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United States Department of Agriculture

Agricultural Research Service


Location: Corn Insects and Crop Genetics Research

Project Number: 5030-22000-017-18-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Aug 1, 2010
End Date: Jul 31, 2014

Associate SNP markers with existing AFLP linkage map and sequence midgut transcriptome for scaffolding RNAseq data.

Feeding damage to corn by larval European corn borer (ECB), Ostrinia nubilalis, is controlled by transgenic hydrids that express the Bacillus thuringiensis (Bt) toxin Cry1F. Field screens have shown the existence of Cry1F resistant ECB phenotypes in midwestern fields, and following mapping of this trait with amplified fragment length polymorphism (AFLP) markers we have identified a quantitative trait locus (QTL) on linkage group (LG) 12. More detailed mapping of this QTL interval will require the generation of a large number of novel genetic markers in order to identify the causal gene(s). To do this, we will predict the presence of single nucleotide polymorphism (SNP) loci from homolgous expressed sequence tag (EST) reads, and develop molecular assays to detect variation using high-throughput genotyping on the SEQUENOM MassARRAY platform. A high number of SNP markers will be used to genotype backcross progeny generated in a biphasic mapping approach that exploits the lack of meiotic recombination in female Lepidoptera, and likely result in a refined QTL interval with a greater number of markers compared to our prior AFLP-based map. Additionally, we will use the Illumina Genome Analyzer II for ultra-deep sequencing to detect changes in quantity and structure (mutational- and splosomal-level) of larval ECB midgut transcripts among full-sib backcross progeny that show a segregating Cry1F resistance trait. This sequencing approach will detect expression changes, termed expression QTL (eQTL), that co-segregate with larval resistance traits. Structural changes in eQTL transcripts will be used to develop additional SNP markers, and applied to genotyping full-sibs within the same backcross pedigrees and refining the original QTL defined by AFLP-mapping. Our approach of using traditional QTL and eQTL analyses will test for both co-segregation of SNP markers (loci) and differentially-expressed transcripts with larval phenotypes. The goal of this research will be to develop a diagnostic molecular assay to detect population-level changes in the frequency of alleles conferring resistance to Cry1F toxin in O. nubilalis, which will be a valuable tool for stakeholders to use in evaluating IRM strategies and recommendations.

Last Modified: 10/19/2017
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