Location: Soil Management and Sugarbeet Research
2021 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
The unit has continued to transition to genomics-guided approaches to prioritize and characterize germplasm to feed the disease resistance trait discovery pipeline, along with executing large scale phenotypic screens of germplasm for the major sugar beet diseases. The unit also continued work on characterizing the interaction between sugar beet and multiple Fusarium spp. (F. oxysporum f. sp. betae, F. commune, and F. secorum) and characterizing the defense response for two sugar beet diseases, Fusarium yellows and Fusarium yellowing decline.
On Objective 1, the unit is spearheading a national effort to utilize genome sequencing data to quickly identify the most common forms of disease resistances in USDA-ARS germplasm releases to prioritize future screening efforts on germplasm lines most likely to harbor new forms of resistance. This year’s progress focused around utilizing a core set of 30 ARS germplasm releases that were evaluated for resistance to curly top, rhizomania, rhizoctonia crown, and root rot, Cercospora leaf spot, root maggot, and root aphid. Whole genome resequencing on these 30 ARS germplasm was completed, along with an additional 100 germplasm lines, to begin the process of discovering genomic regions associated with resistance against the above diseases. Using a variety of bioinformatics approaches combined with the phenotypic data from these disease nurseries, we developed higher quality molecular markers linked to resistance genes compared to those previously being used for this objective. For example, the genomic region containing resistance to rhizomania was mapped to chromosome 3 of the sugar beet genome. Currently, there are two deployed resistance genes to rhizomania available to growers, Rz1 from Beta vulgaris, and Rz2 introgressed from Beta vulgaris spp. maritima. The 30 ARS germplasm entries were used to identify a molecular marker nearby a candidate gene for rhizomania resistance. This new molecular marker for Rz1 is being validated in an allelic set of Rz1 and Rz2 genetic stocks. This approach is being used to identify markers in this germplasm panel for resistances to the other diseases screened for this year. We have also begun the process of re-screening the 64 Beta vulgaris subspecies maritima accessions for Rz2 using a recently published molecular marker marking the causal variant that confers resistance to rhizomania. These new molecular markers are also being applied to confirm parent selection for trait introgression.
On Objective 2, screening of sugar beet germplasm for resistance to the novel sugar beet disease Fusarium yellowing decline (Sub-objective 2.A) has been completed, and data are currently being analyzed. We have completed experimental treatments for characterizing the metabolome of sugar beet during infection with F. commune and F. secorum and have collected and pre-processed all samples for mass spectrometry analysis (Sub-objective 2. B). Due to impacts from Covid, the collaborator who performs mass spectrometry analysis (Colorado State University) has been unable to process samples. We are currently submitting samples to Colorado State University to begin the processing and mass spectrometry analysis in Fall 2021 to identify metabolites associated with Fusarium yellowing decline and Fusarium yellows in sugar beet.
Accomplishments
1. USDA’s germplasm repository tapped for sugar beet genes offering resistance to disease. The development of new lines of sugar beets to defend against emerging diseases is critical to American sugar production, but conventional breeding for resistance can be slow and arduous. ARS scientists in Fort Collins, Colorado, used novel screening tools to rapidly identify DNA markers for disease resistance from sugar beets within the USDA National Plant Germplasm System repository of plant genetic resources. This important scientific advancement sets the stage for a new strategy to use existing genome resequencing datasets of ARS sugar beet releases to dramatically speed up the process of public prebreeding for disease resistance from decades to years.
Review Publications
Dorn, K.M., Fenwick, A.L., Strausbaugh, C.A. 2021. Beet curly top resistance in USDA-ARS Ft. Collins germplasm, 2020. Plant Disease Management Reports. 15.
Dorn, K.M., Fenwick, A.L., Strausbaugh, C.A. 2021. Beet curly top resistance in USDA-ARS plant introduction lines of sugar beet, 2020. Plant Disease Management Reports. 15.
Negi, P., Pandey, M., Dorn, K.M., Nikam, A., Devarmuth, R., Srivastava, A., Suprasanna, P. 2020. Transcriptional reprogramming and enhanced photosynthesis drive inducible salt tolerance in sugarcane mutant M4209. Journal of Experimental Botany. 71(19):6159-6173. https://doi.org/10.1093/jxb/eraa339.
Raduski, A., Herman, A., Pogoda, C., Dorn, K.M., Van Tassel, D., Kane, N., Brandvain, Y. 2021. Patterns of genetic variation in a prairie wildflower, silphium integrifolium, suggest a non-prairie origin and untapped variation available for improved breeding. American Journal of Botany. 108(1):145-158. https://doi.org/10.1002/ajb2.1603.
Jaikumar, N.S., Dorn, K.M., Baas, D., Wilke, B., Kapp, C., Snapp, S. 2020. Nucleic acid damage and DNA damage repair are affected by freezing stress in annual wheat (Triticum aestivum) and by both plant age and freezing in its perennial relative (Thinopyrum intermedium). American Journal of Botany. 107(12):1693-1709. https://doi.org/10.1002/ajb2.1584.
