the long-term advancement of sugar beet germplasm improvement efforts, now incorporating genome sequencing and bioinformatics approaches. The research project continued to focus on the discovery of new sources of disease resistance in sugar beet and sugar beet crop wild relative germplasm, introgressing these traits into a sugar beet background, and initiating new lines of research to identify the genomic regions containing the specific genes that impart disease resistance. The unit continued the expansion of this line of research into distant relatives of sugar beet as potential sources of new forms of disease resistance. On Objective 1, the research team completed the release of two new sugar beet genetic stocks with disease resistance traits introgressed from sea beet (Beta vulgaris spp. maritima), a key sugar beet crop wild relative. The genetic stocks FC308 (PI701378) and FC309 (PI700990) are inbred lines that are being released alongside genome sequencing resources to provide researchers new tools to study plant-pathogen interactions. FC308 and FC309 should also be useful parents in breeding programs aimed at improving resistance to Sugar Beet Cyst Nematode and Fusarium Yellows, respectively. This release is part of a USDA-ARS effort to develop sugar beet lines with more uniform resistance to a single disease, enabling trait mapping, functional genomics, and plant-pathogen interaction research. FC308 harbors the sugar beet nematode resistance gene derived from the sugar beet crop wild relative Beta vulgaris spp. maritima, as confirmed by previously identified molecular markers linked to this source of resistance. FC309 is uniform in its resistance to Fusarium Yellows, a troublesome fungal pathogen in much of the Midwest and Western United States beet sugar production regions. Both genetic stocks are self-fertile diploid inbred lines that segregate for both hypocotyl color and multigerm seed. Both lines are also susceptible to Rhizoctonia Crown and Root Rot. Whole genome sequencing datasets and gene space assemblies are being released alongside the germplasm under National Center for Biotechnology Information BioProject PRJNA923373 and PRJNA563463. To aid in the mapping of resistance traits from the Beta vulgaris spp. maritima background, the team also developed the first fully phased, chromosome-scale genome assembly of a Beta vulgaris spp. maritima plant that exhibited strong resistance to Rhizoctonia Root and Crown Rot. Finally, one germplasm which exhibits strong resistance to both Cercospora Leaf Spot and Rhizoctonia Root and Crown Rot derived from previous USDA-ARS pre-breeding lines was also released as FC729 (PI703023). On Objective 2, the work continued on the expansion of the project into examining transcriptomic responses of resistant and susceptible sugar beet germplasm to infection with Fusarium oxysporum F19. Utilizing the stable resistance to Fusarium Yellows found in the new genetic stock FC309, the team completed the development of a standard area diagram for Fusarium Yellows rating to improve ongoing disease screening efforts. Genomic regions linked to the Fusarium Yellows resistance in FC309 were identified from an F2 mapping population using the bulked segregant analysis and high throughput DNA sequencing approach. Transcripts in these genomic regions exhibiting differential expression in the RNAseq experiment completed in the previous year have been identified and are being prioritized for functional validation in planta. This is the final report for this project which terminated in March 2023. See the report for the replacement project, 3012-21220-011-000D, “Genomic mining of sugar beet crop wild relative germplasm resources for new sources of disease resistance” for additional information.

Accomplishments
1. An improved map of the sugar beet genome. Pests and pathogens continually threaten U.S. sugar beet production. Plant breeding efforts to improve resistance against these threats is ongoing, and now uses DNA sequencing technology to find regions of the genome linked to resistance. A national team of ARS researchers and collaborators published the most complete map of the sugar beet genome to date. This new map of the EL10 sugar beet genome is being used internationally to identify new genetic sources of resistance to multiple pests and pathogens.

Review Publications
McGrath, J.M., Funk, A., Galewski, P., Ou, S., Townsend, B., Davenport, K., Daligault, H., Johnson, S., Lee, J., Hastie, A., Naegele, R.P., Dorn, K.M. 2022. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). DNA Research. 30(1). Article edsac033. https://doi.org/10.1093/dnares/dsac033.
Dorn, K.M., Strausbaugh, C.A. 2022. USDA-ARS pre-breeding germplasm evaluated for Rhizomania and storage rot resistance in Idaho, 2021. Plant Disease Management Reports. 16. Article eV125.
Dorn, K.M., Strausbaugh, C.A. 2022. USDA-ARS plant introduction lines evaluated for rhizomania and storage rot resistance in Idaho, 2021. Plant Disease Management Reports. 16. Article eV126.
Dorn, K.M., Strausbaugh, C.A., Galewski, P.J. 2022. Beet curly top resistance in USDA-ARS NPGS Plant Introduction lines, 2021. Plant Disease Management Reports. 16. Article eV166.
Wigg, K., Brainard, S., Metz, N.J., Dorn, K.M., Goldman, I. 2023. New QTL associated with Rhizoctonia solani Kühn resistance identified in two table beet x sugar beet F2:3 populations using a new table beet reference genome. Crop Science. 63(2):535-555. https://doi.org/10.1002/csc2.20865.
Metz, N.J., Fenwick, A.L., Yeater, K.M., Nielson, A.L., Floyd, B.A., Sowder, B.M., Dorn, K.M. 2022. Evaluation of Rhizoctonia root and crown rot resistance in USDA-ARS Fort Collins germplasm releases, 2020. Plant Disease Management Reports. 16. Article eV173.
Dorn, K.M., Fenwick, A.L., Metz, N.J., Yeater, K.M., Nielson, A.L., Floyd, B.A., Sowder, B.M. 2022. Evaluation of USDA-ARS Beta vulgaris pre-breeding germplasm for resistance to Rhizoctonia crown and root rot, 2021. Plant Disease Management Reports. 16. Article eV162.
Dorn, K.M., Metz, N.J., Fenwick, A.L., Yeater, K.M., Nielson, A.L., Floyd, B.A., Sowder, B.M. 2022. Evaluation of Beta PIs from the USDA-ARS, NPGS for Rhizoctonia crown and root rot resistance, 2021. Plant Disease Management Reports. 16. Article eV161.
Dorn, K.M., Metz, N.J., Fenwick, A.L., Todd, O.E., Kumar, A., Yeater, K.M., Nielson, A.L., Floyd, B.A., Sowder, B.M. 2023. Evaluation of Beta PIs from the USDA-ARS, NPGS for Rhizoctonia crown and root rot resistance, 2022. Plant Disease Management Reports. 17. Article eV103.
Dorn, K.M., Strausbaugh, C.A., Galewski, P.J. 2023. Beet curly top resistance in USDA-ARS Plant Introduction lines, 2022. Plant Disease Management Reports. 17. Article eV033.