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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

2015 Annual 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 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.

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.

Progress Report
Early season sugar beet development continued to be a focus of the East Lansing genetics, genomics, and germplasm enhancement effort. Two major thrusts are geared towards 1) understanding sugar beet germination under stress that leads to a consistent 30% loss of stand in growers fields, and 2) understanding the transition from juvenile to adult plant growth that occurs circa 5 weeks after germination and, if transitioned earlier, could result in significant additional yield to growers at harvest. Along these lines, transcriptomes of seeds germinating at temperature extremes were examined. Results indicate that relatively few germplasms exhibit improved germination responses at high- or low-temperatures. Responses to high- and low-germination temperatures are not obviously correlated. Further, transcriptomes of two germplasms that showed either good high- or low-temperature germination did not show any obvious correlations in the suites of genes that were differentially expressed relative to optimal germination temperatures. In general, response to improved low-temperature germination was largely characterized by genes whose expression was up-regulated, whereas response to improved high-temperature germination was characterized by genes whose expression was largely down-regulated. During development, initial transcriptome analyses showed the expected transitional phase, and these promising results have been expanded to include additional biological replicates as well as an additional germplasm (a low biomass red table beet). Gene identification has relied on comparative searches with databases of known genes, however results have been equivocal and additional means of gene identification are needed. High resolution mapping via genome sequencing was initiated in one genetic population, and shown to be limited in utility due to limitations of the current sugar beet genome sequence having an excessive number of fragments, and lack of sequence information for both parents. To ameliorate this, a reference-quality sugar beet genome sequencing effort was initiated and is in progress, and also draft sequences are being generated for parent accessions of the genetic populations generated to date. These genomic materials should allow better gene identification by plant phenotype rather than by comparative structure-function relationships as is currently performed. Root rots have been a major constraint on beet yield for many years and further have been identified as the most important yield-limiting diseases affecting beets in the last three to five years. The same pathogens are known to affect a number of rotation crops, but interactions between pathogens of beet as well as between beet pathogens and rotation crop pathogens are not well understood. Root rot pathogens affecting beet show high genetic variability that does not relate to current methods of classification. Molecular testing of Rhizoctonia solani has identified three genetically distinct groups that affect beet rather than the two groups used in previous classification. New classification methods are being developed to allow for improved tracking of the pathogens as well as investigation of the interaction with beet and rotation crops which may help to explain some of the variability in strains found in different growing regions. In addition, a correlation has been observed between these genetic groups and variable responses with crop growth stage for at least one rotation crop, dry bean. Such varied responses will allow for targeted assessment of differences in the crop at these growth stages that could aid in resistance breeding in the future. 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. Over 1,000 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. From FY14, over 2,000 roots were selected, vernalized, and selfed in the greenhouse for inbred seed production in FY15, and over 300 were selected for greenhouse and field seed production for open-pollinated population enhancement. Multiple wild and unadapted germplasms have been incorporated into these population improvement schemes. 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. Experiments to determine the role of pathology and genetics in stored beets were initiated, with good results in that different germplasm showed delayed susceptibility to storage rot pathogens, with the caveat that storage at low temperatures induces the flowering response and concomitantly roots from all tested germplasm become increasingly susceptible and germplasm varies both in the rate of flowering response and increased disease susceptibility. Correlation was found between the rate of change in the two physiological processes, which opens up new areas for research. Resistance was identified with reduced disease severity throughout the course of the experiments, and no correlation between resistance to different pathogens was found. One of these germplasms will be released in FY15.

1. Storage rot resistance sugar beet germplasm. Sugar beets are harvested and stored in large outdoor piles for one to three months during the winter prior to processing. Post-harvest deterioration and root rots severely impact the integrity of the sugar beets and leads to substantial loss of sucrose yield. ARS scientists at East Lansing, Michigan developed enhanced sugar beet germplasm with excellent storage characteristics and resistance to common storage rot diseases. The genetic background of this trait includes good sucrose yield potential, good field and disease nursery performance, and smooth-root architecture. The availability of this enhanced germplasm will allow development of hybrids with good storage characteristics during the sugar beet processing campaign. A delay in storage losses of a month would save the industry approximately $1 million per year in Michigan alone.

Review Publications
Rosenzweig, N., Hanson, L.E., Franc, G.D., Stump, W.L., Jiang, Q.W., Clark, G., Stewart, J., Kirk, W.W. 2015. Use of PCR-RFLP analysis to monitor fungicide resistance in Cercospora beticola populations from sugarbeet (Beta vulgaris) in Michigan, United States. Plant Disease. 99:355-362.
Hanson, L.E., Goodwill, T.R., McGrath, J.M. 2015. Beta PIs from the USDA-ARS NPGS evaluated for resistance to Cercospora beticola, 2014. Plant Disease Management Reports. 9:FC001.
McGrath, J.M., Hanson, L.E., Panella, L.W. 2015. Registration of SR98 sugar beet germplasm with resistances to Rhizoctonia seedling and crown and root rot diseases. Journal of Plant Registrations. 9:227-231.
Pan, L., Lu, R., Zhu, Q., McGrath, J.M., Tu, K. 2015. Measurement of moisture, soluble solids, and sucrose content and mechanical properties in sugar beet using portable visible and near-infrared spectroscopy. Postharvest Biology and Technology. 102:42-50.