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

Location: Plant Science Research

2019 Annual Report

Objectives
Objective 1. Identify genes and mechanisms underlying defense response and quantitative disease resistance to foliar fungal pathogens and ear stalk rots in maize. Sub-objective 1.A. Validate and fine-map QTL alleles underlying multiple disease resistance in maize. Sub-objective 1.B. Test the effects of candidate SLB resistance genes using transgenic and mutant analysis. Sub-objective 1.C. Assess the resistance of diverse lines to Anthracnose stalk rot. Sub-objective 1.D. Validate the roles of genes associated with variation in the maize hypersensitive response (HR). Sub-objective 1.E. Validate the effects of candidate QTL identified in genome-wide association studies of Fusarium ear rot. Objective 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. Objective 3. Evaluate diverse maize germplasm for potential in specialty food products by conducting agronomic and disease evaluations. Sub-objective 3.A. Evaluate open-pollinated varieties for food quality and agronomic production characteristics. Sub-objective 3.B. Develop populations with lower grain protein content for use in metabolic disorder diets.

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 developed F2:3 Populations mapping populations to validate and fine-map genes underlying multiple disease resistance in maize. ARS researchers identified and genotyped maize plants carrying transposal element insertions in candidate SLB resistance genes. ARS researchers developed constructs for transient expression to validate the roles of genes associated with variation in the maize hypersensitive response (related to disease resistance). ARS researchers evaluated corn lines from three different crosses segregating for previously identified ear rot resistance gene regions in the field for ear rot resistance. ARS researchers completed two cycles of genomic selection for resistance to Fusarium ear rot in a maize population. ARS researchers screened 100 heirloom and open-pollinated corn varieties in the field for agronomic performance and grain quality. Researchers evaluated diverse inbred lines and hybrids in the field for grain protein content, and a subset of those for specific amino acid contents.

Accomplishments
1. Demonstration that a gene involved in the synthesis of lignin is also important for resistance to at least two diseases. Maize diseases cause significant yield losses. Genes that confer resistance to multiple diseases are a valuable tool to protect the maize crop. The gene that encodes the enzyme caffeoyl-CoA O-methyltransferase was identified as a gene that conferred significant levels of resistance to two maize diseases; southern corn leaf blight and grey leaf spot. ARS scientists at Raleigh, North Carolina, used a variety of methods to identify the gene, these include: using mutants in which the gene was mis-expressed, using transgenic plants in which the gene was over-expressed and mapping the position of the gene in the maize genome. This finding helps us understand one of the ways that plants can defend themselves against disease. Several maize breeding companies have shown interest in this work and it is likely that they will consider this gene when breeding future varieties of maize.

Review Publications
Gage, J., Jarquin, D., Romay, M., Lorenz, A., Buckler IV, E.S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gardiner, J., Good, B., Hirsch, C., Holland, J.B., Hooker, D., Knoll, J.E., Kolkman, J., Kruger, G., Lauter, N.C., Lawrence-Dill, C., Lee, E., Lynch, J., Murray, S., Nelson, R., Petzoldt, J., Rocheford, T., Schnable, J., Schnable, P., Scully, B.T., Smith, M., Springer, N., Srinivasan, S., Walton, R., Weldekidan, T., Wisser, R., Xu, W., Yu, J., De Leon, N. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications. 8:1348. https://doi.org/10.1038/S41467-017-01450-2.
Swartz, K., Gutaker, R.M., Benz, B., Blake, M., Bukowski, R., Holland, J.B., Kruse-Peeples, M., Lepak, N.K., Prim, L., Romay, M.C., Ross-Ibarra, J., Sanchez-Gonzalez, J., Schmidt, C., Schuenemann, V.J., Krause, J., Matson, R.G., Weigel, D., Buckler IV, E.S., Burbano, H.A. 2017. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science. 357:512-515.
Stagnati, L., Lanubile, A., Samayoa, L., Bragalanti, M., Giorni, P., Busconi, M., Holland, J.B., Marocco, A. 2019. A genome wide association study reveals markers and genes associated with Fusarium kernel rot resistance in a maize diversity panel. Journal of Experimental Botany. 9:571-579.
Samayoa, L.F., Dunne, J.C., Andres, R.J., Holland, J.B. 2018. Harnessing maize biodiversity. In: Bennetzen, J., S. Flint-Garcia, C. Hirsch, and R. Tuberosa (Eds.) The Maize Genome. Springer, Switzerland. Book Chapeter. pg. 335-366.
Alkhalifah, N., Campbell, D., Falcon, C., Miller, N., Romay, M., Walls, R., Walton, R., Yeh, C., Bohn, M., Buckler IV, E.S., Ciampitti, I., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hooker, D., Kaeppler, S., Knoll, J.E., Lauter, N.C., Lee, E., Lorenz, A., Lynch, J., Moose, S., Murray, S., Nelson, R., Rocheford, T., Rodriguez, O., Schnable, J., Scully, B.T., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R., Xu, W., Ertl, D., Schnable, P., De Leon, N., Spalding, E., Edwards, J.W., Lawrence-Dill, C. 2018. Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. Biomed Central (BMC) Plant Biology. 11:452. https://doi.org/10.1186/s13104-018-3508-1.
Morales, L., Marino, T.P., Wenndt, A.J., Fouts, J.Q., Holland, J.B., Nelson, R.J. 2018. Dissecting symptomatology and fumonisin contamination produced by Fusarium verticillioides in maize ears. Phytopathology. 108:1475-1485.
Holland, J.B. 2018. Two steps on the path to maize adaptation. Current Biology. 28(18):PR1098-R1101.
Morales, L., Zila, C.T., Moreta Mejia, D.E., Montoya Arbelaez, M., Balint Kurti, P.J., Holland, J.B., Nelson, R.J. 2019. Diverse mechanisms of resistance to Fusarium verticillioides infection and fumonisin contamination in four maize recombinant inbred line families. Toxins. 11:86.
Yang, C., Samayoa, L., Bradbury, P., Olukolu, B.A., Xue, W., York, A.M., Tuholski, M.R., Wang, W., Daskalska, L.L., Neumeyer, M.A., Sanchez-Gonzales, J., Romay, M.C., Glaubitz, J.C., Sun, Q., Buckler IV, E.S., Holland, J.B., Doebley, J.F. 2019. The genetic architecture of teosinte catalyzed and constrained maize domestication. Proceedings of the National Academy of Sciences. 116:5643-5652.
Sarinelli, J.M., Murphy, J.P., Tyagi, P., Holland, J.B., Johnson, J.W., Mergoum, M., Mason, R.E., Babar, A., Harrison, S., Sutton, R., Griffey, C.A., Brown Guedira, G.L. 2019. Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel. Theoretical and Applied Genetics. 132:1247.
He, Y., Kim, S., Balint Kurti, P.J. 2019. A maize Cytochrome b-c1 complex subunit protein ZmQCR7controls variation in the hypersensitive response. Planta. 249:1477-485.
Lopez-Zuniga, L.O., Wolters, P., Davis, S., Kolkman, J., Nelson, R., Hooda, K.S., Rucker, E., Thomason, W., Wisser, R., Balint Kurti, P.J. 2019. Using maize chromosome segment substitution line populations for the identification of loci associated with multiple disease resistance. G3, Genes/Genomes/Genetics. 9(1):189-201.
Xiaodong, X., Olukolu, B., Yang, Q., Balint Kurti, P.J. 2018. Identification of a locus in maize controlling response to a host-specific toxin derived from Cochliobolus heterostrophus, causal agent of Southern Leaf Blight. Molecular Plant-Microbe Interactions. 131:2601-2612.