Progress 10/01/22 to 09/30/23
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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. Artificial Intelligence (AI)/Machine Learning (ML) No work in this area at the location in FY 23. ACCOMPLISHMENTS 01 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.
Impacts
(N/A)
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.
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Progress 10/01/21 to 09/30/22
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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 01 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.
Impacts
(N/A)
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.
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Progress 10/01/20 to 09/30/21
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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. Record of Any Impact of Maximized Teleworking Requirement: The program has been delayed in greenhouse projects and screening limited on ability to produce new materials in the greenhouse and growth chambers. Because of limited access, we were unable to inoculate some greenhouse trials in a timely manner. Those plants grew too old for using (would have been a very different age than other times through the experiment). Thus, we have had to restart plants or delay experiments. We also experienced delays in contacting others, such as sources of potential germplasm and APHIS regulators for movement of materials. We were able to hire a new geneticist, but travel and telework restrictions delayed arrival. That, along with shipping and hiring delays, has slowed the ability to get the breeding program going. ACCOMPLISHMENTS 01 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.
Impacts
(N/A)
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.
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Progress 10/01/19 to 09/30/20
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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 01 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.
Impacts
(N/A)
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.
- 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.
- 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.
- 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.
- 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.
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Progress 10/01/18 to 09/30/19
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Nucleotide-binding (NB-ARC), leucine-rich-repeat genes (NLRs) account for 60.8% of resistance (R) genes molecularly characterized from plants. NLRs exist as large gene families prone to tandem duplication and transposition, with high sequence diversity among crops and their wild relatives. This diversity can be a source of new disease resistance. Using the conserved NB-ARC domain as a model, 231 tentative NB-ARC loci were identified in a highly contiguous genome assembly of sugar beet, revealing diverged and truncated NB-ARC signatures as well as full-length sequences. Comparison of sugar beet NB-ARC domains to validated R genes from monocots and eudicots suggested extensive B. vulgaris-specific subfamily expansions. The NLR landscape in the rhizomania resistance Rz region of Chromosome 3 was characterized, identifying 26 NLR-like sequences spanning 20 Megabases of genome sequence. This work presents the first detailed view of NLR family composition in a member of the Caryophyllales, builds a foundation for additional disease resistance work in Beta vulgaris, and demonstrates an additional nucleic-acid-based method for NLR prediction in non-model plant species. 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. The Great Lakes production region is experiencing increasing issues with foliar leaf spots. In the 2018 season, a combination of three foliar diseases was estimated to cause over $27 million in losses to the local industry (Michigan Sugar company personal communication). One of these, Cercospora leaf spot, has been a long term issue. An ongoing collaboration to examine diversity and management of this disease has been expanded to additional labs and research. We found the pathogen can be present much earlier than previously known. This information is being used to modify current management recommendations. Another major leaf spot, Alternaria leaf spot, was determined by our program to be an increasing problem in the region starting in 2010. Since 2016, it has been contributing to economic losses, especially in parts of the growing region where Cercospora leaf spot has been less of an issue. There is limited information on the pathogen(s) causing Alternaria leaf spot. Our research indicates the strains from sugar beet are similar to isolates from Solanaceous crops, and can cause disease on tomato, potato, as well as other rotation crops in the region such as dry bean. A better understanding of this interaction can aid in management of this new issue. We also were able to produce disease with both the field and greenhouse inoculations. This allows us to improve screening of sugar beet germplasm from the breeding program. Germplasm was identified that showed varying susceptibility to Alternaria after inoculation. The methods need improvement for consistency, but show potential for identification of resistance in the USDA breeding material and commercial lines. As well as leaf spots, root rots and other soil-borne diseases remain a constraint on beet yield. We have initiated testing of genetic markers for one of the major soil-borne pathogens that were developed in our lab, and found high variability within fields. This will be further tested for utility to compare management methods and crop rotation for their impact on sugar beet pathogens. In 2018, Fusarium yellows was identified in a number of fields in Michigan. This has been limited in the region, but may be increasing. Isolates have been collected and are being compared to isolates from other growing regions. Sugar beet germplasm is being screened for disease reaction for all disease pressures in the Great Lakes region. 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). Sugar accumulation is a complex trait, and varies by crop-type. Measures of diversity and differentiation across the beet genomes detected regions involved in sugar accumulation, and significantly, identified the genes controlling sugar accumulation. Annotations of these genes suggest differences in development, physiology, and metabolism underlie crop-type differentiation. This information is essential for improving beet quality traits, as well as recovering specific crop-types after wide hybridization with crop wild relatives to access useful and novel disease resistance genes. Accomplishments 01 Genetics of crop-type differences in beet. Diversification in end use is a hallmark in a number of crop species. Beta vulgaris is a species complex composed of diverged populations including sugar, fodder, table, and leaf (chard) cultigroups. Using population genetic and statistical methods on whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, ARS researchers in East Lansing, Michigan, and colleagues determined relationships between accessions based on identity-by-state and shared genetic variation. Extensive shared (e.g. non-unique) genetic variation was seen within and between cultigroups. Lineage specific variation within crop-types supported a shared demographic history within each cultigroup, while analysis revealed strong cultigroup differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation within a cultigroup. This information is being used by sugar beet and table beet breeders to better delineate target traits, modify selection schema, and develop haplotype markers for better breeding efficacy. 02 Assess diversity among Alternaria species, a sugar beet pathogen becoming of high priority to the Great Lakes. Alternaria leaf spot on sugar beet historically was a minor issue in the United States, with little need to manage the disease. Since 2016, researchers in East Lansing, Michigan, have found this disease has been causing increasing economic losses in the Great Lakes region. Using a combination of molecular and morphological methods, a high level of fungicide resistance was found in Alternaria isolates from sugar beet in the Great Lakes region, which likely contributes to increased disease levels in growers' fields. Isolates were found to belong to the Alternaria alternata species complex. This is a different species than was reported on sugarbeet in the Western United States and shows similarity to species affecting other crops such as potato. Isolates from sugar beet could infect both potato and tomato, with at least one isolate screened showing high virulence on all three crops. This information is being used to help develop management recommendations and to select isolates for use in screening of sugar beet germplasm for disease susceptibility.
Impacts
(N/A)
Publications
- Broccanello, C., Chiodi, C., Funk, A., McGrath, J.M., Panella, L.W., Stevanato, P. 2018. Comparison of three PCR-based assays for SNP genotyping in sugar beet. Plant Methods. 14:28.
- McGrath, J.M., Panella, L.W. 2019. Sugar beet breeding. In: Panella, L.W., editor. Plant Breeding Reviews. Volume 42. Somerset, New Jersey: John Wiley & Sons, Inc. p. 167-218.
- Rosenzweig, N., Hanson, L.E., Mambetova, S., Jiang, Q., Guza, C., Stewart, J., Somohano, P. 2019. Fungicide sensitivity monitoring of Alternaria spp. causing leaf spot of sugarbeet (Beta vulgaris) in the Upper Great Lakes. Plant Disease.
- Wang, J., Sang, H., Jacobs, J.L., Oudman, K.A., Hanson, L.E., Chilvers, M. 2019. Soybean sudden death syndrome causal agent Fusarium brasiliense present in Michigan. Plant Disease. 103:1234-1243.
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Progress 10/01/17 to 09/30/18
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Annotating the beet genome followed repeat masking, ab initio gene finding based on transcript evidence, and resolution to consensus- predicted gene models using the MAKER annotation pipeline. Results predicted 24,255 proteins, 88.5% of the 27,421 predicted in RefBeet. Transcript evidence for gene prediction was derived from C869 (the EL10 progenitor) developing roots (3 � 10-weeks post-germination), mature leaves, and seedlings of other germplasm germinated under aqueous stress conditions, including 150 mM NaCl, 0.3% hydrogen peroxide, and biologically extreme temperatures (10 and 41 degrees Celsius). Transcript sets also included young leaves and the set of transcripts used for annotating RefBeet. For putative functional annotation, three sources were used, in the priority: 1) UniProt, 2) Pfam-A, and 3) Uniref90. If no functional annotation was found in these three highly curated sets, proteins were assigned to the class �hypothetical' proteins. These reasonably stable protein annotations were used to estimate features of the coding portion of the EL10.1 genome assembly. 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. Root rots are a perennial constraint on beet yield and have been identified as the most important yield-limiting diseases affecting beets. The same root pathogens are known to affect several rotation crops. Interactions between pathogens of beet, as well as between beet pathogens and rotation crop pathogens, are not well understood. To improve the ability to examine interactions and the effects of crop rotations, a set of genetic markers were developed to examine pathogen diversity and rapidly identify known strains, especially in the pathogenic fungi Rhizoctonia solani and Fusarium species. Initial testing indicates high diversity in sugar beet isolates. Isolates are being collected from other hosts, and additional regions, including other ARS research locations. One of the newly identified pathogens on sugar beet in the region, a Colletotrichum species has now been identified multiple years, with samples also being submitted to the national plant diagnostic network lab in the region. These are being characterized as a new disease in the area that affects seedlings as well as causing a mild leaf spot. In addition to root rots, foliar diseases are a re-emerging issue in the industry as current management options show reduced efficacy. Sensitivity to three of the major fungicides used for Cercospora leaf spot management has been decreasing, and disease control failures were reported in the Great Lakes region. This has put an increased emphasis on identification of host resistance and understanding the disease cycle. Ongoing tests show infective spores are present earlier than previously thought, which is affecting timing of management applications. In addition to Cercospora leaf spot, Alternaria leaf spot has been increasing in the region, and currently is recognized as a recurring issue in Michigan. Isolates from the area show tolerance to all three of the major fungicides used for foliar disease management. Efforts are ongoing to develop a screening method for variety response to Alternaria. 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. The EL10 genome was leveraged to explore synteny beet and other plants (synteny: from the Latin "same strand", meaning genes that have common, linked chromosome positions across two or more species). Three species related to beet [Caryophyllales; Amaranthaceae, aka Chenopods (=goose foot)]; Amaranthus hypocondriacus, Chenopodium quinoa, and Spinacia oleracea, as well as two unrelated Rosid species [Vitis vinifera (grape) and Arabidopsis thaliana (a model plant)] were compared for genes that have retained genetic linkage through their evolutionary histories. Collinear blocks were identified using the program MCScanX, which uses a reciprocal blast between predicted protein datasets. Genome evolution within the Caryophyllales showed significant genome variation in chromosome numbers, the number of syntenic regions, and the sizes of syntenic regions relative to beet. On average, genome variability increased with phylogenetic distance. A greater number of syntenic regions with fewer members per region were found in species that resolve more distantly from sugar beet. Accomplishments 01 Reclassification of Rhizoctonia with molecular insights. Root rots have been a major constraint on beet yield for many years and have been identified as the most important yield-limiting diseases affecting beets. Root rot pathogens affecting beet show high genetic variability that does not relate to current methods of classification. Molecular testing of Rhizoctonia solani, done in collaborative work by ARS scientists in East Lansing and Salinas, California has identified three genetically distinct groups that affect beet rather than the two groups used in previous classification and has shown the prior groups are not relevant based on genetic relatedness. New classification methods allow for improved tracking of the pathogens as well as for investigation of the interaction with beet and rotation crops which may help to explain some of the variability in strains found in different growing regions. Research in East Lansing has shown a correlation between these genetic groups and variable responses with crop growth stage for at least one rotation crop, dry bean. Varied responses will allow for targeted assessment of differences in the crop at these growth stages that could aid in resistance breeding in the future. It also allows for assessment of alternative disease management strategies, such as impact of crop rotation on the pathogen population. The research is causing interest in other locations, with ARS scientists, university researchers, and company breeders submitting isolates for characterization within the new phylogenetic schema and asking for assistance in identifying the types of R. solani in their growing regions or being used in breeding programs.
Impacts
(N/A)
Publications
- Pethybridge, S.J., Kikkert, J.R., Hanson, L.E., Nelson, S.C. 2018. Challenges and prospects for building resilient disease management strategies and tactics for the New York table beet industry. Agronomy. 8:112.
- Funk, A., Galewski, P., McGrath, J.M. 2018. Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome. Plant Journal. 95(4):659-671.
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