Location: Plant Science Research
2023 Annual Report
Objectives
1. Identify genes and mechanisms underlying defense response and quantitative disease resistance to foliar fungal pathogens and ear stalk rots in maize. [NP301, C1, PS1A]
1.A. Validate and fine-map QTL alleles underlying multiple disease resistance in maize.
1.B. Test the effects of candidate SLB resistance genes using transgenic and mutant analysis.
1.C. Assess the resistance of diverse lines to Anthracnose stalk rot.
1.D. Validate the roles of genes associated with variation in the maize hypersensitive response (HR).
1.E. Validate the effects of candidate QTL identified in genome-wide association studies of Fusarium ear rot.
2. Test new methods of genomics-assisted breeding for quantitative disease resistance in maize to improve productivity and food safety. Conduct genomic selection for resistance to Fusarium ear rot. [NP301, C1, PS1A]
3. Evaluate diverse maize germplasm for potential in specialty food products by conducting agronomic and disease evaluations. [NP301, C1, PS1B]
3.A. Evaluate open-pollinated varieties for food quality and agronomic production characteristics.
3.B. Develop populations with lower grain protein content for use in metabolic disorder diets.
4. Manage and coordinate the Southeastern component of a multi-year, multi-site, cooperative program of maize genetic resource evaluation, genetic enhancement, inbred line development, and information sharing which will broaden the genetic base for U.S. maize. [NP301, C1, PS1A, PS1B]
5. Evaluate temperate, subtropical, and tropical maize genetic resources for adaptation, yield, resistance to ear, stalk, and foliar diseases, tolerance to environmental extremes, and selected value-added, product quality traits. Record and disseminate evaluation data via the GEM database, GEM website, GRIN-Global, and other data sources. [NP301, C2, PS2A]
6. Breed and release maize populations and inbred lines with primarily 50% unadapted/50% temperate pedigrees which contribute to U.S. maize more diverse genetic resistance to diseases, tolerance to environmental extremes, higher yield, unique product qualities, other valuable new traits, or which enable maize trait analysis and allelic diversity research. [NP301, C1, PS1B]
6.A. Evaluate additional nursery rows of breeding crosses for grain yield.
6.B. Evaluate additional field trial plots for disease resistance.
6.C. Evaluate new breeding populations for tolerance to environmental extremes, and selected value-added, product quality traits.
This research will be implemented by increasing the number of nursery rows and field trial plots focused on improving yield; disease resistance; value-added, product quality traits; and related breeding values of maize populations and inbred lines in the southeastern United States.
Approach
We selected 37 near-isogenic lines carrying the 30 most effective multiple disease resistance genes based on previous evaluations. We will produce F2:3 mapping populations of about 100 lines each and rate their disease reactions in replicated field trials. SNP markers will be used to test the effect of each QTL in mostly homogeneous genetic backgrounds.
We previously identified 16 candidate genes for southern leaf blight resistance based on detailed genome-wide association analysis. To functionally characterize these genes, we will first identify and assess lines in which a Mu transposon has inserted into the candidate gene. Also, we will over-express or silence the gene of interest using transgenesis and evaluate the resulting disease phenotypes. We also identified 6 candidate genes associated with modulation of the maize hypersensitive response. We will test if these candidate genes can suppress hypersensitive response using transient expression assays in Nicotiana benthamiana, test if their proteins interact physically with the hypersensitive response trigger protein Rp1-D21 using co-immunoprecipitation assays, and also attempt to identify UnifomMu insertional mutants in these candidate genes and determine whether mutation of these genes affects the hypersensitive response.
We will assess resistance to Anthracnose stalk rot in 30 diverse maize inbred lines grown in replicated field trials under artificial inoculation. We will test the effects of candidate QTL identified in previous genome-wide association studies of Fusarium ear rot in three new biparental cross families. The new lines will be genotyped at SNP markers previously associations with ear rot resistance and grown in replicated field trials under artificial inoculation with Fusarium. Statistical tests of association between SNP genotypes and ear rot resistance in these new populations will be used to independently evaluate their effects.
We will test the effectiveness of genomic selection in a genetically broad-based population. S1 lines from this population were densely genotyped and evaluated across multiple environments to create a training model for genomic selection. Four cycles of genomic recurrent selection will be conducted among individual plants in this population. One cycle of phenotypic selection among replicated S1 lines will be conducted in parallel in the same time frame. Lines resulting from both procedures will be tested in common field trials to compare the effectiveness of genomic and phenotypic selection in this population.
Field evaluations and traditional breeding approaches will be applied to corn populations derived from heirloom populations to find the best sources of agronomic and food quality performance and to initiate within-population selection for improvements in these traits. Traditional breeding methods will also be implemented in crosses between corn lines with lower protein content to attempt to obtain varieties with lower protein content to serve as alternative foods for patients with metabolic disorders.
Progress Report
This is the final report for project 6070-21220-016-000D which terminated in February 2023. With our collaborators, ARS scientists in Raleigh, North Carolina identified a receptor kinase gene that confers southern leaf blight susceptibility and we showed that it appears to function as a suppressor of the basal defense response. We have confirmed the roles of several genes in the modulation of the maize hypersensitive defense response.
We genotyped and evaluated lines derived from backcrossing a Fusarium ear rot-resistant variety to a commercially-developed inbred for resistance to Fusarium ear rot. We initiated new breeding populations for low protein content by crossing our best low protein content lines from the initial cycle of line development.
We coordinated 10,000 yield plots from Raleigh, North Carolina with 4,700 planted in North Carolina by the USDA-ARS Germplasm Enhancement of Maize (GEM) project, 1,900 planted in North Carolina in cooperation with the North Carolina official variety testing program, and the rest planted by five cooperators at various locations throughout the Southeast and Midwest. The results of second year trials will determine which entries are recommended to the GEM project cooperators. Disease evaluation continues in 2023 for resistance to aflatoxin accumulation, with trials conducted by collaborators in Mississippi, Texas, and Georgia. Over 100 new breeding crosses were observed for agronomic traits of interest.
PROJECT FINAL SUMMARY REPORT:
We identified and validated a number of multiple disease resistance loci in maize. We identified and validated a number of loci and genes involved in modulating the defense response in maize (and in sorghum). With our collaborators, we identified a receptor kinase gene that confers southern leaf blight susceptibility and we showed that it appears to function as a suppressor of the basal defense response.
We completed multiple cycles of both phenotypic and genomic selection for resistance to Fusarium ear rot from the same base population. We demonstrated that both genomic and phenotypic selection were effective in this population, and that genomic selection implemented in two cycles per year would be more effective than phenotypic selection, but genetic variation loss needs to be monitored and genomic prediction model retraining is probably required every four generations or less.
We evaluated 80 open-pollinated maize varieties for a range of traits over several environments and used these data to measure the phenotypic similarities among the varieties, identifying clusters of related varieties. A subset of populations was subjected to two cycles of recurrent selection for basic agronomic traits, resulting in rapid improvements in some traits. We also demonstrated that selection for low protein content in grain was effective.
During the course of this project almost two thousand GEM entries (F3 lines) were evaluated in first-year trials, with just over 250 advanced to second year trials. In total, over 42,000 yield trial plots were coordinated by the project in Raleigh, North Carolina with just under 40% of these planted by cooperators and the rest planted in North Carolina by the Raleigh GEM project. Over 1,000 new breeding crosses were developed and evaluated, with approximately 70 of those selected for use in the development of new GEM families. Also, during the project period more than 50 maize lines from the tropics were evaluated for use in development of diverse new breeding crosses and several promising sources were identified, including lines from the International Center for the Improvement of Maize and Wheat in Mexico, the Suwan Farm in Thailand, and other sources. Approximately 7,200 nursery rows and 1,400 isolation rows were planted at Central Crops Research Station in Clayton, North Carolina, over the last 5 years; since 2021 isolated hybrid production has been contracted out and several thousand rows have been grown under contract in Illinois, allowing researchers in Raleigh to focus more attention on corn nursery efforts. Almost 4,000 additional nursery rows were planted in Homestead, Florida and Puerto Vallarta, Mexico during the fall and winter months to improve cycle times and speed up the process of germplasm development and release. Five germplasm lines were recommended to cooperators during the project period.
Accomplishments
1. A gene that suppresses the defense response and suppresses fungal disease resistance. ARS researchers in Raleigh, North Carolina, are working to identify genes in maize that can be introduced or modified to improve disease resistance in the field. This will allow the reduced use of fungicides and a more robust maize crop. With their collaborators, they identified a receptor kinase gene that confers southern leaf blight susceptibility and showed that it appears to function as a suppressor of the basal defense response. They published this work in New Phytologist journal. Perhaps, counter-intuitively, the identification of susceptibility genes may be as important as the identification of resistance genes. Susceptibility genes control processes in the host that the pathogen exploits through its pathogenesis mechanisms, so if these processes can be disrupted, it may result in durable increases in resistance. Unlike many resistance genes, susceptibility genes can be easily targeted for editing using CRISPR-based mechanisms.
Review Publications
Rogers, A., Bian, Y., Krakowsky, M.D., Peters, D.W., Turnbull, C., Nelson, P., Holland, J.B. 2022. Genomic prediction for the germplasm enhancement of maize project. The Plant Genome. 15:4. https://doi.org/10.1002/tpg2.20267.
Kudenov, M., Krafft, D., Scarboro, C., Doherty, C., Balint Kurti, P.J. 2023. Hybrid spatial-temporal Mueller matrix imaging spectropolarimeter for high throughput plant phenotyping. Applied Optics. 62:2078-2091. https://doi.org/10.1364/AO.483870.
Lima, D., Castro Aviles, A., Alpers, T., Mcfarlan, B., Kaeppler, S., Ertl, D., Romay, C., Gage, J., Holland, J.B., Beissinger, T., Bohn, M., Buckler, E., Edwards, J., Flint-Garcia, S., Hirsch, C., Hood, E., Hooker, D., Knoll, J., Kolkman, J., Liu, S., Mckay, J., Minyo, R., Moreta, D.E., Murray, S., Nelson, R., Schnable, J., Sekhon, R., Singh, M., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Washburn, J.D., Weldekidan, T., Wisser, R., Xu, W. 2023. 2018-2019 field seasons of the maize genomes to fields (G2F) G x E project. BMC Genomic Data. 24:29. https://doi.org/10.1186/s12863-023-01129-2.
Chen, C., Zhao, Y., Tabor, G., Nian, H., Phillips, J., Wolters, P., Yang, Q., Balint Kurti, P.J. 2023. A leucine rich repeat receptor-like kinase gene confers susceptibility to southern leaf blight of maize. New Phytologist. 238:1182-1197. https://doi.org/10.1111/nph.18781.
Kloppe, T., Whetten, R.B., Kim, S., Powell, O., Luck, S., Douchkov, D., Whetten, R., Hulse-Kemp, A.M., Balint Kurti, P.J., Cowger, C. 2023. Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a. New Phytologist. 238:1546-1561. https://doi.org/10.1111/nph.18809.
Choquette, N.E., Holland, J.B., Weldekidan, T., Drouault, J., De Leon, N., Flint Garcia, S.A., Lauter, N.C., Murray, S., Xu, W., Wisser, R. 2023. Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize. New Phytologist. 238(2):737-749. https://doi.org/10.1111/nph.18769.
Scarboro, C.G., Doherty, C.J., Balint Kurti, P.J., Kudenov, M.W. 2022. Multistatic fiber-based system for measuring the Mueller matrix bidirectional reflectance distribution function. Applied Optics. 61(33):9832-9842. https://doi.org/10.1364/AO.470608.
