Location: Northwest Irrigation and Soils Research
2023 Annual Report
Objectives
1. Develop genetic markers that will allow for marker-assisted breeding; develop superior sugar beet germplasm with priority traits, such as high sucrose and resistance to various diseases; and release improved breeding materials, including doubled haploid lines, inbred lines, and genetic mapping populations.
1.1. Develop elite germplasm with curly top, Rhizoctonia crown and root rot (RCRR), Cercospora leaf spot (CLS), and storage rot resistance, and high sucrose and low impurities. (Eujayl, Strausbaugh)
1.2. Conduct whole genome sequencing of elite germplasm lines for genetic variation analysis for RCRR resistance. (Eujayl, Strausbaugh)
1.3. Establish a large complement of single nucleotide polymorphism (SNP) markers for genotyping mapping populations and germplasm for curly top and RCRR resistance. (Eujayl, Strausbaugh)
2. Dissect disease development pathways and host-pathogen interactions, and design improved disease management strategies and screening procedures in sugar beet.
2.1. Investigate the interaction between the most common Leuconostoc van Tiegham haplotypes and the various genetic subgroups of R. solani. (Strausbaugh)
2.2. Investigate the use of RNA interference (RNAi) for the control of Beet curly top virus (BCTV). (Strausbaugh, Eujayl)
2.3. Develop additional management strategies for curly top and pest control in sugar beet. (Strausbaugh)
Approach
The proposed research is a coordinated cooperative effort between USDA-ARS, university scientists, and industry partners which will improve sucrose yield in sugar beet production. Elite sugar beet germplasm will be developed to increase sucrose content, while reducing impurities and improving disease resistance and management options for Beet curly top virus (BCTV), Rhizoctonia solani, and storage rot fungi. The first objective is non-hypothesis research focused on improving or identifying novel traits of interest, releasing elite germplasm with these traits, and sequencing lines to map and develop markers for these traits. Genetic markers will allow for marker-assisted breeding and release of superior sugar beet germplasm. Backcrossing, mass selection, and recurrent selection will be used to produce populations and lines with disease resistance, low impurities, and high sucrose content. Doubled haploid lines from this germplasm will be used to produce hybrids and segregating populations for genetic mapping. Whole genome sequencing will be conducted using PacBio technology and optical mapping. This effort will be complemented with gene expression profiling via RNA-Seq and Iso-Seq to identify differentially expressed genes caused by R. solani infection. A large complement of single nucleotide polymorphism (SNP) markers for genotyping mapping populations and germplasm for curly top and Rhizoctonia crown and root rot resistance will be developed. If additional sources of high sucrose or disease resistance are needed, additional high sucrose parental lines and plant introduction accessions will be screened. The second objective is hypothesis driven research which advances our knowledge of disease development and interactions to improve disease management strategies and screening procedures in sugar beet production. The interaction between Leuconostoc and R. solani will be investigated, since Leuconostoc haplotypes will possibility vary in their ability to create more root rot through a synergistic interaction with genetic subgroups of R. solani. Root inoculations in field studies will be conducted with bacterial isolates representing the predominant haplotypes for L. mensenteroides and L. pseudomesenteroides and R. solani isolates representative of the diversity present in anastomosis groups found in sugar beet. Five weeks after inoculation, rotted tissue will be measured and the pH associated with that tissue will be established. Isolations from the leading edge of the rot from randomly selected roots will be conducted to complete Koch’s postulates. Based on the results from the interaction studies, fungal-bacterial combinations exhibiting the synergistic interaction will be evaluated further through inhibition and enzyme assays. To improve management options for BCTV, the use of RNA interference (RNAi) and foliar insecticides will be investigated. If RNAi proves successful, RNAi will also be investigated for the control of R. solani.
Progress Report
This the final report for project 2054-21220-005-000D, Development of Elite Sugar Beet Germplasm Enhanced for Disease Resistance and Novel Disease Management Options for Improved Yield, which has been replaced by a new project 2054-21220-006-000D, Decipher Molecular Mechanisms for Genetic Variations in Agronomically Important Traits to Improve Sugar Beet Disease Resistance and Yield.
In support of Objective 1, three breeding lines (PI683514, PI683515, and PI683516) were developed with better tolerance to Cercospora leaf spot than current commercial sugar beet cultivars. Additionally, these same breeding lines expressed high resistance to Fusarium yellows. In support of the efforts to improve curly top resistance, a large pool of differentially expressed genes was obtained and the CRK8-gene family showed consistent overexpression when plants were infected with Beet curly top virus (BCTV). Based on this research, DNA markers were developed to identify hybrids in the absence of morphological markers between parental lines. The deployment of these markers expands the possibility of using hybridization between many parental lines. A high-density marker set was also developed to track BCTV resistance based on PacBio sequences. The sequences were assembled to identify the specific variation underpinning the durable BCTV resistance within the KDH13 genome, which has superior resistance to BCTV. This sequencing established a high-density marker dataset distributed globally across the genome. These markers can be used to track genomic segments in populations where KDH13 is used as parental material to improve BCTV resistance in commercial sugar beet cultivars. Also in support of Objective 1, ARS researchers identified a mutant line (KEMS12-FP17) that can be planted in September in Kimberly, Idaho, survive the winter, and continue to grow in the spring. Only 28 percent (%) of the plants in the mutant line bolted, while 100% of the plants in the commercial cultivar bolted. This line may serve as a starting point to establish a combination of bolting resistance and frost tolerance in commercial sugar beet cultivars.
In support of Objective 2, ARS researchers investigated late season Rhizoctonia root rot in sugar beet which can lead to complete yield loss in Idaho. ARS researchers at Kimberly, Idaho, were the first to establish the interaction between Rhizoctonia and Leuconostoc and then conducted studies to better understand this interaction. Both isolations and tissue pH suggest late season sugar beet root rot is primarily associated with Leuconostoc and secondary organisms. However, damage was minor without both Rhizoctonia solani AG-2-2 and Leuconostoc strains present when internal rot initiates. Thus, if adequate resistance to R. solani is present in a sugar beet cultivar, little or no rot will be caused by Leuconostoc and other contaminants. These data serve to emphasize the need for incorporating good resistance to R. solani into commercial sugar beet cultivars. Also, by understanding the enzymes which lead to the disease becoming established, control measures can be developed to alleviate the problem. ARS researchers at Kimberly, Idaho, have identified the three enzymes (cellulase, polygalacturonase, and pectin lyase) associated with initiating this root rot problem. Global mRNAseq analysis identified candidate genes and highly co-expressed gene modules that might be critical in host plant defense and pathogenesis. In the future, targeting R. solani cell-wall-degrading enzymes could be an effective strategy to mitigate root damage and losses during its interaction with Leuconostoc.
Also in support of Objective 2, researchers determined that the primary fungi associated with sugar beet storage rot were Botrytis cinerea, Penicillium spp., and an Athelia-like sp. The primary Penicillium spp. were P. expansum and a previously undocumented species. Based on a polyphasic taxonomic approach utilizing both molecular data and macro- and micromorphological characteristics, the undocumented species was designated Penicillium cellarum Strausbaugh & Dugan, sp. nov. The Athelia-like sp. was also a fungus first discovered by ARS researchers in Kimberly, Idaho. The primary fungal pathogen on roots in indoor piles was B. cinerea, but the incidence of the fungi in outdoor piles varied with location and year. However, almost complete control of fungal growth in some outdoor piles could be achieved with the combination of tarps, ventilation pipe, and finding a location with access to cool ambient air. These data emphasize for the sugar beet industry that given the right location, mechanical control measures alone are adequate for management of fungal root rots even after 120 days in storage under ambient conditions.
Additional research focused on Curly top of sugar beet which is a serious, yield-limiting disease in semi-arid production areas caused by BCTV. BCTV is primarily controlled through host resistance, but effectiveness for some sources of resistance appears to be strain specific. Thus, agro-inoculation clones have been developed to assist investigations into the mechanisms controlling curly top resistance in sugar beet. The ARS researchers conducted a survey of commercial sugar beet fields for BCTV from 2012 to 2015 and determined that there was a shift from the Severe strain being dominant in 2006 to being undetectable at times during recent years. Through this study, a new strain of BCTV was identified and designated Kimberly. The role of sugar beet leaf bacteriome in resistance against BCTV was also investigated using sugar beet breeding lines developed at Kimberly that are resistant and susceptible to the virus. The leaf microbial community that might contribute to resistance against both BCTV and the insect vector that carries the virus was established. Specific bacterial strains (e.g. Brevibacillus sp.) identified in this study are being evaluated for their insecticidal and antiviral properties in sugar beets. These results will assist in the development of novel biocontrol strategies against the virus if the strains prove to be worthy of commercial development. Recently, the contribution of miRNA mediated regulation of metabolic pathways and cross-kingdom RNA interference (RNAi) was investigated for sugar beet resistance to BCTV, which will be useful in developing RNAi-based tools for limiting BCTV. Seed and foliar treatments to aid in the control of the BCTV vector, the beet leafhopper, were also investigated but these treatments were not more effective than the current best commercial insecticides.
Additional research on sugar beet storage focused on the influence of rhizomania caused by Beet necrotic yellow vein virus (BNYVV), a major yield-limiting disease of sugar beet that was found to also influence the roots ability to resist freezing. When comparing roots grown in soil with high BNYVV levels compared with those grown with trace levels, researchers determined that sugar beet roots of a BNYVV susceptible cultivar had elevated frozen tissue levels at both -3.3°C (7 to 63% with high BNYVV and 0% with trace) and -4.4°C (63 to 90% with high BNYVV and 13 to 27% with trace). No increase in frozen tissue occurred at higher temperatures or with BNYVV resistant cultivars. Consequently, BNYVV will not only lead to yield and sucrose loss in susceptible sugar beet cultivars, but also lead to more frozen root tissue as temperatures drop below -2.2°C. Based on these observations, the air used to cool sugar beet roots in nonfrozen piles throughout the winter should not drop below -2.2°C to maximize sucrose retention.
Accomplishments
