Location: Crop Germplasm Research
2023 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire genetic resources of cotton and its wild relatives; maintain their safety, genetic integrity, health and viability; and distribute them and associated information worldwide. [NP301, C2, PS2A]
Objective 2: Develop more effective genetic resource maintenance, evaluation, and genetic marker characterization methods and apply them to priority genetic resources of cotton and its wild relatives. Record and disseminate evaluation and characterization data and digital images via GRIN-Global, CottonGen, and other data sources. [NP301, C2, PS2A]
Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for cotton genetic resource and information management. [NP301, C2, PS2A]
Objective 4: Devise more efficient and effective cotton genetic enhancement approaches and apply them to generate breeding stocks incorporating genes from cotton land races and wild relatives for improved yield, fiber quality, seed quality, and/or resistance/tolerance to biotic and abiotic stresses. [NP301, C1, PS1A, PS1B]
Objective 5: 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. [NP301, C1, PS1A]
Objective 6: 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. [NP301, C1, PS1A; C3, PS3A]
Objective 7: Develop, improve, and manage an efficient and effective database and bioinformatics system, CottonGen, for efficiently exploiting cotton genetic variation. [NP301, C4, PS4A]
Objective 8: 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. [NP301, C1, PS1A; C3, PS3A]
Approach
The Gossypium genus is composed of at least 50 recognized species of differing ploidy levels and contains a wealth of genetic variability ranging from highly improved allotetraploid species to wild diploid species. The National Cotton Germplasm Collection contains much of the diversity of the genus, and its long-term objectives are to acquire, conserve, characterize, evaluate, and distribute accessions, with the goal of making these resources available for genetic improvement efforts within and outside the USDA. Under the current project, we will make efforts to acquire new germplasm through plant explorations and exchanges that target current gaps in the Collection. To make the inherent variability of the Collection useful, it must be described and evaluated. For this reason, this project will generate phenotypic descriptions of genetic resources, and evaluate these materials for drought stress tolerance, agronomic traits, and fiber quality. Recent advances in cotton molecular genetics have provided the molecular markers needed to measure genetic diversity, characterize new acquisitions, ascertain areas of deficiency, and maintain the integrity of accessions while regenerating the Collection. Recognizing that parts of the Collection are not readily usable due to species incompatibilities, day-length flowering responses, and the perennial nature of accessions, pre-breeding efforts are needed to improve access to and utility of these portions of the Collection. Information generated by this project will be made publicly available in the GRIN-Global and/or CottonGen databases.
Progress Report
Significant progress was made in FY 2023 on all eight project objectives. Under Objective 1, accessions from the National Cotton Germplasm Collection (NCGC) were increased in three environments: 170 accessions were planted, and 120 accessions were growing from previous years’ plantings at the Costa Rica Cotton Winter Nursery; 150 diploid accessions (Gossypium arboreum and G. herbaceum) were increased at College Station, Texas, in field plots during the summer; and 420 critical accessions were increased in USDA greenhouses at College Station. Also under Objective 1, 36 seed orders with 3,552 accessions were filled for domestic and international requests, following all Animal and Plant Health Inspection Service and importing country phytosanitary requirements. In work under Objective 2, phenotypic descriptors and digital images were collected for accessions grown in the field and greenhouses at College Station and in the Costa Rica Cotton Winter Nursery. Under Objective 2, project scientists coordinated the work of collaborators to identify and characterize sources of tolerance to the critically important bacterial blight (Xanthomonas citri pv. Malvacearum) pathogen. Under Objective 3, best management practices (BMPs) were updated for the NCGC covering local management of genetically engineered cotton accessions. In work under Objective 4, research continued to evaluate cotton seed oil phenotypes in multiple environments with data collection in progress in two environments. In support of research to increase oleic acid in cotton seed, marker assisted selection was used to identify plants with the allele for increased oleic acid, and G. hirsutum and G. barbadense backcross populations were selfed. Under Objective 5, polymorphic DNA markers were mapped in interspecific tetraploid cotton populations, and a set of DNA markers associated with flowering traits were identified. In work under Objective 6, high-quality sequence data was obtained for a cultivated G. herbaceum diploid genome and made available through the GenBank and CottonGen databases. Nine G. hirsutum, and four G. barbadense genome assemblies were compared using multiple genome analysis strategies. Under Objective 7, the CottonGen database was supported and updated with eleven genome assemblies, 28,700 molecular markers, 27,600 phenotypic datapoints, and 418 quantitative trait loci. During FY 2023, CottonGen served 413,658 pages to the user communities and was accessed 65,484 times by cotton researchers from 176 countries. Research under Objective 8 continued on genetic analysis of priority traits important to the cotton industry; the work was conducted both in field and greenhouse environments. These traits include fiber quality, heat tolerance, and male sterility; each is important in ongoing work by breeders to improve the crop for U.S. farmers. Over the life of this project, all research objectives were addressed and largely met. Genetic resources within the NCGC were successfully regenerated and distributed. A major focus was on increasing seeds of critical accessions (those with low quantities or poor viability). Over 75% of the NCGC has been characterized with standardized morphological descriptors and digital images and made available to the cotton community through updates to the GRIN-Global and CottonGen databases. New accessions were added to the NCGC, and accessions were identified and provided to collaborators to support screening for emerging pathogens including Fusarium oxysporum f. sp. vasinfectum Race 4 (FOV4), cotton leafroll dwarf virus, and bacterial blight (Xanthomonas citri pv. Malvacearum). Best management practices were developed for working with transgenic accessions. Genetics projects evaluated cottonseed oil content and oleic acid content. Major advances were made in assembling and/or improving the genome sequences of diploid and tetraploid cotton species. Thousands of molecular markers and core subsets of markers were identified for germplasm characterization and identification of loci for traits of interest. The CottonGen database was expanded with large datasets and new bioinformatic features including a breeding information management system. Biotic and abiotic stress tolerance was defined for incorporation into new cotton cultivars through traditional, transgenic, or gene-editing approaches. This project expired in FY 2023 and was replaced by 3091-21000-048-000D, which is continuing and expanding upon the work.
Accomplishments
1. Genome sequence of a diploid cotton cultivar. Gossypium herbaceum is one of the four types of cultivated cotton. This type is grown and is well-adapted in Africa, yet it lacks desired fiber quality. The genome sequence is essential to identify the sources of these desirable adaptations and use them for improving cotton in other regions being adversely affected by environmental conditions. ARS researchers at College Station, Texas, working with national and international collaborators, sequenced, assembled, and annotated the genome of this species. The genome sequence provides the building blocks to further define the genetic control and development of cotton fiber, as well as to identify genes for tolerance to environmental stressors. The genome sequence also serves as a blueprint for further research on the evolution of cotton and is a valuable tool for use by plant breeders in genetically improving the crop.
2. Molecular mechanisms regulating cotton fiber length. Cotton fiber characteristics affect the price received by the producer as well as processes in textile manufacturing. Having a better understanding of these characteristics can help producers earn a premium price, and help textile manufacturers receive a higher quality cotton. Fiber length is a major indicator of cotton fiber quality, but the differences in physical and chemical properties between short fibers and long fibers are not well characterized. ARS researchers at College Station, Texas, and New Orleans, Louisiana, in cooperation with non-ARS colleagues, utilized fiber samples from accessions in the U.S. National Cotton Germplasm Collection to define the physical and chemical differences between short and long cotton fibers. Differences in key chemical pathways were established that will facilitate identifying genes and common pathways that significantly influence cotton fiber length. This research is a significant contribution to ongoing efforts focused on improving fiber quality, specifically cotton fiber length. The cultivars that will be developed with increased fiber length because of this accomplishment will provide economic benefit to cotton growers and will improve the intermediate and end products of textile manufacturing.
Review Publications
Morales, K., Bridgeland, A.H., Kater, H., Udall, J.A., Yu, J., Thompson, M. 2022. Homology-based identification of candidate genes for male sterility editing in Upland cotton (Gossypium hirsutum L.). Frontiers in Plant Science. Article e2022.1006264. https://doi.org/10.3389/fpls.2022.1006264.
Kushanov, F., Komilov, D., Turaev, O., Ernazarova, D., Amanboyeva, R., Gapparov, B., Yu, J. 2022. Genetic analysis of mutagenesis that induces photoperiod insensitivity of wild cotton Gossypium hirsutum subsp. Purpurascens. Plants. 11(22). https://www.mdpi.com/2223-7747/11/22/3012#.
Ramaraj, T., Grover, C.E., Azalea, M., Arick II, M.A., Jareczek, J., Leach, A., Peterson, D., Wendel, J.F., Udall, J.A. 2022. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3, Genes/Genomes/Genetics. 13(2). https://doi.org/10.1093/g3journal/jkac308.
Grover, C.E., Arick II, M.A., Thrash, A., Sharbrough, J., Hu, G., Yuan, D., Miller, E.R., Ramaraj, T., Peterson, D.G., Udall, J.A., Wendell, J.F. 2022. Dual domestication, diversity, and differential introgression in Old World cotton diploids. Genome Biology and Evolution. 14(12). https://doi.org/10.1093/gbe/evac170.
Meng, Q., Gu, J., Xu, Z., Zhang, J., Tang, J., Wang, A., Wang, P., Liu, Z., Rong, Y., Xie, P., Hui, L., Udall, J.A., Grover, C.E., Wendell, J.C. 2023. Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.). Industrial Crops and Products. Article e116471. https://doi.org/10.1016/j.indcrop.2023.116471.
Kim, H.J., Liu, Y., Thyssen, G.N., Naoumkina, M.A., Frelichowski, J.E. 2023. Phenomics and transcriptomics analyses reveal deposition of suberin and lignin in the short fiber cell walls produced from a wild cotton species and two mutants. PLOS ONE. 18. Article e0282799. https://doi.org/10.1371/journal.pone.0282799.
Restrepo-Montoya, D., Hulse-Kemp, A.M., Scheffler, J.A., Haigler, C., Hinze, L.L., Love, J., Percy, R.G., Jones, D.C., Frelichowski, J.E. 2022. Leveraging national germplasm collections to determine significantly associated categorical traits in crops: Upland and Pima Cotton as a case study. Frontiers in Plant Science. 13:837038. https://doi.org/10.3389/fpls.2022.837038.
