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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #430561

Research Project: Genome Wide Association Analysis to Genes

Location: Plant Genetics Research

Project Number: 5070-21000-040-03-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Dec 1, 2016
End Date: Nov 30, 2018

Objective:
The main challenge addressed by this research is that current Genome Wide Association Analysis (GWAS) strategies do not result in “cloned” genes or perfect molecular markers to use in breeding programs. The objective of this research is to develop and validate a research strategy and supporting bioinformatics tools and resources to enable efficient identification of genes that control phenotypes.

Approach:
Our research strategy is a proof of concept approach using a validated data set of cloned genes to test different strategies and modify existing bioinformatics tools to complete the pipeline to provide gene information that can be immediately utilized in soybean germplasm and variety development. We have selected the cloned genes to represent different categories of variation (for example, genes with common or rare variant alleles and genes with multiple variant alleles). Our strategy for bioinformatics tool modification and development is to have the computer science team work closely with the molecular biology team to determine the desired outcome and communicate the most effective way to achieve the outcome by either modifying an existing tool or building a new tool. We previously successfully collaborated to develop a visualization tool, for trait-related genomic visualization and applied the tool for the analysis of major soybean maturity gene haplotypes based on 72 sequenced soybean genomes.