Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-005-44-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jan 1, 2020
End Date: Dec 31, 2020
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.
In this year, sequencing will be completed for the third batch of lines (fourth if additional lines are identified of interest) and data will be analyzed. 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. 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.