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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #434010

Research Project: Identifying Historically Important Genes in Cultivated Cotton Cultivars Through Deep Sequencing Analysis

Location: Genomics and Bioinformatics Research

Project Number: 6066-21310-005-29-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2018
End Date: Dec 31, 2018

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

Fiber quality and yield are the primary concern of current cotton producers. Studying the evolution and similarities among historic and current cultivated material will allow for identification of genes and gene combinations that have been historically under selection by breeders due to the superior phenotypic traits provided by these genetic combinations. Current studies have been focused on domestication and evolutionary differences utilizing wild Gossypium hirsutum, but studies of cultivated materials will allow for more immediate access to superior genetic combinations that have been successful in traditional cultivar development. Deep sequencing has proven useful in detailed pedigree breeding programs, where parental genotypes can be used for imputation into large downstream populations in conjunction with lower cost genotyping to improve statistical power by increasing number of markers (Livne et al., 2015). A set of historically important cotton cultivars have been identified and sequencing of an initial set is being done with USDA-ARS funding. The available resources are limited to covering the sequencing of the initial set and are insufficient for a dedicated bioinformatics effort needed to analyze such large-scale genomic information. This project will provide the funds for a dedicated bioinformatician to focus on this effort and related goals of cotton improvement through three specific aims as follows. 1) Develop a HapMap of sequence variants. 2) Identify historically important variants. 3) Empower targeted biological studies with population scale data. 4) Connect sequence variants with phenotypes of interest, including fiber yield, fiber quality, and Fusarium wilt (FOV) resistance.