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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #436007

Research Project: Identifying historically important genes in cotton through deep sequencing (2019)

Location: Genomics and Bioinformatics Research

Project Number: 6066-21310-005-34-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2019
End Date: Dec 31, 2019

This project will focus on bioinformatics analysis of deep sequencing data from current and historically important cultivated Gossypium (G.) hirsutum lines (available through the USDA and the National Germplasm Collection) in order to determine genes associated with yield, fiber quality, and resistance to Fusarium wilt. Comparisons of genes of interest will enhance researcher’s abilities to decipher mechanisms responsible for increasing the commodity value of current cotton production. Sequence data available from collaborators will be analyzed with the aim of determining factors to enhance development of new cotton cultivar varieties with higher fiber yield and quality and Fusarium tolerance.

A pilot set of four lines was used in the previous project to optimize the pipeline for informatics analysis. The highest quality Gossypium (G.) hirsutum genome available at the time of analysis will be used for reference to establish a variant collection between all sequenced lines. Single Nucleotide Polymorphisms (SNPs) determined between sequenced historically important cultivated G. hirsutum lines will be used in this study for targeted analyses in relation to selection across time and genes of interest in relation to phenotypes of interest for validation. We will also collaborate with the Haigler lab on bioinformatics analyses that will aid the generation of longer and finer fiber through candidate gene analysis.