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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

2014 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:
Germplasm enhancement activities were conducted with field trials and greenhouse seed increases in Michigan encompassing evaluation and selection for resistance to Cercospora leaf spot and Rhizoctonia seedling and root diseases, and assessment of stand establishment potential. Thirteen hundred distinct entries, not including those submitted for the official leaf spot nursery, were evaluated. From these trials, individuals with superior characteristics were selected for seed multiplication for eventual release to industry, public breeders, and other interested parties as enhanced germplasm. From FY13, over 2,500 roots were selected, vernalized, and selfed in the greenhouse for inbred seed production, and over 500 were selected for field seed production for open-pollinated population enhancement. Multiple wild and unadapted germplasm have been incorporated into these population improvement schemes. Marker discovery and genetic analyses activities were very productive using next-generation sequence acquisition technologies for marker development using single nucleotide polymorphism technologies and whole genome mapping-by-sequencing approaches. Bioinformatic capacity was honed to ease the computational load from the high volume of data generated by these new genomic technologies. A deep transcript profile of expressed genes was obtained from seed germinated under temperature stress and growth-promoting environments, as well as during early season development. Results confirm and extend previous observations on seedling vigor biochemical pathways, including signal transduction and transcription factor pathways, by which seedling vigor is better defined and thus amenable to selection for improved vigor. Simplifying phenotypic selection through development of new methods yielded positive results. A comprehensive survey of sugar beet disease-causing fungal pathogens present in the Great Lakes growing areas confirms presence of known pathogens and suggests involvement of others whose precise roles are being ascertained. For instance, diseases caused by Fusarium oxysporum appear to be gaining prominence as seedling and root rotting issues are increasing in the Great Lakes growing region and elsewhere. Experiments to determine the role of pathology and genetics in long-term storage were continued, with good results in that different germplasm showed delayed susceptibility to storage rot pathogens. New avenues of phenotyping were explored with promising results. Video image analyses for determination of Cercospora leaf spot severity led to a ‘best paper’ publication. Near-infrared analyses of sucrose content of intact and cut sugar beet roots led to a first stage prediction model.


4. Accomplishments
1. Draft sequence of the C869 sugar beet genome. Sugar beet 'C869' is a diploid, self-fertile, germplasm that was released to the public and has been used extensively as the seed parent of the recombinant inbred lines. One inbred plant was chosen for genomic sequencing due to its vigorous growth and consistent characteristics. ARS scientists in East Lansing, Michigan (in collaboration with scientists in the UK and Belgium) assembled these sequences to cover approximately 60% of the beet genome, and most known sugar beet genes are contained within this assembly. This draft genome assembly is an excellent resource to identify genes and create genetic markers to dissect the agronomic traits of sugar beet. A better understanding of genetic traits can improve breeding efforts in both the public and private sectors.

2. Cercospora leaf spot disease progression limited by high temperature. Cercospora leaf spot on sugar beet is endemic to the Great Lakes growing region and requires intensive management using both fungicides and genetic resistance to achieve acceptable control. Even a low level of leaf spot in the fields has a measurable reduction on grower profitability, and climate models are used to assist in managing fungicide applications for maximum efficiency with minimal fungicide input. The causal organism, Cercospora beticola, is adept at developing resistance to such fungicides, thus judicious use of the few safe and effective fungicides is required to ensure sustainability of the sugar beet crop. The current climate model assesses Cercospora leaf spot risk on the basis of accumulated heat units and moisture levels (i.e. disease severity values). ARS scientists and industry collaborators at East Lansing, MI demonstrated that temperatures above 96 F (35.5 C) inhibit growth of the fungus, which suggests that the climate model should be adjusted by excluding these durations from the disease severity value calculation, and thereby delay fungicide application to periods where fungicides will have their maximal effect.


Review Publications
Merlington, A., Hanson, L.E., Bayma, R., Hildebrandt, K., Steere, L., Kirk, W.W. 2014. First report of Fusarium proliferatum causing dry rot in Michigan commercial potato (Solanum tuberosum) production. Plant Disease. 98:843.
Hanson, L.E., Goodwill, T.R., McGrath, J.M. 2014. Beta PIs from the USDA-ARS NPGS evaluated for resistance to Cercospora beticola, 2013. Plant Disease Management Reports. 8:FC170.
Trueman, C.L., Hanson, L.E., Rosenweig, N., Jiang, Q.W., Kirk, W.W. 2013. First report of QoI insensitive Cercospora beticola on sugarbeet in Ontario, Canada. Plant Disease. 97:1255.
Meng, Q.X., Hanson, L.E., Douches, D.D., Hao, J.J. 2013. Managing scab diseases of potato and radish caused by Streptomyces spp. using Bacillus amyloliquefaciens BAC03 and other biomaterials. Biological Control. 67(3):373-379.
Rojas, A., Kirk, W.W., Gachango, E., Douches, D.S., Hanson, L.E. 2014. Tuber blight development in potato cultivars in response to different genotypes of Phytophthora infestans. Journal of Phytopathology. 162(1):33-42.
Kirk, W.W., Hanson, L.E., Franc, G.D., Stump, W.L., Gachango, E.N., Clark, G., Stewart, J. 2012. First report of strobilurin resistance in Cercospora beticola in sugar beet (Beta vulgaris) in Michigan and Nebraska, USA. New Disease Reports. Available: http://dx.doi.org/10.5197/j.2044-0588.2012.026.003.