Location: Sugarbeet and Bean Research
2021 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: The reference sugar beet genome for ARS germplasm release C869 (a.k.a EL10) has been posted online (MS ID#: BIORXIV/2020/298315MS). Additional genomes have been sequenced in collaboration with the ARS genetics program at Fort Collins, Colorado. Putative resistance genes are being identified and analyzed. Selection continues on germplasm and Recombinant Inbred Lines (RILs) in the long-term disease nurseries and greenhouse, 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 responses in collaboration with ARS geneticists at Beltsville, Maryland, and East Lansing, Michigan.
Objective 2: Seedling disease testing was conducted with genetically characterized strains, demonstrating diverse responses to factors such as low temperature. A paper from the research has been accepted for publication in a scientific journal. Screening for disease in seedlings has revealed the presence of a pathogen not previously known to occur on sugar beet in the U.S. Genetic characterization shows a close relationship to a pathogen common on soybean in the U.S., and that the isolates are a different species from the causal agent previously reported in Asia. We are working with the Animal and Plant Health Inspection Service (APHIS) on this finding new to the area and are examining response of ARS germplasm to the fungus. We continue to develop genetic markers and use genetic information to examine Rhizoctonia solani. Co-inoculation of Rhizoctonia solani and Fusarium species in beets was conducted. We continue to observe synergism, which enhances disease severity even when plants are resistant to one of the two pathogens.
Objective 3: In collaboration with ARS scientists from Beltsville, Maryland, potential polygalacturonase inhibitor proteins (PGIPs) have been identified. We are investigating interaction with pathogen genotypes (with Objectives 1 and 2) and have sequences to develop genetic markers. We have also begun to look at differences in nitrogen usage between crop types.
Accomplishments
1. Interaction of plant growth stage and disease. Rhizoctonia solani is a soilborne fungus that causes major sugar beet losses annually worldwide. Adult beet plant resistance to the fungus was found not to be expressed in many seedlings. ARS scientists at East Lansing, Michigan, examined the seedling interaction further, including impact of temperature and pathogen strain on disease (seedling damping-off). It was found that strains varied significantly in their response to low temperatures, with 77% of 35 isolates tested able to cause disease at lower temperatures than usually considered the minimum for risk of Rhizoctonia damping-off. Rhizoctonia solani is known to be a species complex. Because variability in physical characters is low, hyphal anastomosis has been used to separate groups (known as anastomosis groups or AG for short). These AG are essentially equal to separate species. Host genotypes responded differently to two of these AG found in seedling beets. Resistance to both major AG, AG 2-2 and AG 4, was observed in USDA germplasm, but the resistance showed evidence of being independent genetically, which was further supported by ARS collaborators in Beltsville, Maryland. They found two beet genes identified in their program responded differently to the two types of Rhizoctonia solani. This information provides some targets for resistance characterization and breeding.
Review Publications
Hernandez, A., Bloomingdale, C., Bublitz, D.M., Hanson, L.E., Wilbur, J.F. 2021. Evaluation of cultural practices to manage Cercospora leaf spot of sugar beet in Michigan, 2019-20. Plant Disease Management Reports. 15. Article V008. https://doi.org/10.1094/PDMR15.
Heck, D.W., Kikkert, J.R., Hanson, L.E., Pethybridge, S.J. 2021. Development of a sequential sampling plan using spatial attributes of Cercospora leaf spot epidemics of table beet in New York. Plant Disease. https://doi.org/10.1094/PDIS-07-20-1619-RE.
