Location: Corn Insects and Crop Genetics Research2011 Annual Report
1a. Objectives (from AD-416)
To screen a previously constructed Bacterial Artificial Chromosome (BAC) library, derived from western corn rootworm (WCR) and held in the Cooperator's laboratory, with 50 validated Single Nucleotide Polymorphism (SNP) loci to determine which clones carry each locus. To prepare DNA from selected BAC clones for high throughput sequencing. To use DNA from backcross pedigrees of WCR to create a genetic linkage map for organophosphate insecticide resistance.
1b. Approach (from AD-416)
A subset of 50 validated Single Nucleotide Polymorphism (SNP) loci derived from Expressed Sequence Tag (EST) sequence data will be used to screen the available western corn rootworm (WCR) Bacterial Artificial Chromosome (BAC) library prepared previously by the Cooperator to determine which clones carry each locus. Screening will be done by PCR at CICGRU. Each superpool contains DNA from 4,608 clones corresponding to twelve 384-well plates of library clones, giving a total of 24 superpools for the entire library. For each superpool, there is an associated "pool plate" that contains 12 pools of DNA from each 384-well plate, 16 pools from each row of all the plates, 24 pools from each column of all the plates, and 24 "diagonal pools." Thus, a PCR amplicon can be associated with an individual BAC using 100 PCR assays (24 to identify the superpool plus 76 to determine the plate, row, and column within the superpool). A genetic linkage map will be constructed with approximately 600 SNP markers developed by CICGRU, using backcross pedigrees of WCR that were collected by the Cooperator and phenotyped for organophosphate resistance. The set of SNP loci to be used in screening will be selected to give an even distribution across the linkage map, but may also target loci for which EST annotations or other information indicates a gene relevant to adaptations to pest management or potential biotechnology applications. PCR primers will be designed from the EST sequences from which the SNP was derived. Optimal PCR conditions for each primer pair will be determined using WCR genomic DNA as a template. In cases where optimal conditions cannot be determined, new primer pairs will be designed and tested. For each SNP locus an initial round of 24 PCR assays followed by agarose gel electrophoresis of the reaction products will determine the superpools that contain the amplicon. Second-round PCR assays and agarose gel electrophoresis on the relevant pool plates will identify the BAC clones containing the amplicon. Because the BAC library is estimated to give 4.6-fold coverage of the WCR genome, we expect, on average, to perform five second-round assays per SNP locus. BAC clones that have been associated with a SNP locus will be digested with HindIII, BamHI, or EcoRI restriction enzymes and separated by agarose gel electrophoresis. The resulting restriction-site fingerprints will be used to arrange the BAC clones associated with each SNP locus into a contiguous region. DNA will be extracted from 1 or 2 BAC clones from each contig associated with a SNP locus for future high-throughput 454 (Roche) pyrosequencing. The clones to be sequenced will be selected to maximize the length of sequence obtained on each side of the SNP.
3. Progress Report
A western corn rootworm bacterial artificial chromosome library was previously constructed. A bacterial artificial chromosome is a type of tool, called a vector, which inserts DNA from any species into a bacterium. Once the foreign DNA has been cloned into the bacterium, many copies of it can be made and sequenced. The library we constructed contains 110,592 clones of long stretches of DNA from the western corn rootworm. DNA preparations representing the entire library, organized into pools and "superpools," were screened for genes of interest using a technique that amplifies small amounts of DNA. Each superpool contains DNA from 4,608 clones corresponding to twelve 384-well plates of library clones, giving a total of 24 superpools for the entire library. For each superpool, there is an associated pool plate containing 12 pools of DNA from each 384-well plate, 16 pools from each row of all the plates, 24 pools from each column of all the plates, and 24 diagonal pools. This kind of arrangement allows efficient screening for particular genes of interest so that a bacterial artificial chromosome clone can be identified and sequenced in its entirety. Based on this initial screening, ten of these clones were identified and selected by USDA-ARS scientists in Ames, IA for complete sequencing by collaborators at the University of Illinois. Sequence analysis has revealed a lot of repetitive regions in this insect's DNA. Such characterization of the structure of the western corn rootworm genome has been crucial in preparing for a genome sequencing project, which is now underway. A genetic linkage map has been constructed using the markers validated in the parent research project. The linkage map shows the relative position of genes, with the genes closer together being more likely to be inherited together. The library will be screened further with single nucleotide polymorphism markers once they are validated in ongoing research within the parent project, and 80 of these genetic markers will be strategically selected for full sequencing based on the new linkage map that the markers have made possible. Progress is monitored through discussions at various technical meetings and conferences attended by both parties, and by frequent email correspondence and telephone calls initiated by both parties.