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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

2017 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:
A high resolution genetic map was obtained for an inbred 'sugar beet x table beet' recombinant inbred population using low-coverage whole genome sequencing of 176 individuals. This activity both increased the available nucleotide sequence resources for beet as well as proved a novel strategy to use these sequence resources as genetic markers to map traits, such as sugar content and seedling vigor. Transcriptomes of seedlings germinated under stress and non-stress conditions were annotated and placed on the genetic map, via the nascent 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. One germplasm was identified for release and will be submitted as SR103. SR103 is a 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. 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, and 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. 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. As well as R. solani, two species of Colletotrichum were identified as causing disease on sugar beets. Greenhouse inoculations confirmed pathogenicity and indicated that USDA germplasm showed differential reactions to both species. In addition to root rots, foliar diseases are an issue, with new major concern emerging in the industry. That is, fungicide resistance has increased in two major foliar pathogens. Cercospora leaf spot agents showed a higher level of tolerance to one of the major fungicide classes, with between 30 and 60% of isolates sampled showed resistance to the demethylase inhibitor class of fungicides as well as quinone outside inhibitors. Alternaria leaf spot has been increasing and was estimated to cause up to 15% of the losses from foliar disease in 2016. Isolates from the area show tolerance to all three of the major fungicides used for foliar disease management. Efforts are underway to develop a screening method for variety response to Alternaria. Germplasm enhancement activities were conducted with individual field trials and greenhouse seed increases in Michigan encompassing selection for resistance to Cercospora leaf spot and stand establishment potential. 955 distinct entries were evaluated. From these trials, individuals with superior characteristics were selected for crossing and seed production for potential release to industry, public breeders, and other interested parties as enhanced germplasm. In FY17, 1,950 roots were selected, vernalized, and selfed in the greenhouse for seed production. Over 100 of these were selected under severe seedling Rhizoctonia pressure. 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 nascent EL10 genome sequence as a reference (see Q4). Four candidate gene regions for total biomass and 225 potential disease resistance genes conforming to the nucleotide binding (NB) subclass generally referred to as NB-ARC were identified. For the 4th year, video footage was obtained for the entire Cercospora nursery over the time course of the infection at 2-4 day intervals. This resource is being used to develop models of Cercospora infection as well as provide unbiased ratings for variety and germplasm disease reactions.

4. Accomplishments
1. Reference genome for sugar beet germplasm EL10. ARS germplasm release C869 (PI 628754) was inbred for five generations with selection for good stand establishment and vigor. One individual plant was chosen for genome assembly and are being multiplied for release as EL10. For genome assembly, which remains an exceptionally difficult process, multiple methods were evaluated. Both short and long whole genome shotgun sequences were used, with the best initial assembly obtained with long reads. This assembly yielded the sugar beet genome in 938 fragments. The initial assembly was improved using multiple methods designed to increase the contiguity of the assembly and decrease the number of fragments to nine, each representing a sugar beet chromosome. This new genome is the most detailed genome representation available for sugarbeet, with the closest match to existing genetic maps. 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
De Lucchi, C., Stevanato, P., Hanson, L.E., McGrath, J.M., Panella, L.W., De Biaggi, M., Broccanello, C., Bertaggia, M., Sella, L., Concheri, G. 2017. Molecular markers for improving control of soil-borne pathogen Fusarium oxysporum in sugar beet. Euphytica. 213:71.
Hatlestad, G., Akhavan, N., Sunnadeniva, R., Elam, L., Cargyle, S., Hembd, A., Gonzalez, A., McGrath, J.M., Lloyd, A. 2015. The beet Y locus encodes an anthocyanin-MYB-like protein that activates the betalain red pigment pathway. Nature Genetics. 47:92-96.
McGrath, J.M., Townsend, B.J. 2015. Sugar Beet, Energy Beet, and Industrial Beet. In: Cruz, V.M.V, Dierig, D.A., editors, Handbook of Plant Breeding. Volume 9. Industrial Crops: Breeding for Bioenergy and Bioproducts. New York, New York: Springer. p. 81-89.
Hanson, L.E., De Lucchi, C., Stevanato, P., McGrath, J.M., Panella, L.W., Sella, L., De Biaggi, M., Concheri, G. 2017. Root rot symptoms in sugar beet lines caused by Fusarium oxysporum f. sp. betae. European Journal of Plant Pathology. doi: 10.1007/s10658-017-1302-x.