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

2020 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 identification of 11.6 million single nucleotide polymorphism (SNP) loci from 81 Gossypium herbaceum and G. arboreum diploid cottons (A-genome) that were mapped to the recently improved G. arboreum reference genome (A-genome). Work under Objective 1 also included mining of SNP and simple sequence repeat (SSR) markers from another recently sequenced diploid genome (D-genome) for G. thurberi. Results of annotation by CottonGen collaborators indicated there are 42,000 SSRs and 132,000 SNPs in this cotton D-genome species. Work under Objective 2 included public release of high-quality sequence data for four species (G. herbaceum, G. arboreum, G. hirsutum, and Gossypioides kirkii) and resequencing data for the 81 diploid cottons through GenBank and CottonGen databases. The describing manuscripts were revised and published in Nature Genetics and Frontiers in Plant Science. Comparative sequence analysis clarified basic chromosome number variation between Gossypioides kirkii (12) and Gossypium species (13). Work under Objective 3 included continued support to the CottonGen database (managed by Cotton Inc.) which serves the broad cotton community worldwide. Fifteen new cotton genomes, approximately 7,000 genetic tools known as molecular markers, 1,000 molecular tools known as quantitative trait loci (QTLs), and 12,000 new phenotypic datapoints were added to the database. CottonGen served 271,000 pages and was accessed nearly 24,000 times by cotton researchers from 155 countries. Work under Objective 4 included defining genetic control of priority traits including cotton fiber/seed properties, and abiotic/biotic stress tolerance for cotton improvement. Arabidopsis regulatory genes that belong to a group called GL2-interacting-repressors (GIRs) were identified and characterized for cotton fiber initiation and development in both diploid and tetraploid cottons. Phenotypes of recombinant inbred lines (RILs) derived from an interspecific cross between the cotton types, TM-1 and 3-79, which represent the sequenced genetic standards for G. hirsutum and G. barbadense, respectively, were measured for abiotic stress and cotton fiber traits. SNP and SSR markers were used to identify QTLs for these traits. In addition, QTL mapping in a SNP-based genetic map was used to identify traits associated with cotton domestication in a segregating F2 population derived from an instraspecific G. hirsutum cross between the wild var. yucatanense (TX2094) and the elite cultivar cv. Acala Maxxa. A new project was initiated with a 3.5-kb gene construct that was designed for synthesis and assembly into a 10.5-kb transformation vector that was obtained from the Arabidopsis Biological Resource Center (ABRC). This plasmid vector was propagated, purified, and validated for cloning and transforming the candidate genes. Research progress under Objective 4 was also made on molecular mechanisms of cotton response to Verticillium disease.

1. Genome sequence of Gossypioides kirkii. While most species in the cotton tribe have a basic chromosome number of 13, one exception named Gossypioides kirkii has a basic chromosome number of 12. Understanding the chromosome number variation in the cotton tribe is essential for plant breeders to effectively transfer desirable traits for cotton improvement. ARS researchers at College Station, Texas, working with national and international collaborators, sequenced, assembled, and compared the genome of Gossypioides kirkii with previously sequenced genomes of Gossypium species. Chromosome fusions and inversions were discovered among a series of structural rearrangements, they primarily occurred in the Gossypium chromosomes, and this in a stepwise manner resulted in the loss of one cotton chromosome in Gossypioides kirkii. The Gossypioides kirkii genome sequence helps plant biologists resolve a long-standing cytogenetic mystery and it provides cotton breeders with a valuable source of genetic variation.

2. Mapping of quantitative trait loci (QTLs) in cotton. Cotton plants produce the leading natural fiber for the textile industry. Improvement of fiber yield and quality requires understanding of complex genetic systems that may be exploited in both cultivated and non-cultivated cottons. ARS researchers at College Station, Texas, working with national collaborators, developed a single nucleotide polymorphism (SNP)-based genetic map and identified 120 putative quantitative trait loci (QTLs) associated with phenotypic changes for fiber and other traits under domestication of the cotton genome. Candidate genes possibly responsible for the traits were annotated with the data currently available. The work reflects a significant contribution of ongoing efforts by cotton researchers to improve cotton productivity and profitability for U.S. cotton producers.

3. Biosynthesis and accumulation of cotton gossypol. Cottonseed contains high-quality protein and oil for food and feed, but its commercial utilization is limited by a toxic compound called gossypol. Many decades of research have been spent by plant scientists, but still little is known about the metabolism of the gossypol compound in cotton. ARS researchers at College Station, Texas, working with international collaborators, demonstrated that gossypol is primarily synthesized and accumulated in the root systems of cotton plants. Gossypol synthesis was not directly related to the production of pigment glands, but the presence of pigment glands was essential for gossypol accumulation. The new knowledge better defines the complexity of gossypol metabolism, and helps cotton breeders enhance the commercial value of cottonseed by altering the metabolic pathway of gossypol in the cotton plant.

Review Publications
Huang, G., Wu, Z., Percy, R.G., Bai, M., Li, Y., Frelichowski, J.E., Hu, J., Wang, K., Yu, J., Zhu, Y. 2020. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics.
Zhao, T., Xie, Q., Li, C., Li, C., Mei, L., Yu, J., Chen, J., Zhu, S. 2020. Cotton roots are the major source of gossypol biosynthesis and accumulation. Biomed Central (BMC) Plant Biology. 20:88.
Udall, J.A., Long, E., Ramaraj, T., Conover, J.L., Yuan, D., Grover, C.E., Gong, L., Arick, M.A., Masonbrink, R.E., Peterson, D.G., Wendel, J.F. 2019. The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Frontiers in Plant Science. 10:1541.
Grover, C.E., Yoo, M., Lin, M., Murphy, M.D., Harker, D.B., Byers, R.L., Lipka, A.E., Hu, G., Yuan, D., Conover, J., Udall, J.A., Paterson, A.H., Gore, M.A., Wendel, J. 2020. Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum L.). G3, Genes/Genomes/Genetics. 10(2):731-754.