2012 Annual Report
1a.Objectives (from AD-416):
Apply molecular genetic markers to genotype European corn borer from populations in North America and Europe, and detect the levels of genetic differences. These data will be used to estimate the level of genetic divergence within and between European corn borer populations based on geography and ecological/demographic factors.
1b.Approach (from AD-416):
Molecular genetic markers that detect variation at Single Nucleotide Polymorphisms (SNPs) within the European Corn Borer (ECB) genome have been developed by USDA-ARS researchers in Ames, Iowa. Assays that detect SNP marker variation are adapted for use on a Sequenom MassARRAY system located at the Center for Plant Genomics at Iowa State University (ISU-CPG). Since assay materials are already available for use in the USDA laboratory, this project will incur nominal additional cost to ARS. DNA samples have already been prepared for ECB collected at the North American sites of North Platte, NE, Crawfordsville, IA, Monmoth, IL, Frankfort, IN, Bowersville, OH, and Oak Corners, NY. Collaborators in Europe have already provided DNA extracts from Rzeszów, Poland, Csongrad, Hungary, and Krasnodar, Russia. Additionally, collaborators in France will be providing DNA samples from 17 collection sites (estimated ship date to USDA in Ames, IA is July 2011). A total of 178 SNP markers will be used to genotype all ECB samples using the Sequenom MassARRAY at the ISU-CPG, and resulting data will be received by the USDA for statistical analyses. Initial criteria for screening markers will include the determination of Hardy-Weinberg Equilibrium (HWE), with deviations calculated by chi-square tests between observed and expected heterozygosities. SNP markers that are in HWE will be used to estimate hierarchical population genetic parameters (Fst, Fis, and Fit), and exact tests for population differentiation using GENEPOP4.06 analysis software. Geographic structuring will be assessed using the Isolation By Distance (IBD) model that tests for correlation between Log of geographic distance between collection sites (in kilometers) and the parameter (Fst/(1-Fst)), and by principal component analysis to estimate other factors that influence genotypic variance among populations. Furthermore, the program STRUCTURE2.1 will be used to indicate the level of co-ancestry between genotypes from collection sites, and estimate the number of distinct breeding populations, level of population subdivision, and rate of migration (genetic exchange) within the ECB populations.
European Corn Borer (ECB) moths were collected at 10 sites in North America, and DNA was successfully extracted and quantified. Additionally, ECB from 35 sites in Europe were obtained from cooperators in France. A total of 1197 DNA samples were genotyped using 118 Single Nucleotide Polymorphism (SNP) on the Sequenom MassARRAY and for two markers located on the mitochondrial genome by USDA-ARS researchers in Ames, Iowa. The SNP data included a marker for the fatty-acyl reductase gene that USDA-ARS researchers in Ames, Iowa developed for the differentiation of pheromone races of ECB. Genotypic data from eight microsatellite loci were contributed by cooperators in France for all 1197 samples. A dataset that combined all genetic markers was completed collaboratively with researchers from Seoul National University, and appropriate analyses of population genetic structure in ongoing.