Location: Sugarbeet and Bean Research
2018 Annual Report
Objectives
Objective 1: Annotate, prospect, and identify genes and genome structure of the ARS release C869 (a.k.a. EL10) reference sugar beet genome, and develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use.
Sub-objective 1.A: Annotate, prospect, and identify genes and genome structure of the EL10 genome.
Sub-objective 1.B: Develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use.
Objective 2: Assess the host range, diversity, and host-pathogen interactions of sugar beet pathogens of high priority to the Great Lakes, including Rhizoctonia, Cercospora, and seedling disease complex, to identify host resistance factors for use in breeding programs.
Objective 3: Identify sugar beet-specific genes and develop genetic markers involved in beet quality and crop type (sugar, fodder, table, or chard) to transfer novel genetic resources from un-adapted to adapted germplasm, for the benefit of all beet crop types.
Approach
1) Explore disease resistance and stress-germination genes in EL10 and related germplasm. Phenotype RIL populations and obtain low-coverage re-sequencing for genetic analysis and mapping. Develop additional genetic populations and enhanced germplasm for release.
2) Develop and utilize genetic markers and other genetic information for enhanced understanding of Rhizoctonia solani and other plant pathogenic fungi. Characterize host-pathogen, host-pathogen-pathogen interactions and host developmental stages that influence disease progression.
3) Evaluate crop genomes for markers and other features important in a breeding context. Evaluate non-beet genomes for features of potential benefit to long-term beet improvement.
Progress Report
Objective 1: Annotate, prospect, and identify genes and genome structure of the ARS release C869 (a.k.a. EL10) reference sugar beet genome, and develop linkage maps aimed at chromosome-level genome assembly for genes of agronomic importance and interest that breeders can use.
Annotating the beet genome followed repeat masking, ab initio gene finding based on transcript evidence, and resolution to consensus-predicted gene models using the MAKER annotation pipeline. Results predicted 24,255 proteins, 88.5% of the 27,421 predicted in RefBeet. Transcript evidence for gene prediction was derived from C869 (the EL10 progenitor) developing roots (3 – 10-weeks post-germination), mature leaves, and seedlings of other germplasm germinated under aqueous stress conditions, including 150 mM NaCl, 0.3% hydrogen peroxide, and biologically extreme temperatures (10 and 41 degrees Celsius). Transcript sets also included young leaves and the set of transcripts used for annotating RefBeet. For putative functional annotation, three sources were used, in the priority: 1) UniProt, 2) Pfam-A, and 3) Uniref90. If no functional annotation was found in these three highly curated sets, proteins were assigned to the class ‘hypothetical' proteins. These reasonably stable protein annotations were used to estimate features of the coding portion of the EL10.1 genome assembly.
Objective 2: Assess the host range, diversity, and host-pathogen interactions of sugar beet pathogens of high priority to the Great Lakes, including Rhizoctonia, Cercospora, and seedling disease complex, to identify host resistance factors for use in breeding programs.
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. To improve the ability to examine interactions and the effects of crop rotations, a set of genetic markers were developed to examine pathogen diversity and rapidly identify known strains, especially in the pathogenic fungi Rhizoctonia solani and Fusarium species. Initial testing indicates high diversity in sugar beet isolates. Isolates are being collected from other hosts, and additional regions, including other ARS research locations. One of the newly identified pathogens on sugar beet in the region, a Colletotrichum species has now been identified multiple years, with samples also being submitted to the national plant diagnostic network lab in the region. These are being characterized as a new disease in the area that affects seedlings as well as causing a mild leaf spot. In addition to root rots, foliar diseases are a re-emerging issue in the industry as current management options show reduced efficacy. Sensitivity to three of the major fungicides used for Cercospora leaf spot management has been decreasing, and disease control failures were reported in the Great Lakes region. This has put an increased emphasis on identification of host resistance and understanding the disease cycle. Ongoing tests show infective spores are present earlier than previously thought, which is affecting timing of management applications. In addition to Cercospora leaf spot, Alternaria leaf spot has been increasing in the region, and currently is recognized as a recurring issue in Michigan. Isolates from the area show tolerance to all three of the major fungicides used for foliar disease management. Efforts are ongoing to develop a screening method for variety response to Alternaria.
Objective 3: Identify sugar beet-specific genes and develop genetic markers involved in beet quality and crop type (sugar, fodder, table, or chard) to transfer novel genetic resources from un-adapted to adapted germplasm, for the benefit of all beet crop types.
The EL10 genome was leveraged to explore synteny beet and other plants (synteny: from the Latin "same strand", meaning genes that have common, linked chromosome positions across two or more species). Three species related to beet [Caryophyllales; Amaranthaceae, aka Chenopods (=goose foot)]; Amaranthus hypocondriacus, Chenopodium quinoa, and Spinacia oleracea, as well as two unrelated Rosid species [Vitis vinifera (grape) and Arabidopsis thaliana (a model plant)] were compared for genes that have retained genetic linkage through their evolutionary histories. Collinear blocks were identified using the program MCScanX, which uses a reciprocal blast between predicted protein datasets. Genome evolution within the Caryophyllales showed significant genome variation in chromosome numbers, the number of syntenic regions, and the sizes of syntenic regions relative to beet. On average, genome variability increased with phylogenetic distance. A greater number of syntenic regions with fewer members per region were found in species that resolve more distantly from sugar beet.
Accomplishments
1. Reclassification of Rhizoctonia with molecular insights. Root rots have been a major constraint on beet yield for many years and have been identified as the most important yield-limiting diseases affecting beets. Root rot pathogens affecting beet show high genetic variability that does not relate to current methods of classification. Molecular testing of Rhizoctonia solani, done in collaborative work by ARS scientists in East Lansing and Salinas, California has identified three genetically distinct groups that affect beet rather than the two groups used in previous classification and has shown the prior groups are not relevant based on genetic relatedness. New classification methods allow for improved tracking of the pathogens as well as for 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. Research in East Lansing has shown a correlation between these genetic groups and variable responses with crop growth stage for at least one rotation crop, dry bean. 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. It also allows for assessment of alternative disease management strategies, such as impact of crop rotation on the pathogen population. The research is causing interest in other locations, with ARS scientists, university researchers, and company breeders submitting isolates for characterization within the new phylogenetic schema and asking for assistance in identifying the types of R. solani in their growing regions or being used in breeding programs.
Review Publications
Pethybridge, S.J., Kikkert, J.R., Hanson, L.E., Nelson, S.C. 2018. Challenges and prospects for building resilient disease management strategies and tactics for the New York table beet industry. Agronomy. 8:112. https://doi.org/10.3390/agronomy8070112.
Funk, A., Galewski, P., McGrath, J.M. 2018. Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome. Plant Journal. 95(4):659-671.
