Location: Sugarbeet and Bean Research
2020 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 submitted for publication. Additional genomes are being sequenced in collaboration with the Fort Collins, Colorado, Genetics program. Putative resistance genes are being identified and analyzed. Selection continues on germplasm and Recombinant Inbred Lines (RILs) in the long-term disease nursery, including re-selection of materials from the National Center for Genetic Resources Preservation (NCGRP) previously reported with varying response to Cercospora leaf spot.
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.
Simple sequence repeat markers have been developed to assess diversity in Rhizoctonia solani on sugar beet. These have been used to analyze strains from different rotation crops and are being assessed for utility in the field with sugar beet. A collaboration has been developed with Cornell University to further assess diversity and host interactions (grant proposal submitted). This will allow assessment of interaction with table beet as well as sugar beet and under a wider range of soil and growing conditions. Genetic analysis is being used to compare putative polygalacturonase genes (PGs) in the pathogens and polygalacturonase inhibitor proteins (PGIPs) in the host. In other systems these affect disease development and host range. Differential responses have been found between dry bean (some with well characterized PGIP systems) and sugar beet (with recently identified PGIP systems).
In addition to Rhizoctonia, screening continues for two other major pathogens in the region--Cercospora beticola, a long-term issue in the region and Alternaria species, a more recently identified problem in the area. Between them, these pathogens are estimated to have caused losses to the industry of over $20 million over the last five years.
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.
Beta vulgaris is a species complex containing several distinct crop-types (sugar, fodder, table, and chard). Selection and drift have sorted ancestral variation in a way that has resulted in pronounced phenotypic differences between these crops. Methods to measure and quantify these differences were developed by focusing on lineage specific genetic variation (i.e. that which is unique to a population or crop type). Historically important genotypes have been identified to examine changes with time and varying levels of selection. Distribution of genetic variation within and between crop types showed extensive shared genetic variation. Lineage specific variation within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a varied pattern of differentiation with respect to crop type. Inferred population size history for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of the major cultivated beet types.
Accomplishments
1. Genetics of Rhizoctonia resistance genes in beet. Rhizoctonia root and crown rot (RRCR) is the most important soil-borne disease of sugar beet in the world. ARS scientists have a long history of breeding for resistance, but the mechanism is not understood, but we know multiple genes are involved. Better knowledge of the resistance mechanism could speed up plant screening and getting resistance into varieties with other desired characters for stakeholders. In collaboration with ARS researchers from Beltsville, Maryland, ARS researchers in East Lansing, Michigan, identified possible resistance genes for RRCR in sugar beet, particularly polygalacturonase inhibitor protein genes (PGIPs). Polygalacturonases are proteins that break down the plant cell wall, especially pectins. When a common model plant, Nicotiana benthemiana (N. benthemiana), a relative of tobacco, was transformed with these genes, the plants showed reduced damage with a single isolate for the causal agent of RRCR, Rhizoctonia solani (R. solani). This model plant was tested with a range of fungal isolates because tests with host plants such as dry bean and beet have shown varied resistance responses to different strains, so screening was done to determine how widespread the interaction might be. Strains that varied in their effect on the N. benthemiana were used for sequencing, and candidate pectin-degrading genes (PGs) identified. Three R. solani strain types varied in PGs, with more found in the type that is most damaging to beet. Variable response was observed depending on the PGs in the fungus and the PGIPs in the host, similar to what has been observed in the dry bean system. Understanding this interaction may allow for targeted selection of resistance depending on the major pathogen type in the growing area. These results could help breeders develop resistant varieties and give new options for disease management to growers.
Review Publications
Pethybridge, S.J., Sharma, S., Hansen, Z., Kikkert, J.R., Olmstead, D.L., Hanson, L.E. 2020. Optimizing Cercospora leaf spot control in table beet using action thresholds and disease forecasting. Plant Disease. 104:1831-1840. https://doi.org/10.1094/PDIS-02-20-0246-RE.
Galewski, P.J., McGrath, J.M. 2020. Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences. BMC Genomics. 21:189. https://doi.org/10.1186/s12864-020-6451-1.
Pethybridge, S.J., Sharma, S., Hanson, Z., Vaghefi, N., Hanson, L.E., Kikkert, J.R. 2019. Improving the fungicide-based management of Cercospora leaf spot in table beet in New York. Canadian Journal of Plant Pathology. https://doi.org/10.1080/07060661.2019.1690048.
Kunert, A.T., Pohlker, M.L., Krevert, C.S., Wieder, C., Speth, K.R., Hanson, L.E., Morris, C., Schmale, D.G., Poschl, U., Frohlich-Nowoisky, J. 2019. Macromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processing. Biogeosciences. 16:4647–4659. https://doi.org/10.5194/bg-16-4647-2019.
Rosenzweig, N., Hanson, L.E., Jiang, Q., Mambetova, S., Guza, C., Stewart, J., Somohano, P. 2020. Temporal population monitoring of fungicide sensitivity in Cercospora beticola from sugarbeet (Beta vulgaris) in the Upper Great Lakes. Canadian Journal of Plant Pathology. https://doi.org/10.1080/07060661.2019.1705914.
