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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

2016 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. 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 five weeks after germination and, if transitioned earlier, could result in significant additional yield to growers at harvest. To these ends, roots of sugar beet and other beet crop types were sectioned at 3, 5, 7, and 9 weeks after emergence to observe development of supernumerary cambial rings, a feature restricted to beets and close allies. Establishment of this unusual vascular system is intimately associated with root width enlargement and initiation of sucrose accumulation. Results suggest that this patterning is similar in all beet crop types (sugar, fodder, table, chard), with the addition that chard displays vascular radiations that result in numerous secondary rootlets (a.k.a.; sprangles, fanginess), much like wild beets. No supernumerary rings were observed at 3 weeks of age, however foci of cambial development were observed by 5 weeks of age. By 7 weeks of age, supernumerary cambial layers were distinct but not fully joined, as they are by harvest. The pattern of ring development suggests a role for a diffusible factor establishing a gradient whereby cambial initials form equidistant from the stele and cortex, xylem initials may form at specific concentrations along this gradient, and cambial cell divisions are initiated in a radial fashion to generate the characteristic ring structures. Transcriptome analyses of the same time points is consistent with this view in that genes with functions related to auxin transport and signaling appear to vary significantly across this temporal juncture. These features are being integrated into the nascent sugar beet genome sequence (see Q4). 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 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. Screening both dry bean and sugar beet showed variable responses for seedling and adult infection on different hosts, which was also associated with recently identified genetic variability in the damping-off and root rot pathogen Rhizoctonia solani. Genetic markers are being developed to help identify and characterize these genetic groups. In addition, a different type of root rot was observed on beets in several fields in two states. Using a combination of molecular and classical methods, this was determined to be Colletotrichum coccodes, a pathogen of several crops such as onion, potato, and tomato, but which has not been reported on beet. Studies in the greenhouse confirmed pathogenicity and indicated that USDA germplasm showed differential reactions to this pathogen. 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 and stand establishment potential. Over 970 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 FY15, over 2,500 roots were selected, vernalized, and selfed in the greenhouse for inbred seed production in FY16, and over 100 were selected for greenhouse and field seed production for open-pollinated population enhancement. Multiple wild and un-adapted germplasms have been incorporated into these population improvement schemes. Genomics enabled screening of disease resistance and yield genes was initiated, using the nascent C869 genome sequence as a reference. Four candidate gene regions for total biomass and 96 potential disease resistance genes conforming to the NB-ARC specification were identified in the MSR inbred population and the C869 reference genome, respectively. For the third 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. High quality reference genome of sugar beet germplasm C869. ARS germplasm release C869 (PI 628754) was inbred for five generations, and up to five individual plants were submitted for whole genome nucleotide sequencing and genome assembly using numerous methods. Two sets of nucleotide sequences were used as inputs; short-read (149-fold genome coverage) and long-read (80-fold coverage). Using only short-reads, an assembly algorithm generated 85% genome coverage in nearly two million scaffolds, which was reduced using linking libraries to about 60,000 scaffolds. Using only long-reads, another assembly algorithm generated 75% genome coverage in 938 scaffolds. Addition of optical mapping technology to the long-read assembly further reduced the number of contigs to a total of 86 scaffolds containing 75% of the genome. This assembly was used to predict 29,713 distinct gene models that were annotated for putative biological function. A total of 236 unique NBS-LRR genes, whose functions are implicated in disease resistance, were recovered including six predicted genes spanning the putative Rz1 / Rz2 locus that controls resistance to Beet necrotic yellow vein virus, the primary pathogen causing rhizomania (crazy root disease), a disease of worldwide importance. A final genome assembly step further reduced the number of scaffolds to nine, the base number of chromosomes in sugar beet. The availability of a complete, high quality sugar beet genome sequence will allow for the rapid identification of genes essential for sustainable sugar beet production and their use in rapidly deploying novel genes from the huge reservoir of genetic potential contained in wild and related species.


Review Publications
Atoum, Y., Afridi, M., Liu, X., McGrath, J.M., Hanson, L.E. 2016. On developing and enhancing plant-level disease rating systems in real fields. Pattern Recognition. 53:287-299.
Hanson, L.E., Goodwill, T.R., McGrath, J.M. 2016. Beta PIs from the USDA-ARS NPGS evaluated for resistance to Cercospora beticola, 2015. Plant Disease Management Reports. 10:FC022.