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ARS Home » Pacific West Area » Kimberly, Idaho » Northwest Irrigation and Soils Research » Research » Research Project #425141

Research Project: Improved Sugar Beet Germplasm and Innovative Disease Management Approaches to Increase Yield and Reduce Product Losses

Location: Northwest Irrigation and Soils Research

2017 Annual Report

1. Identify molecular markers and their genetic map positions for priority sugar beet traits, including host plant resistance to curly top, root rots, and abiotic stresses. [NP301, C1, PS1B] 1.1. Whole genome re-sequencing of sugar beet public breeding line KDH13 for genetic variation analysis. 1.2. Identify a large representative set of single nucleotide polymorphism (SNP) markers for genotyping of mapping populations and germplasm. 1.3. Construct high density genetic linkage map to identify DNA markers closely linked to genes regulating resistance to curly top. 2. Improve germplasm screening procedures for host plant resistance, and incorporate disease management options into production practices through enhanced understanding of plant pathogen etiology and interactions with host resistance, pests, and abiotic stresses. [NP303, C3, PS3A] 2.1. Investigate curly top species variation and/or the presence of new curly top species in sugar beet. 2.2. Refine management strategies for curly top and pest control in sugar beet. 2.3. Establish the etiology and management options for an Athelia-like fungus associated with stored sugar beet roots. 2.4. Characterize and exploit the interaction of Rhizoctonia solani and Leuconostoc mesenteroides in sugar beet root rot to improve disease management options. 2.5. Determine the effect of rhizomania in the field on freeze damage to sugar beet roots in storage. 3. Identify novel sources of host plant resistance to diseases (curly top, rhizomania, and root rots), storage, and abiotic stresses (drought and frost), and incorporate them into adapted germplasm. [NP301, C1, PS1A]

Establish a research program to coordinate, interact and collaborate with university scientists to provide sustainable integrated disease and pest management strategies for sugar beet. New sugar beet germplasm with enhanced disease resistance and agronomic qualities will be developed, along with innovative and improved disease management strategies. Specific focus has been placed on alleviating crop losses due to curly top, rhizomania, root rots, spoilage during storage, and seedling frost injury. Genetic research will identify molecular markers associated with curly top resistance and establish their genetic map position. Understanding the etiology of pathogens associated with curly top, rhizomania, root rots, and storage losses, i.e., fungal decay, will lead to improved disease management options and screening methods. Using genetic methods with germplasm from the disease screening nurseries (curly top, rhizomania, Rhizoctonia-bacterial root rot, and storage), we will identify novel genes regulating traits of interest ultimately leading to public release of improved germplasm. New germplasm will be used by the sugar beet industry to enhance disease resistance and improve yields in commercial cultivars. The new genetic and pathogen knowledge generated will also allow our stakeholders to reduce losses by improved disease and postharvest storage management.

Progress Report
Under Objectives 1 and 3, the array of differentially expressed genes (DEGs) from 56 comparisons between healthy plants and plants infested with beet leafhoppers infected by one, two or three of the Beet curly top virus (BCTV) strains was used to screen for BCTV. The DEG sequences were compared with known sequences in the GenBank to identify resistance gene analogues. A high level of cysteine-rich receptor like proteins, which accounted for up to 11% (171 members) of the significant DEG between resistant and susceptible lines, were identified. Additionally, several other gene-families linked to regulating metabolic pathways were identified. Confirmation of the digital comparison results were confirmed using sequence-based quantitative polymerase chain reaction analysis (qPCR). Sugar beet lines KEMS06, KEMS6-600 and KEMS08 were evaluated for Cercospora leaf spot, Fusarium wilt and Aphanomyces root rot for three seasons. These lines showed better resistance to Cercospora and Fusarium than the commercial resistant checks. These lines will be released and registered as parental lines by the end of 2017. KDH4-9 will be released as new genetic stock for curly top resistance. Transfer of curly top resistance genes from KDH13 to other valuable germplasm has been proven. These populations will be used for selection, development and release of multi-trait germplasm. Seed was harvested from 56 doubled haploid lines that are homozygous for resistance to one of three diseases: curly top, rhizomania or Rhizoctonia root rot. These seeds will be the basis for future germplasm releases if novel genes can be found for disease resistance and other traits of interest. Additionally, they will be used for developing genetic mapping populations. Inbred lines were identified that exhibited differential responses to different BCTV-strains. This suggests that some sources of resistance to BCTV are strain specific. Additional experiments were conducted to assess resistance to single strains and combinations of strains using doubled haploid and inbred lines. If all sources of resistance prove to be strain specific, then a different resistance gene will be required for each strain. Also, all strains will need to be included when screening for resistance in order to maintain resistance under commercial production. Breeding lines KPS24 and KPS25, which have high sucrose content (>20%), were evaluated under field conditions in 2016 and 2017, and high sucrose was confirmed. Both lines were hybridized with KDH4-9 and KEMS12 to incorporate curly top and rhizomania resistance genes, respectively. The progenies of these crosses were evaluated in 2017. Several breeding lines were evaluated for frost tolerance and the ability to survive through the winter. Mutant line KEMS12 was identified as frost tolerant and winter-hardy. This line regrew in the spring without bolting and produced normal harvestable roots. The mature roots that overwintered were vernalized to induce flowering and seed production. Enough seed was produced to conduct a field trial to evaluate sucrose production from this line when it is planted in the fall of 2017 and harvested in the fall of 2018. Planting sugar beet in the fall would extend the growing season and reduce complications or delays that occur due to weather in the spring. Advanced inbred lines and doubled haploid lines were identified for release. Breeding parental lines KEMS06, KEMS06-600 and KEMS08 are mutants with resistance to Cercospora. Additionally, advanced inbred lines (F5) were developed with combined resistance to BCTV and Beet necrotic yellow vein virus, and segregating populations were produced for combined BCTV resistance and high sucrose traits. In support of Objective 2, a survey to investigate the current BCTV population in Idaho was conducted. When compared with samples collected in an earlier survey (2006-2007), there has been a reduction of the Severe strain in commercial sugar beet fields. Based on whole genome sequencing, the Severe and California/Logan primer sets appear to be strain specific. However, the Worland primer set detects the Worland, Colorado, and Kimberly1 strains. Whole genomes have been sequenced for 69 isolates and deposited in GenBank. The paper establishing 11 strains for BCTV (including the Kimberly1 strain) and the survey results were recently published. Isolates of three BCTV strains were provided to the University of Idaho where agro-inoculation clones were developed. These data will help to develop new management options for curly top in sugar beet. Seed and foliar insecticide treatments to control the beet leafhopper vector for BCTV were evaluated and the length of efficacy was established for the two most promising products (Poncho as a seed treatment and Asana as a foliar treatment). The Poncho seed treatment could still reduce BCTV symptoms 77 days after planting, while Asana reduced symptoms for at least 28 days after application. To build upon these initial studies, an additional experiment was initiated to identify new products with different chemistries. The studies conducted to establish new management options to reduce sucrose losses from sugar beet storage were successful and published. The predominant fungi isolated from symptomatic roots were an Athelia-like sp., Botrytis cinerea, Penicillium spp., and Phoma betae. Additional studies have identified the distribution of the three predominant fungi in outdoor and indoor sugar beet storage piles in Idaho. Pathogenicity tests and strain identification studies for these fungi were completed. A novel Penicillium sp. was found in this work and published as Penicillium cellarum Strausbaugh & Dugan, sp. nov. A study to determine the influence of rhizomania on freezing of sugar beet roots was conducted. The fungi isolated from the root lesions were primarily Botrytis cinerea, Penicillium spp., and Phoma betae.

1. A novel Penicillium sp. causing rot in stored sugar beet roots was discovered in Idaho. Penicillium vulpinum, along with a number of other fungi, can lead to rot of stored sugar beet roots. ARS researchers at Kimberly, Idaho, determined that the Penicillium isolates associated with necrotic lesions on sugar beet roots in storage study were different from P. vulpinum and other recognized Penicillium species. A polyphasic taxonomic approach utilizing both molecular data and macro- and micromorphological characteristics determined the sugar beet isolates were a new species designated as Penicillium cellarum. These data will allow for more targeted management of root rots of stored sugar beet roots.

2. Beet curly top virus strains associated with sugar beet. Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by beet curly top virus (BCTV). BCTV is primarily controlled through host resistance, but effectiveness for some sources of resistance appear to be strain specific. ARS researchers at Kimberly, Idaho, conducted a survey from 2012 to 2015 and determined that there was a shift from the Severe strain being dominant in commercial sugar beet fields in 2006 to being undetectable at times during recent years. Eleven new BCTV strains were identified during the recent survey, including the strain Kimberly1. If the California/Logan, Colorado, and Worland BCTV strains continue to predominate in sugar beet, the host resistance genes for these strains should be a priority for incorporation into commercial sugar beet plants.

3. Development of DNA markers to detect Beet Curly Top Virus resistance. Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by beet curly top virus (BCTV). Currently the only method to select parental lines with resistance to BCTV is a direct destructive method of infecting plants with the virus. Developing DNA markers from genic regions or genes that regulate the trait would be the ideal method to screen for BCTV resistance. A large pool of differentially expressed genes were obtained and the CRK8-gene family showed consistent overexpression caused by infection with three BCTV strains. Quantitative polymerase chain reaction (qPCR) analysis supported the digital analysis and DNA markers were developed to identify hybrids in the absence of morphological markers between parental lines. The deployment of these markers expands the possibilities of using hybridization between many parental lines to detect BCTV resistance.

Review Publications
Strausbaugh, C.A., Eujayl, I.A., Martin, F.N. 2016. Pathogenicity, vegetative compatibility, and genetic diversity of verticillium dahliae isolates from sugar beet. Canadian Journal of Plant Pathology. 38(4):492-505.
Strausbaugh, C.A., Panella, L.W. 2017. Beet curly top resistance in USDA-ARS plant introduction lines, 2016. Plant Disease Management Reports. 11:V082.
Eujayl, I.A., Strausbaugh, C.A. 2017. Beet curly top resistance in USDA-ARS Kimberly sugar beet germplasm lines, 2016. Plant Disease Management Reports. 11:V081.
Strausbaugh, C.A., Eujayl, I.A., Wintermantel, W.M. 2017. Beet curly top virus strains associated with sugar beet in Idaho, Oregon, and a Western U.S. collection. Plant Disease. 101:1373-1382.
Panella, L.W., Strausbaugh, C.A. 2016. Ft. Collins sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2015. Plant Disease Management Reports. 10:FC168.
Strausbaugh, C.A., Wambolt, C. 2016. Commercial sugar beet cultivars evaluated for rhizomania resistance and storability in Idaho, 2015. Plant Disease Management Reports. 10:FC187.
Strausbaugh, C.A., Wambolt, C. 2016. Experimental sugar beet cultivars evaluated for rhizomania resistance and storability in Idaho, 2015. Plant Disease Management Reports. 10:FC186.
Eujayl, I.A., Strausbaugh, C.A. 2016. Kimberly sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2015. Plant Disease Management Reports. 10:FC185.
Panella, L.W., Strausbaugh, C.A. 2017. Evaluations of Ft. Collins sugar beet germplasm for rhizomania and storage rot resistance in Idaho, 2016. Plant Disease Management Reports. 11:FC101.
Panella, L.W., Strausbaugh, C.A. 2017. Beet curly top resistance in USDA-ARS Ft. Collins germplasm, 2016. Plant Disease Management Reports. 11:V084.