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United States Department of Agriculture

Agricultural Research Service

Research Project: New Technologies for the Dissection of Complex Phenotypic Traits in Lepidoptera

Location: Corn Insects and Crop Genetics Research

Project Number: 3625-22000-017-10
Project Type: Reimbursable

Start Date: Mar 01, 2010
End Date: Feb 27, 2014

Objective:
Our first objective is to use "Next-Generation" Sequencing (NGS) on the Illumina Genome Analyzer II for ultra-deep sequencing of midgut transcripts, and detect changes in quantity and structure (mutational- and splicosomal-level) among transcripts from multiple full-sib Cry1Ab resistant and susceptible Ostrinia nubilalis larvae from backcross pedigrees. Our second objective is to describe expression differences between phenotypes, termed expression quantitative trait loci (eQTL), which co-segregate with phenotypic traits. Our third objective is to use single nucleotide polymorphisms (SNPs) within eQTL transcripts as markers for genotyping full-sibs within the same backcross pedigrees as used to define eQTL.

Approach:
Control measures suppress populations of larval Lepidoptera, but applications present challenges for long-term sustainability. Phenotypic plasticity within populations can form differential response of multiple genes or gene pathways to common environments and control practices. Portions of quantitative phenotypic variation within populations is attributed to differential response at the transcriptional level. As a robust microarray alternative, we will use "Next-Generation" Sequencing (NGS) by the Illumina Genome Analyzer II for ultra-deep sequencing of midgut transcripts to detect changes in quantity and structure (mutational- and splicosomal-level) among transcripts from multiple full-sib Cry1Ab resistant and susceptible Ostrinia nubilalis larvae from backcross pedigrees. Constitutive expression level changes between phenotypes, termed expression quantative trait loci (eQTL), that co-segregate with phenotypic traits will be identified. Transcript levels of genes within a gene regulatory network co-segregate, such that validation of eQTL involvement in trait determination cannot use futher expression assays. Structural changes in eQTL transcripts will be used for single nucleotide polymorphism (SNP) marker development, and markers applied to genotyping full-sibs within the same backcross pedigrees (mentioned above). Subsequent QTL analyses will test for co-segregation of genomic loci for candiate eQTL with the larval phenotype. These procedures for lepidopteran transcriptome analysis by NGS technologies include protocols for contig assembly, gene annotation, and SNP and splice variant predictions. NGS data will have added value due to analysis of different larval phenotypes segregating in pedigrees, such that eQTL will be identified. NGS application also will be achieved through validation of eQTL via QTL mapping of associated SNP loci.

Last Modified: 7/31/2014
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