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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #434423

Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

2018 Annual Report

Objective 1: Evaluate the cotton primary and secondary gene pools, as well as natural and synthetic cotton populations that are maintained in the USDA NPGS and cotton research community to identify useful genetic variability for industry-relevant traits, and provide information to breeders, along with augmented, and/or improved core sets of effective DNA markers. Sub-objective 1A: Augment and improve core sets of cotton SSR and SNP markers to effectively exploit the genetic variation of cotton germplasm and populations. Sub-objective 1B: Develop a core set of SSR markers for G. thurberi to allow for improved molecular characterization of this wild diploid Gossypium species. Objective 2: Sequence, refine, and annotate priority genomes of cotton species and accessions that contain genes controlling traits important to the cotton industry, and work with breeders to use these and previously identified cotton sequences to identify genomic regions for effective selections. Objective 3: Develop, improve, and manage an efficient and effective database and bioinformatics system, CottonGen, for efficiently exploiting cotton genetic variation. Objective 4: Identify key genes and genetic elements in cotton genomes, and use the information in selecting and verifying a range of priority agronomic traits, including biotic and abiotic stress resistance, and fiber and seed properties from materials contained in the USDA NPGS and cotton research community.

This project will provide the cotton industry with advanced genomic information and bioinformatic tools to enhance and accelerate the analysis and exploitation of genetic variability in the complex Gossypium genus. Current information suggests that genetic variation in cultivated cotton is limited, and that the overall structure of genetic variation in the Gossypium genus is not adequately resolved. More powerful tools are required to exploit the genetic potential of wild or uncultivated genotypes. Our recently completed genome assemblies of the Upland cotton genetic standard TM-1 and its probable progenitors provide a template for further sequencing efforts. Resequencing other cultivated and wild cotton species and/or accessions will allow comparative exploration for effective identification and manipulation of beneficial genes otherwise buried within Gossypium germplasm collections. In the current project, we will specifically develop and improve core sets of DNA markers tailored to individual cotton species, generate novel genome sequence information, and identify key genes or genetic elements linked to priority traits for improving agronomics, fiber and/or seed quality, and resistance to biotic/abiotic stresses. In cooperation with Cotton Incorporated, this project will provide support, coordination, and oversight to CottonGen, a database of genomic, genetic, and breeding resources managed by Washington State University. A primary goal of this project is to provide effective tools and information to identify and elucidate genetic variation within the U.S. National Cotton Germplasm Collection that is maintained by our sister germplasm project. New biological information developed by the project will be made publicly available in the GenBank and CottonGen databases.

Progress Report
This is a new project that replaced 3091-21000-038-00D and which is continuing and expanding upon the work of the precursor project. Work under this new project in FY 2018 addressed two FY 2019 milestones (Complete sample preparations of priority cotton species and germplasm accessions, Objective 1; and Improved Tripal database with new cotton data and tools, Objective 3). The preparation was initiated for cotton plant materials, experimental procedures, database management, and collaboration with national and international partners. Preliminary studies showed that resequencing genomes of representative Gossypium species and accessions facilitates exploitation of genetic variation to be used in cotton molecular breeding (Objective 2). Work was initiated with cooperators to further develop/expand the capabilities of CottonGen and associated bioinformatics tools including the Breeding Information Management Systems (BIMS) for effective management of cotton breeding data (Objective 3).