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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Research Project #425071

Research Project: Genetic Dissection of Traits for Sugar Beet Improvement

Location: Sugarbeet and Bean Research

2018 Annual Report


1a. Objectives (from AD-416):
Objective 1: Apply high-resolution genetic mapping and transcriptome profiling to identify genes in sugar beet and related species that contribute traits (e.g. early season development and stand persistence) to sustainable crop and biomass production. Sub-Objective 1.A: Generate genetic maps in the context of recombinant inbred lines (RILs). Sub-Objective 1.B: Discover genes via transcriptome profiling with emphasis on early season traits such as vigor, stand establishment, and transition from heterotrophic growth through sucrose accumulating capacity. Sub-Objective 1.C: Develop additional RIL and genetic populations and enhanced germplasm for release. Objective 2: Characterize diverse populations of root rotting pathogens of sugar beet at the molecular level, and identify genetic components that affect host-pathogen interactions to minimize disease losses. Objective 3: Develop improved screening methods that provide better resolution of young plant development and disease reactions that enable more rapid and effective selection of improved germplasm for release to the sugar beet community.


1b. Approach (from AD-416):
Selfed families will be created from self-fertile materials generated to dissect the genetic control of high priority sugar beet disease resistances. A program of phenotypic selection is followed by selecting mother roots from field nurseries and selfing these hybrids in the greenhouse. A genome sequence will be constructed and molecular markers will be developed from sugar beet nucleotide sequences, located to one of the nine beet chromosomes, and compared with segregation of disease and agronomic traits to identify genetic control. A genetic linkage map will be created for eventual isolation of specific genes that control agronomic and disease traits. Transcript profiling will be employed for gene discovery, however these tools are new for germplasm enhancement and their use has not been well explored. Examining transcript of profiles during sugar beet emergence and development, and during abiotic and biotic stress will allow deduction of important physiological and biochemical clues to the plant responses to stress and development that can be used towards more rigorous application in germplasm enhancement. Traditional sugarbeet population improvement approaches will be deployed for open pollinated, self-incompatible germplasm for release to industry. Production of improved populations will follow from mother root selection under field, greenhouse, or laboratory conditions of one or more germplasm sources, followed by random inter-mating, and harvest of seed from either individual plants, genetically related individuals, or as an entire population. The prevalence of different sugar beet pathogens in the Michigan agro-ecosystem will be ascertained, and used to develop high priority targets for transcript profiling. Differential disease reactions to Fusarium oxysporum and Rhizoctonia solani, for instance, alone and in combination, will form the basis to better characterize the disease infection process and assist in identifying targets of opportunity for breeding intervention. Novel approaches for screening populations for traits will be tested, such as Near-Infrared Spectroscopy and image analysis, and deployed to phenotype high priority traits. Populations and their progeny showing good agronomic and disease performance will be folded into the general agronomic and disease nursery evaluations, and released to industry as enhanced germplasm.


3. Progress Report:
Objective 1: Apply high-resolution genetic mapping and transcriptome profiling to identify genes in sugar beet and related species that contribute traits (e.g., early season development and stand persistence) to sustainable crop production of biomass. Representatives of the "RTA" recombinant inbred population were screened for resistance to Rhizoctonia seedling disease in the field and greenhouse. A novel method for early detection using a handheld photosynthesis meter demonstrated a temperature differential of 2-5 degrees Celsius between selected infected and non-infected susceptible RTAs and controls, and was not observed in resistant materials where temperature did not vary. Test sequencing was performed for evaluation of population structure, which for this population may be sub-optimal as a traditional genetic mapping population. Transcriptomes of seedlings germinated under stress and non-stress conditions were used to annotate the EL10 genome sequence (see Q4). Additional recombinant inbred populations were screened for response to seedling pathogens. Host resistance has been identified to at least three of the major seedling diseases in the area. Smooth-rooted germplasm with excellent sugar content, high yield, and good to excellent tolerance to the range of pathogens currently important to Great Lakes growers was identified and will be released to industry in 2019. Objective 2: Characterize diverse populations of root rotting pathogens of sugar beet at the molecular level and identify genetic components that affect host-pathogen interactions to minimize disease losses. 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. Screening both dry bean and sugar beet with the same pathogen isolates showed variable responses for seedling and adult infection on different hosts. For the damping-off and root rot pathogen Rhizoctonia solani, this response shows an association with pathogen genetic variability. Genetic markers were developed to help identify and characterize Rhizoctonia genetic groups, and shows there are at least three, rather than two genetic groups in R. solani AG 2-2 as previously thought, that affect sugar beet and dry bean. Work is ongoing to understand how these genetic groups interact with host genotypes. Seedling response to diverse pathogens varied with temperature, and isolates were identified that caused more damage at cool soil temperatures when growers plant the crop. In addition to root rots, foliar diseases are a major concern re-emerging in the industry. For Cercospora leaf spot, an increased level of tolerance to at least three of the major fungicide classes is being reported by the industry. Fungicide resistance screening and management is thus an increasing priority. In addition to Cercospora leaf spot, Alternaria leaf spot has been increasing in the region and has been classified by Michigan Sugar as a priority issue. Alternaria isolates from the region showed tolerance to all three fungicides used for foliar disease management. A screening method for variety response to Alternaria is being developed in preparation for breeding enhanced germplasm. Objective 3: Develop improved screening methods that provide better resolution of young plant development and disease reactions that enable more rapid and effective selection of improved germplasm for release to the sugar beet community. Germplasm enhancement activities were conducted with individual field trials and greenhouse seed increases in Michigan encompassing selection for resistance to Cercospora leaf spot, Rhizoctonia seedling disease, and stand establishment potential. In FY18, 1,019 distinct entries were evaluated. From these trials, individuals with above average characteristics were selected for crossing and seed production for potential release to industry, public breeders, and other interested parties as enhanced germplasm. In FY18, 1,423 roots were selected and vernalized, and seed was produced in the greenhouse. Multiple wild and un-adapted germplasms have been incorporated into these population improvement activities. Genomics-enabled screening of disease resistance and yield genes was initiated, using the EL10 genome sequence as a reference (see Q4). 231 potential disease resistance genes conforming to the NB-ARC specification were identified, including genes for rhizomania resistance, perhaps the disease of most concern for the sugar beet industry worldwide. Forty-nine (49) additional East Lansing USDA-ARS breeding lines and historical crop type germplasm were sequenced to examine diversity and signatures of selection for gene discovery.


4. Accomplishments
1. A reference genome for sugar beet germplasm is needed for dissecting the genetic basis of traits needed for sustainable sugar beet production. ARS germplasm release C869 (PI 628754) was inbred for five generations with selection for good stand establishment and vigor. One individual inbred plant, designated 'EL10', was chosen for genome sequencing and assembly. For genome assembly, which remains an exceptionally difficult process, multiple methods were evaluated. The best initial assembly represented the sugar beet genome in 938 discrete fragments. This initial assembly was improved using multiple methods and ultimately decreased the number of fragments to nine, each representing one sugar beet chromosome. The nine fragments obtained were consistent with published genetic maps and the fragmented RefBeet genome, and thus this assembly now represents the most detailed genome representation for sugar beet. The availability of a complete, high quality sugar beet genome sequence allows for the rapid identification of genes essential for sustainable sugar beet production. It is being used to discover novel genes from the huge reservoir of genetic potential contained in wild and unadapted germplasm.


Review Publications
Trueman, C.L., Rosenzweig, N., Somohano, P., Hanson, L.E. 2017. First report of DMI insensitive Cercospora beticola on sugar beet in Ontario, Canada. New Disease Reports. 36:20.
Broccanello, C., McGrath, J.M., Panella, L.W., Richardson, K.L., Chiodi, C., Biscarini, F., Barone, V., Baglieri, A., Squartini, A., Concheri, G., Stevanato, P. 2017. A SNP mutation affects rhizomania-virus content of sugar beets grown on resistance-breaking soi. Euphytica. 214:14.
Hanson, L.E., Goodwill, T.R., Corder, H.J., McGrath, J.M. 2017. Beta Plant Introductions from the USDA-ARS NPGS evaluated for resistance to Cercospora beticola, 2016. Plant Disease Management Reports. 11:FC028.
Rosenzweig, N., Hanson, L.E., Pratt, D., Stewart, J., Somohano, P. 2017. First report of QoI resistance in Alternaria spp. infecting sugar beet (Beta vulgaris) in Michigan, USA. New Disease Reports. 36:5.