Location: Northwest Irrigation and Soils Research
2025 Annual Report
Objectives
Objective 1: Identify traits with the potential to increase productivity and sustainability of sugar beet while reducing economic losses due to beet curly top, Rhizoctonia root rot, rhizomania, postharvest storage losses, Cercospora leaf spot, and frost.
Sub-objective 1.A: Develop elite germplasm with novel sources of resistance to BCTV, C. beticola, R. solani, BNYVV, and storage rots.
Sub-objective 1.B: Develop sugar beet lines with freezing/frost protection.
Objective 2: Develop new sugar beet genetic stocks and breeding lines capable of resolving the genetic determinants of agriculturally important traits, and provide the material and markers to breeders for efficient trait utilization.
Sub-objective 2.A: Generate experimental populations for gene discovery.
Sub-objective 2.B: Generate new and novel agronomically important traits using DNA mutagenesis.
Objective 3: Create in-depth genomic resources that are trait-focused and apply molecular genetics methods to decipher the molecular mechanisms, genes, and gene products influencing important phenotypic variation.
Sub-objective 3.A: Delineate molecular mechanisms related to diverse traits in sugar beet genotypes exhibiting CLS and rhizomania resistance and the non-bolting phenotype.
Sub-objective 3.B: Evaluate the role of sugar beet host-associated bacterial and fungal microbiome in resistance against beet curly top, rhizomania, and post-harvest storage quality.
Sub-objective 3.C: Investigate the interaction between different sugar beet germplasm sources and strains of BCTV found in sugar beet to identify different sources of resistance and how their gene expression and molecular resistance mechanisms may differ.
Sub-objective 3.D: Develop additional management strategies for beet curly top and pest control in sugar beet.
Approach
The Sub-objective 1A research goal is to release elite sugar beet germplasm with novel sources of resistance to Beet curly top virus (BCTV), Rhizoctonia solani, Beet necrotic yellow vein virus (BNYVV), Cercospora beticola,and storage rots. To achieve this goal PI lines and breeding populations will be characterized for their resistance level by screening in disease nurseries. Additional screening will be conducted on germplasm not previously investigated, if novel sources are not found initially.
The Sub-objective 1B research goal is to release elite sugar beet germplasm with freezing/frost tolerance by using a leaf syringe agroinfiltration system to transiently express recombinant proteins in sugar beet leaves. Tobacco or Arabidopsis could be utilized to characterize these proteins, if sugar beet is uncooperative.
The Sub-objective 2A research goal is to discover novel disease resistance genes by screening progeny of F2 derived, synthetic, and recurrent selection populations, and F3 families in disease nurseries. If extreme weather events are encountered, enough seed will always be saved to allow for additional plantings.
The Sub-objective 2B research goal will be to generate new agronomically important traits (such as frost tolerance, non-bolting, etc.) through DNA mutagenesis and link them to specific loci in the sugar beet genome. If no beneficial mutations are identified, the M2 and M3 lines can still be useful for discovery of important genes through loss of function.
Sub-objective 3A will test the hypothesis that mutation-induced changes in gene expression and protein/metabolite production in the sugar beet lines will positively affect pathogen resistance and negatively affect bolting. Genomic analysis of sugar beet EMS mutant lines when combined with RNAseq, proteomics, and metabolite analysis will provide genomic markers associated with the trait of interest. If something unexpected happens with the experiments, we have sufficient seed to replicate the experiments.
Sub-objective 3B will test the hypothesis that host plant specific microbiome can positively affect disease resistance. Sugar beet leaf microbiome changes based on 16S and ITS sequencing in response to BCTV, BNYVV, and post-harvest storage will be investigated in resistant and susceptible lines. If something unexpected happens with the experiments, we have sufficient seed to replicate the experiments.
Sub-objective 3C will test the hypothesis that sugar beet cultivars/lines with different sources of resistance will vary in their response to BCTV strains. BCTV clones will be infiltrated into sugar beet leaves to evaluate their responses in lines previously shown to exhibit differential responses to BCTV strains. If the leaf-infiltration clones prove to be unstable, stab-inoculation clones can be used.
Sub-objective 3D will test the hypothesis that seed and foliar insecticide treatments can be used to supplement or extend the control of BCTV and pests beyond that provided by neonicotinoid seed treatments and host resistance by screening in field plots. If extreme weather events are encountered, enough seed will always be saved to allow for additional plantings.
Progress Report
This report documents the progress for project 2054-21220-006-000D, Decipher Molecular Mechanisms for Genetic Variations in Agronomically Important Traits to Improve Sugar Beet Disease Resistance and Yield, which began in January 2023.
In support of Objective 1, 48 plots were used for genetic screening of eight sugar beet lines for Beet curly top virus (BCTV) resistance under field conditions. Two new breeding lines developed by ARS researchers at Kimberly, Idaho, exhibiting strong curly top resistance will be released next year.
For Objective 2, progress has been made in 2025 to identify and develop Cercospora leaf spot (CLS) resistance traits into USDA breeding populations. The CLS resistance trait from KEMS06 was introgressed into important Kimberly sugar beet breeding germplasms. Characterization of KCercS06, the Cercospora susceptible sibling cohort line of KEMS06, was performed. These two lines are nearly isogenic to each other but differ in their Cercospora resistance. This is a significant resource for sugar beet disease resistance breeding as it allows mapping the genetic determinants in the genome responsible for the Cercospora resistance trait in KEMS06. Progress has also been made in the introgression of CLS from KEMS08 (PI 683816), another important breeding line developed at Kimberly that possesses higher resistance than KEMS06, into several USDA breeding lines and hybrid populations. Heritability of the KEMS08 CLS resistant trait is being tracked following the methodology used with the KEMS06 germplasm. Over the past year, ARS researchers have backcrossed male sterile KEMS08 lines so that they have bulk seed with 50% male sterile trait ratio. This is currently being leveraged to determine the dominant/recessive nature of the CLS resistance trait for stakeholders when released.
To assist sugar beet breeders in introgressing the Cercospora resistance traits from KEMS06 and KEMS08 into elite cultivars, ARS researchers identified unique Single Nucleotide Polymorphisms (SNPs) associated with these lines through next generation sequencing, and the SNPs were incorporated into a 4,000 SNP panel array (4K Chip). The 4K Chip project is a collaborative effort between ARS sugar beet researchers at Fort Collins, Colorado; East Lansing, Michigan; Fargo, North Dakota; Kimberly, Idaho; and Madison, Wisconsin. The goal of the 4K Chip project is to build a unified high throughput SNP array marker assisted selection (MAS) pipeline to expedite sugar beet breeding.
Under Objective 3 ARS researchers at Kimberly, Idaho, used different multi-omics tools to dissect mechanisms of genetic resistance in a sugar beet double haploid breeding line developed at Kimberly, KDH4-9, that shows strong Beet curly top virus (BCTV) resistance. Graded-pool whole-genome sequencing, transcriptome, and metabolome analysis were used to rapidly map quantitative trait locus (QTL) in a mapping population resulting from a genetic cross between KDH4-9 and a susceptible line. Resistance associated QTLs were found to be primarily localized in chromosome 3 along with a few minor QTLs localized in chromosomes 1 and 2. The putative genomic markers associated with resistance in KDH4-9 will be valuable for future trait introgression into commercial cultivars by sugar beet seed companies.
Nanoparticles, namely silica nanoparticles that are ecofriendly and possess antiviral, insecticidal, and plant growth promoting properties, are currently being evaluated alone or in combination with pyrethroid insecticide (Asana) to identify possible alternatives to neonicotinoid insecticides against BCTV under field conditions. In addition, CRISPR inhibition (CRISPRi) transgenic sugar beet plants targeting critical BCTV genome elements have been advanced to generate F1 seeds for future characterization of BCTV resistance in these transgenic lines.
Using genome and transcriptome sequencing, whole genome assembly, along with metabolome analysis, putative mechanisms and genes associated with rhizomania resistance in the KEMS12 mutant line (developed at Kimberly, Idaho) were identified. This line was shared with a sugar beet seed company for further evaluation of resistance against European beet necrotic yellow vein virus strains. The information obtained from this work will improve rhizomania resistance in commercial cultivars by using this mutant line as potentially a new source of resistance. A manuscript related to this work has been submitted.
A QTL mapping method using graded-pool whole-genome sequencing and transcriptome analysis of an F1 population resulting from a genetic cross between KEMS12 and a susceptible line exhibiting resistance and susceptibility, was implemented. Resistance associated QTLs were primarily found to be localized in chromosomes 2, 6, and 8. The putative rhizomania resistance markers identified in KEMS12 will be valuable for future trait introgression into commercial cultivars by sugar beet seed companies.
New mechanisms involving the role of Beet necrotic yellow vein virus (causal agent for rhizomania), derived small non-coding RNAs, in viral pathogenicity and counter resistance mechanisms in the KEMS12 line were demonstrated. A manuscript related to this work has been submitted. Viral genes potentially associated with pathogenicity are currently being targeted using RNA interference (RNAi) technology to develop transgenic sugar beet lines with improved rhizomania resistance.
Methods to control post-harvest storage loss (which can account for greater than 55 percent loss of sucrose) in sugar beets are limited and not highly efficient. The efficacy of an ecofriendly and convenient physical treatment, cold plasma, to improve long term post-harvest indoor storage was demonstrated. Lower doses of cold plasma reduced disease symptoms by 30-54 percent and higher dose increased (16-25 percent) biomass retention. Sucrose retention increased (up to 18 percent), depending upon dose and genotype. Microbiome analysis showed a reduction in pathobiome such as Proteobacteria, Basidiomycota in cold plasma treated samples. Metabolome analysis showed enrichment of glycerophospholipid metabolites. The results demonstrate the potential of cold plasma technology and its future application at the commercial level.
A panel of previously sequenced wild sugar beet relatives (Beta Vulgaris subsp. Maritima) representing diverse geographic locations across Europe and the Mediterranean area was investigated for cold tolerance. Using environmental variables associated with their geolocations, ARS researchers were able to associate genotypes possibly linked to freezing tolerance and to identify putative genetic markers. Seeds of germplasm representing environmental extremes have been acquired and are currently being evaluated for freezing tolerance. This will aid in future introgression of freezing tolerance trait in sugar beet breeding lines possessing other economically important traits. A vector construct to overexpress a Lolium perenne ice recrystallization inhibition protein-like (IRI3) gene in sugar beet is currently underway. This gene has been shown to confer freezing tolerance in Arabidopsis, tomato, and potato.
Historical data related to wind events, air temperature patterns, vegetation, and disease incidence in sugar beet were used to demonstrate large scale dispersal of beet leafhopper. Combining wind and temperature forecasts in the future could be a valuable tool for timely spraying of insecticides to control beet leafhopper in sugar beets in the future.
Accomplishments
1. Identifying Neonicotinoid insecticide alternatives to control Beet curly top virus in sugar beet. Sugar beet is highly susceptible to the Beet curly top virus (BCTV) which is transmitted by the insect pest, beet leafhopper. BCTV significantly reduces sugar yield in semi-arid growing regions in the U.S. Neonicotinoid insecticide seed treatments are extremely effective but potentially face regulatory restrictions. ARS researchers in Kimberly, Idaho, evaluated alternative treatments with phytohormones, namely jasmonic acid and methyl jasmonate, in combination with pyrethroid insecticide, the current best alternative to neonicotinoids. Combining phytohormones with pyrethroid insecticide reduced BCTV symptoms by negatively affecting virus transmission by the insect vector and increased root and sugar yield by 22-24% compared to pyrethroid insecticide alone. This research establishes an effective treatment option for controlling BCTV in sugar beet if future use of neonicotinoid insecticides is restricted.
2. New resistance to Rhizoctonia crown and root rot and rhizomania discovered in sugar beet breeding lines. Rhizomania and Rhizoctonia crown and root rot in sugar beet result in significant loss of root yield and sugar production. Genetic sources of resistance to both diseases are highly limited. ARS researchers at Kimberly, Idaho, identified potential new sources of genetic resistance to these diseases through evaluations in disease nurseries under natural infection conditions. This work can be used by sugar beet seed companies to improve resistance to rhizomania and Rhizoctonia crown and root rot in commercial cultivars.
3. Identified markers associated with improved post-harvest disease resistance in sugar beet. Fungal and bacterial diseases account for more than 20% of sugar beet sucrose loss during indoor storage. ARS researchers at Kimberly, Idaho, determined the role of the root microbial community and metabolites in disease resistance in southern Idaho commercial indoor storage buildings. Putative microbial and metabolite-related markers associated with improved post-harvest disease resistance were identified using global analysis of root microbes and metabolites in resistant and susceptible sugar beet germplasms. This work will be used to prioritize future breeding strategies by sugar beet seed companies to reduce storage losses.
4. Fungal pathogens found in outdoor sugar beet piles in Idaho can impact human health as well as cause sugar loss. Sugar beet roots in outdoor storage piles are subjected to fungal growth causing significant sugar loss. ARS researchers at Kimberly, Idaho, assessed incidence, distribution, and pathogenicity of fungi associated with outdoor storage piles in southern Idaho. Cladosporium spp. were the only fungi detected on the root surface of uncovered piles and Cladosporium spp. and Botrytis cinerea were detected in covered piles. Pathogenicity tests demonstrated Botrytis cinerea caused the most rot, while Cladosporium spp. caused little to no rot. This work will guide management strategies to prevent sugar losses in outdoor piles. This research also suggests that workers should take precautionary measures because Cladosporium spp. is known to affect human health.
Review Publications
Vincill, E.D., Eujayl, I.A., Majumdar, R., Strausbaugh, C.A. 2025. Introgression of the Cercospora leaf spot (CLS) disease resistance trait from KEMS06 sugar beet germplasm into two double-haploid breeding lines, KDH4-9 and KDH13. Journal of Sugar Beet Research. 62(1):2-16. https://doi.org/10.5274/jsbr.62.1.2.
Strausbaugh, C.A., Wenninger, E.J., Jackson, L.K., Vincill, E.D. 2024. Host and shelter plants for the beet leafhopper, which vectors curly top viruses and phytoplasmas in southern Idaho. PhytoFrontiers. 4(4):591-601. https://doi.org/10.1094/PHYTOFR-03-24-0022-R.
Majumdar, R., Kandel, S.L., Strausbaugh, C.A., Singh, A., Pokhrel, S., Bill, M. 2024. Root microbiome and metabolome traits associated with improved post-harvest root storage for sugar beet breeding lines under southern Idaho conditions. International Journal of Molecular Sciences. 25(23). Article 12681. https://doi.org/10.3390/ijms252312681.
Strausbaugh, C.A., Wenninger, E.J., Jackson, L.K., Vincill, E.D. 2024. Wind-mediated dispersal of beet leafhoppers and pine pollen in southern Idaho. PhytoFrontiers. 4(4):498-503. https://doi.org/10.1094/PHYTOFR-06-24-0073-SC.
Strausbaugh, C.A. 2025. Incidence, distribution, and pathogenicity of fungi growing on sugar beet roots on top of outdoor piles in Idaho. Plant Disease. 109(7):1478-1488. https://doi.org/10.1094/PDIS-12-24-2663-RE.
Strausbaugh, C.A., Majumdar, R., Vincill, E.D. 2025. Commercial sugar beet cultivars evaluated for rhizomania resistance and storability in Idaho, 2023. Plant Health Progress. 26(1):116. https://doi.org/10.1094/PHP-12-24-0148-PDMR.
Strausbaugh, C.A., Chu, C.N. 2025. Fargo sugar beet germplasm evaluated for Rhizoctonia crown and root rot resistance in Idaho, 2024. Plant Health Progress. 26(2):244. https://doi.org/10.1094/PHP-01-25-0029-PDMR.
Majumdar, R., Strausbaugh, C.A., Wenninger, E.J. 2025. Foliar and seed treatment products for the control of beet curly top in Idaho sugar beet, 2024. Plant Health Progress. https://doi.org/10.1094/PHP-02-25-0042-PDMR.
Strausbaugh, C.A., Majumdar, R., Vincill, E.D. 2025. Experimental sugar beet cultivars evaluated for rhizomania resistance and storability in Idaho, 2023. Plant Health Progress. 26(2):243. https://doi.org/10.1094/PHP-12-24-0149-PDMR.