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

Location: Crop Germplasm Research

2024 Annual Report

Objectives
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.

Approach
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).

Progress Report
Work by this project under Objective 1 in FY 2024 identified underutilized cotton genetic resources to genotype; also, a set of cotton accessions was selected to apply sequence-based genotyping methods. These plants were grown in the greenhouse, and leaf tissue was obtained for future DNA extraction. Applications were made to the National Park Service and the Florida Department of Environmental Protection for permits to explore and collect seed of wild cotton in parks of South Florida. Under Objective 2, project staff assisted GRIN-Global users, including first-time foreign users, in searches and selections of accessions of cotton from the National Cotton Germplasm Collection for scientific or educational purposes, distributing seed to users as requested, and adding over 100,000 data points to the GRIN-Global and CottonGen public databases. Routine seed increases for the National Cotton Germplasm Collection included accessions of the Asiatic and African diploid cotton sub-collection which were germinated for viability assessment; approximately 600 of these accessions were cultivated in greenhouses, summer field plots, or the Costa Rican Cotton Winter Nursery (CWN) for seed multiplication and phenotype characterization. Under Objective 3, cotton accessions with varying seed sizes were obtained for future field evaluations; families and selections were made for seed increase in the CWN. Objective 4 work identified several priority cotton accessions for genome sequencing. High-quality genome sequences including Gossypium hirsutum 'PSC355' and other Upland cottons that harbor fiber yield and quality, nematode resistance, gene regulation, and trait divergence were publicly released through GenBank and/or CottonGen databases, providing additional resources for understanding cotton evolution, domestication, and germplasm utilization for cotton breeding. Two F2 populations that showed phenotypic segregation for cotton fiber traits were planted in the field. Leaf tissue was collected for DNA extractions and individual plant fiber samples were collected for phenotyping. More than two dozen candidate genes for heat tolerance and male sterility were identified in major dicot and monocot plant genomes; these candidate genes were evaluated by homologous DNA and protein sequence analysis. A set of DNA markers was identified that detect genomic changes in the interspecific hybridization and synthetic polyploidization between diploid and tetraploid cotton species. These markers provide cotton breeders with valuable tools to introduce new genetic variation from wild cottons to improve fiber yield and quality under adverse environments. Objective 6 work provided information resources and tools for the CottonGen database which serves the international cotton community. New information resources made available included cotton genome assemblies, molecular markers, phenotypic datapoints, and quantitative trait loci. Results from genome wide association studies were added along with gene expression datasets. The database user manual was updated, and short training videos were released to facilitate use of database tools.

Accomplishments
1. Genomic resources for cotton breeding. A narrow gene pool in cotton limits future genetic gains with plant breeding practices. Precision breeding with genomic and biotech approaches offers potential solutions, contingent upon accurate cultivar-specific knowledge for plant breeders to use. ARS researchers at College Station, Texas, working with collaborators, developed high-quality genomes for three American 'Upland' cotton cultivars (UGA230, UA48 and CSX8308) and their genetic standard reference (TM-1). Considerable genomic variation was observed among these four Upland cotton genomes, overlapping with genomic introgressions from American 'Pima' cotton, gene regulation, and trait divergence. Genes for cotton fiber development were enriched that will contribute to the enhanced fiber quality in modern cotton cultivars. This accomplishment provides an important foundation to guide breeders in improving cotton yield, quality, and sustainability.

Review Publications
Yu, J., Jung, S., Cheng, C., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D., Campbell, B.T., Udall, J.A., Main, D. 2021. CottonGen: The community database for cotton genomics, genetics, and breeding research. Plants. 10(12). Article 2805. https://doi.org/10.3390/plants10122805.
Zeng, L., Hinze, L.L., Fang, D.D., Delhom, C.D., Zhang, J. 2023. Analysis of a cotton introgression population derived through multiple generations of random mating in multiple-parents crosses. Euphytica. 219. Article 101. https://doi.org/10.1007/s10681-023-03213-1.
Chaudhary, M.T., Majeed, S., Rana, I.A., Zulfiqar, A., Jia, Y., Du, X., Hinze, L.L., Azhar, M.T. 2024. Impact of salinity stress on cotton and opportunity for improvement through conventional and biotechnological approches. BMC Plant Biology. Article e24:20. https://doi.org/10.1186/s12870-023-04558-4.
Majeed, S., Chaudhary, M.S., Mubarik, M.T., Rana, I.A., Shaban, M., Tan, D.K., Jia, Y., Du, X., Hinze, L.L., Azhar, M.T. 2023. Genetics of biochemical attributes regulating morpho-physiology of upland cotton under high temperature conditions. Journal of Cotton Research. 7. Article 3. https://doi.org/10.1186/s42397-023-00164-9.
Sreedasyam, A., Lovell, J., Mamidi, S., Khanal, S., Jenkins, J., Plott, C., Kempton, B., Li, Z., Shu, S., Carlson, J., Goodstein, D., Santiago, L., Kirkbride, R., Calleja, S., Campbell, B.T., Koebernick, J., Dever, J., Scheffler, J.A., Pauli, D., Jenkins, J.N., Mccarty Jr, J.C., Williams, M., Boston, L., Webber, J., Udall, J.A., Chen, Z., Bourland, F., Stiller, W., Saaki, C., Grimwold, J., Chee, P., Jones, D., Schmutz, J. 2024. Genome resources for three modern cotton lines guide future breeding efforts. Nature Plants. https://doi.org/10.1038/s41477-024-01713-z.
Ning, W., Rogers, K., Hsu, C., Magbauna, Z.V., Pechanova, O., Arick Ii, M.A., Kayal, E., Hu, G., Peterson, D.G., Udall, J.A., Grover, C., Wendel, J.F. 2024. Origin and diversity of the wild cottons (Gossypium hirsutum) of mound key, Florida. Scientific Reports. 14. Article 14046. https://doi.org/10.1038/s41598-024-64887-8.
Khidirov, M., Ernazarova, D., Rafieva, F., Ernazarova, Z., Toshpulatov, A., Umarov, R., Kholova, M., Udall, J.A., Yu, J., Kushanov, F., Oripavo, B., Kudratova, M., Gapparov, B., Khidirova, M., Komilov, D.N., Turaev, O. 2023. Genomic and cytogenetic analysis of synthetic polyploids between diploid and tetraploid cotton (Gossypium) species. Plants. 12(24). Article 4184. https://doi.org/10.3390/plants12244184.
Bell, A.A., Robinson, F., Quintana, J., Hinze, L.L., Harris, J.N., Liu, J., Wagner, T.A., Prom, S., Saladino, V., Zheng, X., Stelly, D., Nichols, R. 2023. Registration of eight germplasm lines of upland cotton resistant to nematodes with elite agronomic performance. Journal of Plant Registrations. 17:536-543. https://doi.org/10.1002/plr2.20290.