Location: Sugarbeet and Bean Research
2023 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. Over the course of this project, the genomes for sugar beet germplasm EL10 was annotated and has now been published as a peer reviewed paper. This chromosome-level genome assembly, with associated linkage maps, has been used to generate additional publications and is now publicly available. Additional putative genes with potential roles in plant development, disease resistance, and other factors of interest 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 NCGRP previously reported with potential resistance to Cercospora leaf spot.
Objective 2. Screening for disease in seedlings has confirmed 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 a new pathogen also was found. A different pathogen with similar morphology also was found later in the season on leaves, but genetic characterization has indicated that more than one species may be involved. Neither of the species currently identified are the same species reported to cause beet anthracnose in Asia, but a study in Japan indicated that an isolate from radish had been re-classified from the previously reported species, Colletotrichum dematium, to one of the same species found in Michigan, C. incanum. We published a first report of this species causing anthracnose of sugar beet and continue to investigate the evidence pathogen diversity. In 2022, a similar fungus was found causing a leaf spot of chard.
During the course of the project, we confirmed that Alternaria species, particularly Alternaria alternata, has become a more significant issue on sugar beet in Michigan than had previously been observed. We confirmed variability in host genotype interactions with isolates, and our results assisted in the industry in identifying particularly susceptible varieties. With reduction of use of these varieties, the Alternaria leaf spot levels have been reduced, but it remains more common than prior to 2010. We used genetic information to analyze Alternaria species associated with sugar beet, common rotation crops, and other crops grown in the region, and uncovered evidence that the same isolates can affect numerous crops in the region, and that there is no evidence for a major shift in the genotypes present with the increase in prevalence in the region. Similar increases in frequency are now being reported in other growing areas in the United States, and information has been requested by researchers and seed companies. A peer-reviewed diagnostic guide on identification and sampling for Alternaria on beet was published.
While screening diverse beet germplasm, we have identified Michigan strains of Fusarium spp. with higher virulence on sugar beet than had previously been reported. Genetic analysis confirms that some of these are in different species in the Fusarium oxysporum species complex. The majority of species identified from beet in Michigan are in this complex, in contrast to the high level of F. secorum found in the Red River Valley. Seedling disease with Fusarium species was again found at high levels in 2023, including some species that are reported to affect beet seedlings, but not adult beets, such as F. acuminatum. With the increasing prevalence of Fusarium in sugar beet in the region, the industry has put this on their high priority list for research.
Throughout the duration of the project, we identified new genetic groups within Rhizoctonia solani AG 2-2, the primary causal agent of Rhizoctonia root and crown rot in beet. This work was done in collaboration with researchers at USDA-ARS, Salinas, California. These genetic groups have shown some variability in host interactions which may help to explain some of the variability previously reported in host-pathogen interactions. Simple sequence repeats (SSRs) were developed to examine diversity, and PCR-primers were developed with an aim to detect the different phylogenetic groups rapidly. These are being tested for specificity and consistency.
Objective 3. Additional beet genomes are being sequenced in collaboration with the Fort Collins, Colorado, Genetics program in addition to wild and weedy beet relatives. Pathogen genomes are being sequenced with the help of the Michigan State University genomics core facility. New climate research and breeding has been initiated for improved response to reduced nitrogen application and for seedling drought resistance. Germplasm testing is being done to examine response to nitrogen levels and drought and develop cost-efficient phenotyping methods for novel genetic resources.
Accomplishments
1. New host and pathogen discovered in Michigan. Knowledge of the disease affecting a crop and region are essential for developing management practices and producing a crop. ARS researchers in East Lansing, Michigan, identified a disease of sugar beet that was previously not known to occur in the United States. A leaf spot was found that produced fungal spores that were not typical of the standard pathogens in the area. The fungus was identified as a Colletotrichum species based on morphology. A disease caused by a Colletotrichum species, anthracnose, caused by C. dematium was previously reported on sugar beet in Japan and on table beet in Prince Edward Island, Canada, but not from the United States. With further testing the fungus from beets in Michigan was determined to be Colletotrichum incanum using a combination of morphology and DNA sequencing. This species caused a leaf spot and seedling damping-off on beet in the greenhouse. Additional isolates have been collected from sugar beet and are being tested and identified. Since the anthracnose can be seedborne, this is important information for seed companies and breeders. Stand establishment has been an issue in Michigan, so it is important to understand what diseases may be causing seedling damping-off to develop appropriate management tools. The local sugar company has initiated sampling to determine how widespread this disease is in Michigan sugar beet. Anthracnose was reported to affect table beet, and C. incanum has been reported on radish and soybean, therefore this also has potential to be a concern for vegetable and soybean producers and researchers in the region.
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.
Harveson, R.M., Neher, O., Hanson, L.E. 2023. Diseases of sugar beet. In: Hollier, C.A., Padgett, G.B., Draper, M.A., editors. Diseases of Field Crops. St. Paul, MN: APS Press. p. 267-286.
Crizon Cortes, S., Hanson, L.E., Miles, L., Wilbur, J., Naegele, R.P. 2022. Diagnostic guide for Alternaria leaf spot on sugar beet, red beet, and chard. Plant Health Progress. 23(4):497-506. https://doi.org/10.1094/PHP-03-22-0025-DG.
Naegele, R.P., Abdelsamad, N.A., DeLong, J.A., Saito, S., Xiao, C., Miles, T. 2022. Fungicide resistance and host influence on population structure in Botrytis spp. from specialty crops in California. Phytopathology. 112(12):2549-2559. https://doi.org/10.1094/PHYTO-03-22-0070-R.
Hanson, L.E., Schlachter, E.M., Minier, D.H., Byrne, J., Wilbur, J.F. 2023. First report of anthracnose on sugar beet (Beta vulgaris) caused by Colletotrichum incanum in Michigan, USA. New Disease Reports. 47(1). Article e12152. https://doi.org/10.1002/ndr2.12152.
Hernandez, A.P., Bublitz, D.M., Wenzel, T.J., Ruth, S., Bloomingdale, C., Mettler, D., Bloomquist, M., Hanson, L.E., Wilbur, J.F. 2023. An in-field heat treatment to reduce Cercospora beticola survival in plant residue and improve Cercospora leaf spot management in sugarbeet. Frontiers in Plant Science. 14. Article 1100595. https://doi.org/10.3389/fpls.2023.1100595.
