Skip to main content
ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #444798

Research Project: Management of Cotton Genetic Resources and Genetic Improvement of Cotton

Location: Crop Germplasm Research

Project Number: 3091-21000-048-000-D
Project Type: In-House Appropriated

Start Date: Mar 27, 2023
End Date: Mar 26, 2028

Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority cotton genetic resources to avoid backlogs in genetic resource and information management. Sub-objective 1.A: Apply core sets of molecular markers to systematically characterize underutilized cotton genetic resources. Sub-objective 1.B: Apply sequence-based methods to develop characterization profiles of cotton accessions to assist in priority genetic resource management activities. Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority cotton genetic resources and associated descriptive information. Sub-objective 2.A: Strategically broaden the genetic diversity conserved by the NCGC through acquisition of cotton and wild relative germplasm from exchanges and explorations. Sub-objective 2.B: Distribute viable seed and associated information for all available accessions to users of the NCGC. Sub-objective 2.C: Maintain safety, genetic integrity, and viability of priority cotton genetic resources and associated descriptive information. Objective 3: Conduct research to develop genetically-enhanced germplasm that broadens the diversity available for improving cotton by incorporating superior traits from cultivars, landraces, and wild relatives into adapted genetic backgrounds and genepools. Sub-objective 3.A: Evaluate cotton accessions and develop germplasm with improved seed traits. Sub-objective 3.B: Conduct research to broaden the diversity available for improving cotton by incorporating diverse alleles from landraces and wild relatives. Objective 4: Conduct research to develop, augment, and/or improve genomic tools for elucidating genetic variability of the primary and secondary cotton gene pools, as well as natural and synthetic cotton populations, and demonstrate effectiveness of these new tools. Sub-objective 4.A: Develop priority genome and pan-genome sequences and assemblies for cotton species and accessions that contain genes controlling traits important to the cotton industry. Sub-objective 4.B: Construct a practical haplotype graph for cotton genomic diversity. Objective 5: Conduct research to identify and manipulate economically valuable genes and/or genetic systems in cotton genomes and apply the information to improve priority traits, such as yield and quality of fiber and seed, and tolerance to biotic and abiotic stress. Sub-objective 5.A: Identify and map genes or QTLs that improve fiber quality. Sub-objective 5.B: Engineer or modify genes/genetic systems for enhanced cotton productivity under abiotic stress conditions. Objective 6: Expand and manage the current cotton database and bioinformatics systems to provide genomics and bioinformatic tools for efficiently exploiting cotton genetic variation for crop improvement. Goal: Coordinate genomic, genetic, and breeding data availability in CottonGen to enrich the delivered content and streamline users' centralized searches for specific information.

The U.S. National Cotton Germplasm Collection (NCGC) contains much of the diversity of the Gossypium genus – with genetic variability ranging from highly improved allotetraploid species to wild diploid species. The long-term goals of this project are to conserve, describe, and distribute accessions of the NCGC, as well as conduct genetic and genomic research to make these resources available to researchers. Cotton growers need cultivars with genetic variability to provide resilience to biotic and abiotic stresses and improved fiber quality to obtain premiums at harvest. Cotton seed industries have been negatively impacted by decreasing seed size which has not been addressed due to increased relative value of fiber. Recent advances in molecular genetics and genome sequencing have provided the molecular markers needed to measure genetic diversity and the basis for tools such as pan-genomes, haplotype graphs, plant transformation, and gene editing to better explore and understand the cotton genomes to address producer and industry needs. Much of this information is available to the cotton community through the CottonGen database. The proposed research will advance cotton germplasm, genomics, and breeding research by characterizing both underutilized and potentially redundant accessions to allow for better use and management of the NCGC (Objective 1); acquiring accessions through plant explorations in the U.S. and Australia as well as continuing to maintain and deliver high quality cotton genetic resources to customers (Objective 2); developing germplasm with improved seed and fiber traits (Objective 3); obtaining cotton genome/pan-genome sequences and developing a practical haplotype graph to fully capture cotton genetic variation (Objective 4); identifying fiber quality genes and developing heat tolerance and male sterility systems through genetic engineering and genome editing (Objective 5); and enhancing the CottonGen database with new content as well as bioinformatic tools to effectively utilize the information for cotton improvement (Objective 6).