Skip to main content
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

2022 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
Work under Objective 1 included mapping of polymorphic simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for cotton germplasm characterization and quantitative trait loci (QTL) identification with interspecific tetraploid cotton populations. DNA sequences were produced for analysis with markers on previously characterized accessions of a diploid cotton wild relative species G. thurberi. Work under Objective 2 included public release, through GenBank and CottonGen databases, of high-quality sequence data for G. anomalum, an African diploid wild relative of cultivated cotton that harbors stress-resistance, cytoplasmic male sterility, and fiber-related traits. Also released to the public were genome assemblies of two nematode-resistant cottons (G. hirsutum) for developing DNA markers to facilitate the transfer of nematode-resistance in breeding programs. Work under Objective 3 included support of and data input to the CottonGen database (managed by Washington State University) which serves the broad cotton community worldwide. Twenty-three new assemblies and/or functional analyses of the cotton genomes were added, approximately 78,000 genetic tools known as molecular markers, 14,000 new phenotypic datapoints, and 276 QTLs were added to the database. A new version of CottonGen was published, a user manual of the breeding information management system (BIMS) was updated, and quarterly newsletters were released. In fiscal year (FY) 2022, CottonGen served 370,273 pages to the user communities and was accessed 58,604 times by cotton researchers from 172 countries. Work under Objective 4 included analysis of the genetic factors that control the priority traits important to the cotton industry. Two new populations of intraspecific Upland cotton F2 plants (G. hirsutum) were grown in the field for mapping genes controlling fiber quality. A regulatory mechanism of gene promotors in response to salt-alkaline stress was revealed during hypocotyl elongation of Sea Island cotton (G. barbadense). Such cellular regulation was found most actively at the cottonseed germination stage. Gene candidates for male sterility in cotton were identified and characterized through a homology-based analysis of DNA and protein sequences with those collected in six other plant species. Multiplex gene cassettes were constructed for simultaneous editing to develop the male sterility lines desirable in breeding superior hybrid cotton. During the life of this project, major accomplishments were made in defining the genetic structure of a number of important cotton types, in developing important new tools to define the genetic make-up of cotton species, and in identifying the genomic sources and locations within the cotton genome that control important agronomic traits such as fiber quality, resistance to environment stresses, etc. This is the final report for this project. In FY 2022, at Area Director initiative and as approved by the Office of National Programs, this project was terminated and the fiscal, physical, and human resources were redirected to the sister project 3091-21000-041-000D. Work under the combined, ongoing project will continue to focus on achieving the objectives and meeting the milestone delineated in each of the two applicable project plans.

1. Genome sequence of wild African cotton. Gossypium anomalum is a wild African diploid cotton species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. This wild cotton species is also a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Lacking a genome sequence for this wild species has hindered the efforts of exploiting such desirable traits for cultivated cotton improvement. ARS researchers at College Station, Texas, working with national and international collaborators, sequenced, assembled, and annotated the genome of this species. The genomic resources and associated information represent a significant contribution in cotton genetics research and will facilitate the work of cotton breeders in improving the crop for farmers worldwide.

2. New version of the CottonGen database. CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data. Since the release of its first version in 2014, CottonGen has been expanded with exponentially increased data input worldwide and fast developed bioinformatics tools available among all crop plants. ARS researchers at College Station, Texas, working with national collaborators, updated the current status and formulated the future direction of CottonGen in a peer-review journal publication. The expanded relational datasets, querying interfaces, and new tools to analyze such datasets will make cotton researchers more efficient in utilizing the information and developing the knowledge to support cotton genetic improvement for enhancement of cotton productivity and profitability in the United States and worldwide.

Review Publications
Rui, C., Zhang, Y., Fan, Y., Han, M., Dai, M., Wang, Q., Chen, X., Lu, X., Wang, D., Wang, S., Gao, W., Yu, J., Ye, W. 2021. Insight between the epigenetics and transcription responding of cotton hypocotyl cellular elongation under salt-alkaline stress. Frontiers in Plant Science. 12. Article 772123.
Kushanov, F.N., Turaev, O.S., Khusenov, N.N., Tulanov, A.A., Amanboyev, R.S., Saha, S., Yu, J., Abdurakhmonov, I. 2021. Application of marker-assisted breeding technology in cotton (Gossypium spp). Frontiers in Plant Science. 12:779386.
Grover, C.E., Yuan, D., Arick, M.A., Miller, E.R., Hu, G., Peterson, D.G., Wendel, J.F., Udall, J.A. 2021. The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. Genes, Genomes, Genetics. Article jkab319.