Location: Sugarbeet and Bean Research
2019 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.
Nucleotide-binding (NB-ARC), leucine-rich-repeat genes (NLRs) account for 60.8% of resistance (R) genes molecularly characterized from plants. NLRs exist as large gene families prone to tandem duplication and transposition, with high sequence diversity among crops and their wild relatives. This diversity can be a source of new disease resistance. Using the conserved NB-ARC domain as a model, 231 tentative NB-ARC loci were identified in a highly contiguous genome assembly of sugar beet, revealing diverged and truncated NB-ARC signatures as well as full-length sequences. Comparison of sugar beet NB-ARC domains to validated R genes from monocots and eudicots suggested extensive B. vulgaris-specific subfamily expansions. The NLR landscape in the rhizomania resistance Rz region of Chromosome 3 was characterized, identifying 26 NLR-like sequences spanning 20 Megabases of genome sequence. This work presents the first detailed view of NLR family composition in a member of the Caryophyllales, builds a foundation for additional disease resistance work in Beta vulgaris, and demonstrates an additional nucleic-acid-based method for NLR prediction in non-model plant species.
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.
The Great Lakes production region is experiencing increasing issues with foliar leaf spots. In the 2018 season, a combination of three foliar diseases was estimated to cause over $27 million in losses to the local industry (Michigan Sugar company personal communication). One of these, Cercospora leaf spot, has been a long term issue. An ongoing collaboration to examine diversity and management of this disease has been expanded to additional labs and research. We found the pathogen can be present much earlier than previously known. This information is being used to modify current management recommendations. Another major leaf spot, Alternaria leaf spot, was determined by our program to be an increasing problem in the region starting in 2010. Since 2016, it has been contributing to economic losses, especially in parts of the growing region where Cercospora leaf spot has been less of an issue. There is limited information on the pathogen(s) causing Alternaria leaf spot. Our research indicates the strains from sugar beet are similar to isolates from Solanaceous crops, and can cause disease on tomato, potato, as well as other rotation crops in the region such as dry bean. A better understanding of this interaction can aid in management of this new issue. We also were able to produce disease with both the field and greenhouse inoculations. This allows us to improve screening of sugar beet germplasm from the breeding program. Germplasm was identified that showed varying susceptibility to Alternaria after inoculation. The methods need improvement for consistency, but show potential for identification of resistance in the USDA breeding material and commercial lines. As well as leaf spots, root rots and other soil-borne diseases remain a constraint on beet yield. We have initiated testing of genetic markers for one of the major soil-borne pathogens that were developed in our lab, and found high variability within fields. This will be further tested for utility to compare management methods and crop rotation for their impact on sugar beet pathogens. In 2018, Fusarium yellows was identified in a number of fields in Michigan. This has been limited in the region, but may be increasing. Isolates have been collected and are being compared to isolates from other growing regions. Sugar beet germplasm is being screened for disease reaction for all disease pressures in the Great Lakes region.
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.
Beta vulgaris is a species complex containing several distinct crop-types (sugar, fodder, table, and chard). Selection and drift have sorted ancestral variation in a way that has resulted in pronounced phenotypic differences between these crops. Methods to measure and quantify these differences were developed by focusing on lineage specific genetic variation (i.e. that which is unique to a population or crop type). Sugar accumulation is a complex trait, and varies by crop-type. Measures of diversity and differentiation across the beet genomes detected regions involved in sugar accumulation, and significantly, identified the genes controlling sugar accumulation. Annotations of these genes suggest differences in development, physiology, and metabolism underlie crop-type differentiation. This information is essential for improving beet quality traits, as well as recovering specific crop-types after wide hybridization with crop wild relatives to access useful and novel disease resistance genes.
Accomplishments
1. Genetics of crop-type differences in beet. Diversification in end use is a hallmark in a number of crop species. Beta vulgaris is a species complex composed of diverged populations including sugar, fodder, table, and leaf (chard) cultigroups. Using population genetic and statistical methods on whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, ARS researchers in East Lansing, Michigan, and colleagues determined relationships between accessions based on identity-by-state and shared genetic variation. Extensive shared (e.g. non-unique) genetic variation was seen within and between cultigroups. Lineage specific variation within crop-types supported a shared demographic history within each cultigroup, while analysis revealed strong cultigroup differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation within a cultigroup. This information is being used by sugar beet and table beet breeders to better delineate target traits, modify selection schema, and develop haplotype markers for better breeding efficacy.
2. Assess diversity among Alternaria species, a sugar beet pathogen becoming of high priority to the Great Lakes. Alternaria leaf spot on sugar beet historically was a minor issue in the United States, with little need to manage the disease. Since 2016, researchers in East Lansing, Michigan, have found this disease has been causing increasing economic losses in the Great Lakes region. Using a combination of molecular and morphological methods, a high level of fungicide resistance was found in Alternaria isolates from sugar beet in the Great Lakes region, which likely contributes to increased disease levels in growers' fields. Isolates were found to belong to the Alternaria alternata species complex. This is a different species than was reported on sugarbeet in the Western United States and shows similarity to species affecting other crops such as potato. Isolates from sugar beet could infect both potato and tomato, with at least one isolate screened showing high virulence on all three crops. This information is being used to help develop management recommendations and to select isolates for use in screening of sugar beet germplasm for disease susceptibility.
Review Publications
Broccanello, C., Chiodi, C., Funk, A., McGrath, J.M., Panella, L.W., Stevanato, P. 2018. Comparison of three PCR-based assays for SNP genotyping in sugar beet. Plant Methods. 14:28. https://doi.org/10.1186/s13007-018-0295-6.
McGrath, J.M., Panella, L.W. 2019. Sugar beet breeding. In: Panella, L.W., editor. Plant Breeding Reviews. Volume 42. Somerset, New Jersey: John Wiley & Sons, Inc. p. 167-218.
Rosenzweig, N., Hanson, L.E., Mambetova, S., Jiang, Q., Guza, C., Stewart, J., Somohano, P. 2019. Fungicide sensitivity monitoring of Alternaria spp. causing leaf spot of sugarbeet (Beta vulgaris) in the Upper Great Lakes. Plant Disease. https://doi.org/10.1094/PDIS-12-18-2282-RE.
Wang, J., Sang, H., Jacobs, J.L., Oudman, K.A., Hanson, L.E., Chilvers, M. 2019. Soybean sudden death syndrome causal agent Fusarium brasiliense present in Michigan. Plant Disease. 103:1234-1243. https://doi.org/10.1094/PDIS-08-18-1332-RE.
