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United States Department of Agriculture

Agricultural Research Service


Location: Plant Science Research

2009 Annual Report

1a. Objectives (from AD-416)
Objectives are to (1) identify genes and genome regions controlling key traits in diverse maize germplasm using multiple populations and novel genetic mapping methods; (2) identify and characterize new sources of resistance to southern leaf blight (SLB), gray leaf spot (GLS), northern leaf blight (NLB), and Fusarium ear rot by developing new near-isogenic line sets, identifying QTL conferring resistance to multiple foliar diseases, and evaluating the known genetic diversity among public maize inbreds; and (3) incorporate favorable alleles from exotic maize into adapted maize lines, with particular emphasis on improvement of resistance to Fusarium ear rot and fumonisin contamination.

1b. Approach (from AD-416)
Develop genetic mapping populations appropriate for identification of favorable alleles in exotic maize by identifying genome regions and specific genes controlling the response to photoperiod in multiple tropical maize inbreds. Develop interconnected multiple populations and novel statistical methods to map specific genes controlling quantitative trait variation in diverse maize. Fine-map QTL for SLB, NLB, GLS, Fusarium ear rot and fumonisin contamination resistance. Characterize specific disease resistance QTL using near-isogenic line pairs. Identify QTL conferring resistance to multiple foliar diseases. Complete multiple environment screening of a 302-line population encompassing the known genetic diversity among public maize inbreds for resistance to SLB, NLB and GLS. Identify new sources of resistance to SLB, Fusarium ear rot, and fumonisin contamination from the GEM program and the NCSU tropical maize breeding program. Develop new lines with elite agronomic performance and enhanced resistance to Fusarium ear rot by backcrossing. Test if selection for resistance to Fusarium ear rot results in improved resistance to contamination by the associated mycotoxin fumonisin.

3. Progress Report
We have made good progress in fine mapping of a Southern Leaf Blight resistance gene on chromosome 3 and have identified several candidate genes. We have also started to fine-map a Southern Leaf Blight resistance gene on chromosome 6 and are making good progress. We have shown that we can reliably score the presence or absence of the gene on a single plant basis in the greenhouse. We have also initiated a project to identify the underlying gene using transposon tagging. Alone and in collaboration with a group at Cornell University, we have looked at several populations for evidence of genes conferring resistance to multiple diseases. We have not yet shown any compelling evidence that they exist in the populations tested. Our working hypothesis is that the more significant genes tend to be disease-specific, while smaller-effect genes (that may not be detectable by conventional analysis) may confer some level of resistance to multiple diseases. We compared pairs of lines differing only for Southern Leaf Blight resistance genes on chromosomes 3 and 6 microscopically and for expression levels of several genes related to infection response. We found no evidence that the specific genes tested slow down the initial stages of infection. Nor did they confer significantly different levels of pathogenesis-related gene expression in response to the early stages of infection. Therefore, they must mediate disease resistance through some other mechanism. Photoperiod response gene regions were identified in multiple maize populations. The Maize Nested Association Mapping population, the largest public genetic mapping resource ever developed, was completed; seed sent to the USDA Maize Genetics Cooperation Stock Center for public release, and genotypic data uploaded to public genome databases for distribution. The genetic basis of flowering time and of Southern Leaf Blight resistance in diverse maize was characterized in detail using this population, revealing that these traits are controlled by many genes, each of which has only small effects on a trait. Genomic regions with low or high recombination rates and chromosomal regions that may be important contributors to hybrid vigor were identified using the Nested Association Mapping population. Superior backcross-derived lines combining resistance to Fusarium ear rot and hybrid yield potential were identified. 50 advanced lines from the USDA Germplasm Enhancement of Maize project and the North Carolina State University maize inbred development programs were tested for resistance to Fusarium ear rot and fumonisin contamination resistance.

4. Accomplishments
1. Maize Nested Association Mapping population Many agriculturally important traits are genetically complex, controlled by many genes, hindering the identification of the causal genes. The Maize Nested Association Mapping population was developed in collaboration with USDA-ARS groups at Ithaca, NY and Columbia, MO and consists of 5000 genetically unique mapping lines derived from 25 crosses, encompassing a large sampling of the genetic diversity of maize. We showed the power of this population to reveal the many genes of small effect that impact flowering time in maize. Seeds of each line and their genotypic marker information were released publicly for use by the maize research community at large. This population and genetic data represent the single most powerful public resource for complex trait analysis of any species.

Review Publications
Eller, M.S., Payne, G., Holland, J.B. 2008. Breeding for Improved Resistance to Fumonisin Contamination in Maize. Toxin Review. 27:371-389.

Zwonitzer, J.C., Bubeck, D.M., Bhattramakki, D., Goodman, M.M., Arellano, C., Balint Kurti, P.J. 2009. Use of backcross recurrent selection and QTL mapping to identify loci contributing to southern leaf blight resistance in a highly resistant maize line. Theoretical and Applied Genetics. 118:911-925.

Holland, J.B. 2009. Increasing Yield. Maize Handbook. 469-482.

Nelson, P., Coles, N., Holland, J.B., Bubeck, D., Smith, S., Goodman, M. 2008. Molecular Characterization of Maize Inbreds with Expired U.S. Plant Variety Protection. Crop Science. 48:1673-1685.

Johal, G., Balint Kurti, P.J., Weil, C. 2008. Mining and harnessing natural variation - a little MAGIC. Crop Science. 48:2066-2073.

Poland, J., Balint Kurti, P.J., Wisser, R., Pratt, R., Nelson, R. 2009. Shades of gray: The world of quantitative disease resistance. Trends in Plant Science. 4:21-29.

Balint Kurti, P.J., Johal, G. 2009. Maize Disease Resistance. Handbook of Maize. 1 p.229-250.

Balint Kurti, P.J., Zwonitzer, J., Wisser, R. 2008. Use of an Advanced Intercross Line Population for Precise Mapping of Quantitative Trait Loci for Gray Leaf Spot Resistance in Maize. Crop Science. 48:1696-1703.

Williams, W.P., Krakowsky, M.D., Windham, G.L., Balint-Kurti, P.J., Hawkins, L.K., Henry, W.B. 2008. Identifying maize germplasm with resistance to aflatoxin accumulation. Toxin Reviews. 27:319-345.

Van Esbroeck, G., Ruiz, J., Sanchez, J., Holland, J.B. 2008. A COMPARISON OF LEAF APPEARANCE RATES AMONG TEOSINTE, MAIZE LANDRACES AND MODERN MAIZE. Maydica. 53:117-153.

Eller, M.S., Robertson-Hoyt, L., Payne, G., Holland, J.B. 2009. Grain Yield and Fusarium Ear Rot of Maize Hybrids Developed From Lines With Varying Levels of Resistance. Maydica. 53:231-237.

Last Modified: 06/22/2017
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