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United States Department of Agriculture

Agricultural Research Service

Research Project: BREEDING SELECTION AND MOLECULAR CHARACTERIZATION FOR IMPROVED SUGAR BEET GERMPLASM
2010 Annual Report


1a.Objectives (from AD-416)
1) Enhance and release sugarbeet germplasm that represents substantially improved populations enriched for novel genetic combinations for the unique Eastern U.S. growing regions;.
2)Develop and exploit sugarbeet and other species nucleotide sequence information for marker-assisted gene discovery, including development and release of simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers; and.
3)Develop simplified phenotyping assays for priority biotic and abiotic stress resistance and early season development suitable for molecular analyses.


1b.Approach (from AD-416)
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. Selfed families will be created from self-fertile materials generated to dissect the genetic control of high priority disease resistances. A program of phenotypic selection is followed by selecting mother roots from field nurseries, selfing these hybrids in the greenhouse, and applying molecular markers. 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. Mapped molecular markers will also be used to integrate sugar beet Bacterial Artificial Clones on the genetic linkage map 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 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. 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 reaction to Fusarium oxysporum, for instance, as an example of a newly discovered pathogen for Michigan, will form the basis for transcript profiling experiments that will better characterize the disease infection process and assist in identifying targets of opportunity for breeding intervention. 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 continue with individual field trials and greenhouse seed increases in Michigan encompassing agronomic evaluation, selection for resistance to Cercospora leaf spot, Fusarium yellows, and Rhizoctonia seedling and root diseases, selection for sugar beet cyst nematode resistance and salt tolerance during germination, and assessment of stand establishment potential. Over 1,000 distinct entries, not including those submitted for the official leaf spot nursery, are being evaluated. From these trials, individuals with superior characteristics will be selected after evaluation of their performance during the current growing season. From FY09, over 4,000 roots were selected, vernalized, and selfed in the greenhouse for inbred seed production, and an equal number 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. In FY10, marker discovery and genetic analyses activities were productive with additional nucleotide sequence acquisition for marker development using single nucleotide polymorphism technologies was initiated using next generation sequencing. A coalition of ARS researchers, and university and industry scientists has been formed to obtain a full-length sugar beet genome sequence. Simplifying phenotypic selection through development of new methods and molecular dissection yielded very positive results. Synergistic interactions between root pathogens including Fusarium, Rhizoctonia, and Rhizopus were demonstrated. The developmental profile of germinating sugar beet seeds before radicle eruption was completed and molecular investigations of stress responses during germination suggest the first 24 hours after imbibition is critical for expression of seedling vigor. The second year of a comprehensive survey of sugarbeet disease-causing fungal pathogens present in the Great Lakes growing areas is continuing - the first survey in over 25 years. Results confirm presence of known pathogens and suggest involvement of others whose precise roles are being ascertained, and unlike the previous year, Aphanomyces seedling disease is a recurring issue for Michigan growers.


4.Accomplishments
1. Salt-tolerant sugar beet germination. An in-depth understanding of response to stress is critical during sugar beet seed germination in order to identify key germplasm and breeding lines for enhancing seedling vigor, and identifying mechanisms of seedling vigor under different germination regimes and in different genetic backgrounds. Sugar beet is tolerant of high salinity except during germination and stand establishment. Germination in sodium chloride solutions was used to characterize germplasm for differential responses to saline conditions, with the result that two different modes of saline germination were found. One mode resulted in a dose-dependent reduction in germination percent, and the other mode showed a time-delayed germination rate but less overall reduction in total germination. Phenotypic evaluation of germination in a range of solutions (0 to 600 mM NaCl) was obtained from 16 breeding lines and two check varieties counted each day for 12 days. No germination occurred at >400 mM NaCl, and germination was inhibited by 50 mM NaCl in the checks and three of the breeding lines. Five of the breeding lines showed no reduction in germination at 150 mM NaCl concentrations, and 11 of the 14 breeding lines appeared as if they were capable of resulting in a full stand at this moderate salt concentration. New germplasm was identified with tolerance to salt stress during germination.

2. Transcript profile of germinating seedlings for gene and marker discovery. An effort to identify as many as practical genes expressed during germination in sugar beet was initiated using next generation, long read sequencing instrumentation. Three genotypes were sampled across seven treatments and 10 time points after imbibition. Developing seeds were also available from one germplasm, and these were also included. Over 360,000 passing reads were obtained with an average length of 197 bases. These reads collapsed into 8,788 tentative consensus sequences, of which 4,203 could be assigned to a similar sequence existing in the beet gene expression database. Thus, the remaining 4,585 sequences may represent new genes whose predictions have been previously unavailable for analyses. These new sequences likely have utility for understanding germination, emergence, and stand establishment in sugar beet, and serve as an additional resource for development of new molecular genetic markers for breeding and germplasm enhancement.

3. Identified a new synergism in root rot for sugar beet. During the pathogen survey, a high proportion of Rhizopus was found in root showing root rot symptoms in the Michigan growing area. In all cases this fungus was associated with another, known strong pathogen of sugar beet. Greenhouse testing demonstrated the potential for a synergistic interaction with Rhizoctonia solani. This information provides one potential explanation for reports of Rhizoctonia root rot resistance not providing the expected level of disease management in fields. In addition, methods developed in this testing are being used to screen ARS germplasm for response to the combined pathogens to improve disease management.


Review Publications
Hanson, L.E. 2010. Interaction of Rhizoctonia solani and Rhizopus stolonifer Causing Root Rot of Sugar Beet. Plant Disease. 94(5):504-509.

Hanson, L.E., Duckert, T.M., Goodwill, T.R., McGrath, J.M. 2010. Beta PIs From the USDA-ARS NPGS Evaluated for Resistance to Cercospora beticola, 2009. Plant Disease Management Reports. Available: http://www.plantmanagementnetwork.org/pub/trial/PDMR/reports/2010/FC005.pdf

El-Zohairy, El-Awady, A., Eissa, H.F., El-Khishin, D.A., Nassar, A., McGrath, J.M. 2009. Differential Expression of Salt Stress-related Genes in Wild Beta vulgaris. Egyptian Journal of Genetics and Cytology. 38:187-206.

Last Modified: 11/20/2014
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