Location: Sugarbeet and Bean Research
2022 Annual Report
Objectives
Objective 1: Annotate, prospect, and identify genes and genome structure of the ARS release C869 (a.k.a. EL10) reference sugar beet genome, and develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use.
Sub-objective 1.A: Annotate, prospect, and identify genes and genome structure of the EL10 genome.
Sub-objective 1.B: Develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use.
Objective 2: Assess the host range, diversity, and host-pathogen interactions of sugar beet pathogens of high priority to the Great Lakes, including Rhizoctonia, Cercospora, and seedling disease complex, to identify host resistance factors for use in breeding programs.
Objective 3: Identify sugar beet-specific genes and develop genetic markers involved in beet quality and crop type (sugar, fodder, table, or chard) to transfer novel genetic resources from un-adapted to adapted germplasm, for the benefit of all beet crop types.
Approach
1) Explore disease resistance and stress-germination genes in EL10 and related germplasm. Phenotype RIL populations and obtain low-coverage re-sequencing for genetic analysis and mapping. Develop additional genetic populations and enhanced germplasm for release.
2) Develop and utilize genetic markers and other genetic information for enhanced understanding of Rhizoctonia solani and other plant pathogenic fungi. Characterize host-pathogen, host-pathogen-pathogen interactions and host developmental stages that influence disease progression.
3) Evaluate crop genomes for markers and other features important in a breeding context. Evaluate non-beet genomes for features of potential benefit to long-term beet improvement.
Progress Report
Objective 1. Annotate, prospect and identify genes and genome structure of the ARS release C869 (a.k.a. EL10) reference sugar beet genome and develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use. The genome for EL10 has been accepted online (MS ID#: BIORXIV/2020/298315MS ) and a peer reviewed paper has been submitted. Additional genomes are being sequenced in collaboration with the Fort Collins, Colorado Genetics program. Putative genes with potential roles in plant development, disease resistance, and other potential factors are being identified and analyzed. Selection continues on germplasm and Recombinant Inbred Lines (RILs) in the long-term disease nurseries, including reselection of materials from the National Center for Genetic Resources Preservation (NCGRP) previously reported with potential resistance to Cercospora leaf spot. Materials are being used for investigations of other genetic response in collaboration with Beltsville Beet Genetics program.
Objective 2. Assess the host range, diversity and host-pathogen interactions of sugar beet pathogesn of high priority to the Great Lakes, including Rhizoctonia, Cercospora, and seedling disease complex, to identify host resistance factors for use in breeding programs. Screening for disease in seedlings has revealed the presence of a pathogen not previously known to occur on sugar beet in the United States. Seedling disease was unusually high in the area in spring of 2022, with Fusarium being the most prevalent pathogen identified, but the new pathogen was also found. Genetic characterization shows close relationship to a pathogen common on soybean in the United States and radish in Japan. The isolate are a different species from the causal agent previously reported in Asia, but the Japanese radish work showed that an isolate from radish had been re-classified from that species to this newer species. We have been in consultation with APHIS to determine risk prior to publication and answering questions from the industry. We have continued development of genetic markers and use of genetic information to examine Rhizoctonia solani and initiated genetic analysis of Alternaria species associated with sugar beet, common rotation crops, and other crops grown in the region. We co-inoculated Rhizoctonia solani and Fusarium species and continued to observe synergism, which enhances disease severity even when plants are resistant to one of the two pathogens.
Objective 3. Identify sugar beet-specific genes and develop genetic markers involved in beet quality and crop type (sugar, fodder, table, or chard) to transfer novel genetic resources from un-adapted to adapted germplasm, for the benefit of all beet crop types.
Identified potential polygalacturonase inhibitor proteins (PGIPs), in collaboration with ARS scientist from Beltsville, Maryland. Investigating interaction with pathogen genotypes (with objective 2) and have found varied levels of both putative PGIPs in plants and corresponding polygalacturonases in pathogens that appear to be associated with disease levels and disease response levels. Breeding and crossing has been initiated to examine response to nutrients and drought.
Accomplishments
1. Identified beet as a new host for an old pathogen (leaf spot). ARS researchers in East Lansing, Michigan, identified a leaf spot, a previously unknown sugar beet disease, which was found to produce fungal spores that were not typical of the standard pathogens in the region. The causal fungus was identified as a Stemphylium species based on morphology. Because there has been a severe disease, yellow leaf spot, caused by a Stemphylium species, S. beticola, in Europe, further testing was initiated. The fungus from beets in Michigan was determined to be Stemphyllium vesicarium. This species is known to cause disease on other crops in the region like onion and asparagus. When tested on sugar beet, it caused a mild leaf spot. The disease produced about a tenth as many lesions as those caused by S. beticola in growth chamber tests. This is the first time Stemphyllium vesicarium has been reported on beet, but a Stemphylium species has been reported to cause a mild leaf spot on Swiss chard (same species as sugar beet), indicating that this also may be an issue on other forms of beet. The disease was mild and could be mistaken for another common leaf spot, Alternaria leaf spot. It is not known how damaging the Stemphylium leaf spot might be in the region, but the presence is important in making informed management decisions, such as when fungicide treatments might be needed. This knowledge is important for diagnosticians and researchers who need to determine pathogens and provide risk assessment, and for growers and field consultants who need to make disease management decisions. It is essential to know when fungicide treatments might be needed (for example to manage Cercospora leaf spot or yellow leaf spot) or likely are not necessary. The information also is important for vegetable producers, to know that beet may harbor inoculum and may not be an appropriate rotation or companion crop for susceptible vegetable crops.
Review Publications
Minier, D.H., Hanson, L.E. 2021. Effect of low temperature on the aggressiveness of Rhizoctonia solani AG 2-2 isolates on sugar beet (Beta vulgaris) seedlings. Plant Disease. 105(10):3111-3117. https://doi.org/10.1094/PDIS-09-20-1990-RE.
Bublitz, D.M., McGrath, J.M., Hanson, L.E. 2021. Weather conditions conducive for the early-season production and dispersal of Cercospora beticola spores in the Great Lakes Region of North America. Plant Disease. 105(10):3063-3071. https://doi.org/10.1094/PDIS-09-20-2004-RE.
Metheny, J., Jayawardana, M.A., Wilbur, J.F., Hanson, L.E. 2022. First report of Stemphylium leaf spot of sugar beet caused by Stemphylium vesicarium. New Disease Reports. 45(2). Article e12084. https://doi.org/10.1002/ndr2.12084.
