Location: Soil Management and Sugarbeet Research
2022 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 advancing sugar beet germplasm improvement efforts using genomics-guided approaches. This work has focused on the discovery of disease resistance traits from sugar beet crop wild relatives and sugar beet pre-breeding germplasm via large-scale phenotypic screens, followed by genetic and genomic approaches to identify the genes underlying resistance. The unit expanded these research aims to include additional sugar beet crop wild relative species as potential sources for novel disease resistance genes.
On Objective 1, the research team advanced new pre-breeding lines with disease resistance traits introgressed from sea beet (Beta vulgaris spp. maritima), a key sugar beet crop wild relative. These included a Fusarium Yellows resistant line (FC309), which has been self-pollinated to ensure genetic and phenotypic heterogeneity, resulting in seed quantities sufficient for a germplasm release later this year. A single self-pollinated and re-phenotyped plant from the FC309 seed lot was also selected for high resolution (PacBio HiFi) genetic sequencing to generate a high-quality genome assembly. To advance resistance gene identification and introgression from sugar beet crop wild relatives, the Beta vulgaris spp. maritima panel of 64 accessions, a key focus of this research objective, was screened for Rhizoctonia Crown and Root Rot resistance in a replicated greenhouse experiment. The research team identified several highly resistant individual plants across multiple accessions. These plants were rescued following the disease rating for self-pollination and tissue collection for high molecular weight DNA isolation for eventual PacBio HiFi genome sequencing and assembly. Upon re-screening to confirm the resistance phenotype, these lines will be used to introgress this Beta vulgaris spp. maritima derived source of Rhizoctonia resistance. The team also completed an additional cycle of selection and self-pollination from the FC709-2 background. A high quality PacBio HiFi-based genome assembly was also produced for a single plant from this new line, FC709-3. To further investigate the genetic sources of Rhizoctonia Crown and Root Rot resistance from the FC709-2 background, the researchers also utilized a comprehensive transcriptomic (RNAseq) analysis to identify genes with expression profiles associated with resistance. The transcriptomic characterization was coupled with genetic mapping experiments utilizing high density genotyping and bulked segregant sequencing of an F2 mapping population to identify the causal resistance genes from FC709-2.
On Objective 2, research expanded beyond metabolic profiling into examining the global transcriptional responses of resistant and susceptible sugar beet germplasm to infection with Fusarium oxysporum F19. A comprehensive, replicated RNAseq experiment consisting of 24 samples identified statistically significant differentially expressed genes, including candidate canonical disease resistance genes. To enable more accurate and reproducible phenotyping of Fusarium Yellows screens in greenhouse and growth chamber experiments, the researchers developed an artificial intelligence-enabled high throughput phenotyping pipeline. Work is ongoing to scale the deployment of this phenotyping pipeline into an automated, large scale greenhouse and field-based phenotyping system for multiple sugar beet diseases.
Accomplishments
1. New sugar beet genome provides breeders with toolbox for pest resistance. Pests and pathogens are a major cause of losses in U.S. sugar beet production, with up to 80% loss reported for some outbreaks. ARS researchers in Fort Collins, Colorado, and collaborators used cutting-edge genome sequencing technologies to develop the most complete genomic maps for sugar beets and their wild relatives. The team identified a group of sugar beet lines and wild relatives that resist Rhizoctonia Crown and Root Rot and sugar beet cyst nematode. These plants can now serve as the basis for using genetic markers to breed this resistance into commercial sugar beet lines. In addition to these sugar beet-specific findings, the approach is transferable to breeding objectives in many important agricultural crops in the U.S. and worldwide.
Review Publications
Nunn, A., Rodriguez, I., Tandukar, Z., Frels, K., Contreras-Garrido, A., Carbonell-Bejerano, P., Zhang, P., Ramos, D., Jandrasits, K., Lanz, C., Brusa, A., Mirouze, M., Dorn, K.M., Jarvis, B., Sedbrook, J., Wyse, D., Otto, C., Langenberger, D., Weigel, D., Marks, M.D., Anderson, J., Becker, C., Chopra, R. 2022. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. Plant Biotechnology Journal. 20(5):944-963. https://doi.org/10.1111/pbi.13775.
Altendorf, K.R., Larson, S.R., Dehaan, L.R., Crain, J., Neyhart, J., Dorn, K.M., Anderson, J.A. 2021. Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass (Thinopyrum intermedium). G3, Genes/Genomes/Genetics. 11(3). Article jkab025. https://doi.org/10.1093/g3journal/jkab025.
Brusa, A., Patterson, E., Gaines, T., Dorn, K.M., Westra, P., Kuepper, A., Sparks, C., Wyse, D. 2021. A needle in a seedstack: An improved method for detection of rare alleles in bulk seed testing through KASP. Pest Management Science. 77(5):2477-2484. https://doi.org/10.1002/ps.6278.
Crain, J., Larson, S.R., Dorn, K.M., DeHaan, L., Poland, J. 2022. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. Theoretical and Applied Genetics. 135:2769-2784. https://doi.org/10.1007/s00122-022-04148-2.
Webb, K.M., Wintermantel, W.M., Broeckling, C.D., Wolfe, L., Yao, L., Hladky, L.L., Clasen Chavez, F. 2020. Metabolic disturbances in sugar beet (Beta vulgaris) during infection with Beet necrotic yellow vein virus. Physiological and Molecular Plant Pathology. 112. Article e101520. https://doi.org/10.1016/j.pmpp.2020.101520.
Woodhall, J.W., Brown, L., Harrington, M., Herbert, K., Keith, S., Webb, K.M., Neher, O. 2020. First report of Binucleate Rhizoctonia (Ceratobasidium) Ag F causing dry rot canker of sugar beet in Idaho. Plant Disease. 104(9). https://doi.org/10.1094/PDIS-06-19-1328-PDN.
Gao, L., Koo, D., Juliana, P., Rife, T., Singh, D., Da Silva, C., Lux, T., Dorn, K.M., Clinesmith, M., Silva, P., Wang, X., Spannagl, M., Monat, C., Friebe, B., Steuernagel, B., Muehlbauer, G., Pozniak, C., Singh, R., Stein, N., Mascher, M., Fritz, A., Poland, J., Walkowiak, S. 2020. The Aegilops ventricosa 2NvS segment in bread wheat: Cytology, genomics and breeding. Theoretical and Applied Genetics. 134:529-542. https://doi.org/10.1007/s00122-020-03712-y.
Dorn, K.M., Fenwick, A.L., Yeater, K.M., Nielson, A.L., Floyd, B.A., Metz, N.J., Sowder, B.M. 2021. Evaluation of Beta vulgaris USDA-ARS germplasm releases for rhizoctonia crown and root rot resistance, 2020. Plant Disease Management Reports. 15. Article eV166.
Dorn, K.M., Strausbaugh, C.A. 2021. Ft. Collins sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2020. Plant Disease Management Reports. 15. Article eV164.
