Research Project: Genetics of Disease Resistance and Food Quality Traits in Corn

Location: Plant Science Research

2020 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
ARS researchers at Raleigh, North Carolina, mapped and validated several loci associated with multiple disease resistance in maize. ARS researchers at Raleigh, North Carolina, identified several genes and loci associated with modulating the maize defense response and we wrote and published a review on the maize hypersensitive defense response. ARS researchers at Raleigh, North Carolina, have also developed a novel introgression line resource which will be of considerable benefit to the maize genetics community. ARS researchers at Raleigh, North Carolina, completed four cycles of genomic selection for resistance to Fusarium ear rot in a maize population. ARS researchers at Raleigh, North Carolina, initiated selection within 12 heirloom populations to develop agronomically improved populations. ARS researchers at Raleigh, North Carolina, made crosses and initiated breeding populations between lines with low protein content and good agronomic performance. ARS researchers at Raleigh, North Carolina, coordinated 7700 Germplasm Enhancement of Maize yield plots with about 3200 planted in North Carolina and the rest planted by six cooperators at various locations throughout the Southeast and Midwest. The results of second year trials will determine which entries are recommended to the Germplasm Enhancement of Maize project cooperators. Disease evaluation continues in 2019 for Gray Leaf Spot, where advanced materials were evaluated at three locations in North Carolina (Laurel Springs, Salisbury, and Waynesville). Over 150 new breeding crosses were observed for agronomic traits of interest. The majority of the breeding crosses were produced by the Raleigh, North Carolina program, but approximately one-third were provided by the Germplasm Enhancement of Maize program in Ames, Iowa.

Accomplishments
1. Discovery of microbe-dependent hybrid vigor in maize. Hybrid vigor is the superior yield observed in hybrids compared to their inbred parents. Hybrid vigor is the basis of commercial corn production in the USA. The physiological and genetic mechanisms linking genomic hybridization to phenotypic superiority remain poorly understood. Nearly all research into the subject thus far has focused on molecular and quantitative genetic processes, with mixed success; meanwhile the influence of the environment on hybrid vigor has been mostly ignored. In collaboration with North Carolina State University scientists, ARS researchers at Raleigh, North Carolina were able to show that when soil microbes are absent or reduced, hybrid vigor of maize is eliminated or greatly weakened. We demonstrated the generality of this phenomenon in three distinct microbial environments: in the lab using a synthetic community of seven bacterial strains, in a growth chamber using a complex microbial community derived from soil, and in the field using four different methods of soil fumigation. This striking, repeatable pattern indicates, for the first time, that hybrid vigor arises, in part, from interactions with microbial neighbors. This finding will be of outstanding interest to biologists across a wide diversity of fields, including both micro- and macro-biologists. In addition, hybrid vigor is the reason hybrid corn dominates corn production in the USA and has been a cornerstone of global food security for decades. Therefore, ARS researchers at Raleigh, North Carolina, findings have high potential to lead to new methods of harnessing the power of hybrid vigor to improve agricultural productivity.

Review Publications
Tuleski, T., Kimball, J., Do Amaral, F.P., Pereira Federal, T.P., Tadra-Sfeir, M.Z., De Oliveira Pedrosa, F., De Souza, E.M., Balint Kurti, P.J., Monteiro, R.A., Stacey, G. 2019. Herbaspirillum rubrisubalbicans as a phytopathogenic model to study the immune system of Sorghum bicolor. New Phytologist. 33:235-246.
He, Y., Christensen, S.A., Karre, S., Johal, G., Balint Kurti, P.J. 2019. A maize polygalacturonase functions as a suppressor of the hypersensitive response and programmed cell death in maize. Biomed Central (BMC) Plant Biology. 19:310.
Balint Kurti, P.J. 2019. The plant hypersensitive response; concepts, control and consequences. Molecular Plant Pathology. 20:1163-1178.
Martin, L., Rucker, E., Thomason, W., Holland, J.B., Wisser, R., Balint Kurti, P.J. 2019. Validation of multiple disease resistance QTL from chromosome segment substitution population in F2:3 family populations. G3, Genes/Genomes/Genetics. 9:2905-2912.
Doblas-Ibanez, P., Deng, K., Vasquez, M., Giese, L., Cobine, P., Kolkman, J., King, H., Jamann, T., Balint Kurti, P.J., De La Fuente, L., Nelson, R., Mackey, D., Smith, L. 2019. Dominant, heritable resistance to Stewart’s wilt in maize is associated with an enhanced vascular defense response to infection with P. stewartii. Molecular Plant-Microbe Interactions. 32:1581-1597.
Kimball, J., Cui, Y., Chen, D., Brown, P., Rooney, W., Stacey, G., Balint Kurti, P.J. 2019. Identification of QTL for target leaf spot resistance in Sorghum bicolor and investigation of relationships between disease resistance and variation in the MAMP response. Scientific Reports. 9:1-9.
Samira, R., Zhang, X., Kimball, J., Cui, Y., Stacey, G., Balint Kurti, P.J. 2019. Quantifying MAMP-induced production of reactive oxygen species in sorghum and maize. Bio-protocol. https://doi.org/10.21769/BioProtoc.3304.
Wagner, M., Busby, P., Balint Kurti, P.J. 2019. Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance. New Phytologist. 225:2152-2165.
Sun, Y., Zhu, Y., Balint Kurti, P.J., Wang, G. 2020. Fine-tuning immunity: Players and regulators for plant NLRs. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2020.02.008.
Wang, Y., Martins, L., Sermons, S.M., Balint Kurti, P.J. 2020. Genetic and physiological characterization of a Calcium deficiency phenotype in maize. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.120.401069.
Camargo Senhorinho, H.J., Dacal Coan, M.M., Marino, T.P., Kuki, M.C., Barth Pinto, R.J., Scapim, C.A., Holland, J.B. 2019. Genome-wide association study of popping expansion in tropical popcorn and field corn germplasm. Crop Science. 59:2007–2019.
Stagnati, L., Rahjoo, V., Samayoa, L.F., Holland, J.B., Busconi, M., Lanubile, A., Marocco, A. 2020. A genome-wide association study to understand the effect of Fusarium verticillioides infection on seedlings of a maize diversity panel. G3, Genes/Genomes/Genetics. 10:1685-1696.
Mcfarland, B.A., Alkhalifah, N., Bohn, M., Bubert, J., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Gage, J.L., Falcon, C.M., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hood, E., Hooker, D., Jarquin, D., Kaeppler, S., Knoll, J.E., Kruger, G., Lauter, N.C., Lee, E.C., Lima, D.C., Lorenz, A., Lynch, J.P., Mckay, J., Miller, N.D., Moose, S.P., Murray, S.C., Nelson, R., Poudyal, C., Rocheford, T., Rodriguez, O., Romay, M., Schnable, J.C., Schnable, P.S., Scully, B.T., Sekhon, R., Silverstein, K., Singh, M., Smith, M., Spalding, E.P., Springer, N., Thelen, K., Thomison, P., Tuinstra, M., Wallace, J., Walls, R., Wills, D., Wisser, R.J., Xu, W., Yeh, C., De Leon, N. Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Research Notes. 13,71 (2020). https://doi.org/10.1186/s13104-020-4922-8.
Wisser, R.J., Fang, Z., Holland, J.B., Teixeira, J.E., Dougherty, J., Weldekidan, T., De Leon, N., Flint-Garcia, S.A., Lauter, N.C., Murray, S.C., Xu, W., Hallauer, A. 2019. The genomic basis for short-term evolution of environmental adaptation in maize. Genetics. 213(4):1479-1494. https://doi.org/10.1534/genetics.119.302780.
Guo, T., Yu, X., Li, X., Zhang, H., Zhu, C., Flint-Garcia, S.A., McMullen, M.D., Holland, J.B., Szalma, S.J., Wisser, R., Yu, J. 2019. Optimal designs for genomic selection in hybrid crops. Molecular Plant. 12(3):390-401. https://doi.org/10.1016/j.molp.2018.12.022.
Morales, L., Repka, A.C., Swarts, K.L., Stafstrom, W.C., He, Y., Sermons, S.M., Yang, Q., Lopez-Zuniga, L.O., Rucker, E., Thomason, W.E., Nelson, R.J., Balint Kurti, P.J. 2020. Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines. Plant Journal. https://doi.org/10.1111/tpj.14787.