2013 Annual Report
1a.Objectives (from AD-416):
The objective of this project is to analyze the genetic and phenotypic characterization data from new inbred lines displaying high and stable resistance to Aspergillus (A.) flavus and aflatoxin accumulation and to new genes and gene-based markers linked to these traits. Genes for resistance will be identified via association analysis orquantitative trait loci (QTL) mapping. New methodologies for efficient association mapping, including parameters for highest statistical power, will be tested. Methods to combine data from QTL mapping with association mapping will be developed.
1b.Approach (from AD-416):
Considerable work has already been done in the mapping of aflatoxin and Aspergillus (A.) flavus resistance in maize, and five fully phenotyped and genotyped quantitative trait loci (QTL) mapping populations and two association mapping panels are currently available for this project. The data must now be analyzed, and utilized to identify germplasm and genes associated with high resistance. In the first year, the analysis of field phenotypes in the International Maize and Wheat Improvement Center (CIMMYT) and Corn Host Plant Resistance Research Unit (CHPRRU) association mapping panels will be done first to account for high genotype by environment interaction (GxE) and potential measurement error, correlations and covariances between traits and population substructure, and best estimators of all phenotypes calculated. This will be followed by initial association mapping of both panels. In year two, testing new methodologies for dealing with multiple testing effects, low power due to imalanced allele frequencies, and other variables affecting association mapping can be done, and further association analyses of the two panels either to confirm genes found in one panel can be identified in the second panel, or combining the two independent association panels to analyze them jointly, to see if power is improved and false positive rate reduced. Finally, in the third year, the association mapping results will be combined with results from QTL mapping studies, in order to cross-validate and also identify genes linked to resistance that cannot be identified in either type of study alone.
The objective of this project is to analyze the genetic and phenotypic data from inbred lines of corn displaying high levels of stable resistance to Aspergillus flavus and aflatoxin accumulation to identify new genes and gene-based markers linked to these traits. Genes for resistance will be identified via association analysis. Here we report work done on the project since it was initiated in February 2012. Inbred lines of corn that had not previously been identified as resistant to aflatoxin accumulation were discovered during the phenotypic characterization of an association mapping panel of 300 inbred lines of corn. The association mapping panel was created by ARS scientists at Mississippi State, Mississippi. The panel included 300 diverse inbred lines. Some lines were selected because of their known resistance to aflatoxin contamination; some were selected from environments where Aspergillus flavus is often epidemic; and others were selected to add genetic diversity to the panel. All lines were crossed with a susceptible inbred line that is adapted to the southern United States. The resulting testcrosses were grown in replicated field trials for two years. Grain samples collected from the field trials were analyzed to determine concentration of aflatoxin. This was completed before the cooperative agreement between ARS and the University of the Republic, Montevideo, Uruguay, was established. The cooperators at the University of the Republic collated and analyzed the phenotypic data collected from the field trials conducted by ARS scientists. The analysis was designed to account for high genotype x environment (G × E) interactions, correlations and covariances between traits, population substructure, and errors in measurement. Best estimators of all phenotypes were calculated. A manuscript reporting the phenotypic data and identifying lines that are potential new sources of resistance to aflatoxin contamination has been prepared. Additional genetic analyses are in progress.