Location: Crop Germplasm Research
2022 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 on all four project objectives during fiscal year (FY) 2022. Under Objective 1, accessions from the National Cotton Germplasm Collection were increased in three environments: 140 photoperiodic Gossypium hirsutum and 10 cotton standards were increased at the Costa Rica Cotton Winter Nursery, 31 accessions were increased at College Station, Texas, in field plots during the summer, and 290 critical accessions were increased in USDA greenhouses at College Station. These increases amounted to 4.8% of the current holdings in the National Cotton Germplasm Collection. Also under Objective 1, 40 seed orders with 1,475 accessions were filled for domestic and international requests, following all Animal and Plant Health Inspection Service/USDA and importing country phytosanitary requirements. In work under Objective 2, phenotypic descriptors and digital images were collected for 150 accessions grown in the field and greenhouses at College Station. Due to travel restrictions, no information was collected on the accessions grown in the Costa Rica Cotton Winter Nursery. Also under Objective 2, more comprehensive simple nucleotide polymorphism (SNP) genotyping of new G. thurberi accessions using next generation sequencing was accomplished; genetic diversity analysis of those genotypes is in progress. Research continued with collaborators to identify and characterize sources of tolerance to the critically important fusarium oxysporum f. sp. vasinfectum (FOV4) virus. Under Objective 3, best management practices (BMP) were reviewed for the National Cotton Germplasm Collection covering local management of genetically engineered cotton accessions. The curator participated in a National Plant Germplasm System sub-committee on Genetically Engineered Organisms and helped edit and formalize BMP policies for the National Plant Germplasm System and the National Cotton Germplasm Collection. In work under Objective 4, research continued to evaluate cotton seed oil phenotypes in multiple environments with data collection completed in one environment and in progress in two additional environments. In support of research to increase oleic acid in cotton seed, both the G. hirsutum and G. barbadense backcross populations were advanced two generations during FY 2022.
Accomplishments
1. Leveraging National Germplasm Collections. Worldwide cotton germplasm collections are essential to collecting and conserving living plant material, solving agricultural production problems, and conserving plant genetic diversity for future needs. To better characterize the diversity of cotton accessions, the U.S. National Cotton Germplasm Collection has been measuring traits in a standardized manner over the past decade. A single trait has multiple states which represent the multiple types found for that trait among cotton accessions, so collecting this trait information is ultimately helping to document the diversity that encompasses all the cotton species in the collection. ARS researchers at College Station, Texas, working with national collaborators, leveraged a curated subset of collected trait data to compare descriptors within three major cotton groups maintained in the collection. This accomplishment demonstrated that many traits have significant relationships between trait states that vary across the three groups, and that plant breeding has broken down these trait relationships over time. Knowledge of these trait relationships will help plant breeders and others interested in cotton improvement to better use the materials available in the germplasm collection; they will also be adaptable to the germplasm collections of other crops to help us learn more concerning the value of the treasure troves of trait data collected both on our cotton germplasm and that of other crops of importance in U.S. agriculture.
2. Cotton plant responses to drought and heat stress. The biochemical status of plant leaves can reveal their tolerance to heat and drought stresses, which can facilitate crop improvement for adaptation to climate change. Leaf reflectance sensing promises to rapidly estimate biochemical status in plant leaves; however, further research is necessary to develop methods for using sensing technology in plant breeding and crop improvement. ARS researchers at College Station, Texas, working with collaborators in Arizona, used hyperspectral sensing to estimate leaf metabolic states among cotton varieties grown under drought stress. This research is a significant contribution to the ongoing efforts of scientists working in high-throughput plant phenotyping; improved cotton cultivars resulting from this effort will benefit society by making available to growers productive cotton cultivars that will be resilient to the adverse effects of anticipated climate changes as they occur over time.
Review Publications
Melandri, G., Thorp, K.R., Broeckling, C., Thompson, A.L., Hinze, L.L., Pauli, D. 2021. Assessing drought and heat stress-induced changes in the cotton leaf metabolome and their relationship with hyperspectral reflectance. Frontiers in Plant Science. 12. Article 751868. https://doi.org/10.3389/fpls.2021.751868.
Majeed, S., Rana, I., Mubarik, M., Atif, R., Yang, S., Chung, G., Jia, Y., Du, X., Hinze, L.L., Azhar, M. 2021. Heat stress in cotton: An interactive review on predicted and unpredicted growth-yield anomalies and mitigating breeding strategies. Agronomy. https://www.mdpi.com/2073-4395/11/9/1825.
Mubarik, M., Majeed, S., Khan, S., Du, X., Frelichowski, J.E., Hinze, L.L., Azhar, M. 2020. Reforming cotton genes: From elucidation of DNA structure to genome editing. Turkish Journal of Agriculture and Forestry. 45:691-703. https://doi.org/10.3906/tar-2012-64.
Ur Rehman, A., Majeed, S., Chaudhary, M., Rana, I., Du, X., Hinze, L.L., Azhar, M. 2021. Intra-plant variability in Gossypium hirsutum L. for heat tolerance related attributes. Agronomy. 11(12). Article 2375. https://doi.org/10.3390/agronomy11122375.
Perkin, L.C., Bell, A.A., Hinze, L.L., Suh, C.P., Arick II, M.A., Peterson, D., Udall, J.A. 2021. Genome assembly of two nematode-resistant cotton lines (Gossypium hirsutum L.). G3, Genes/Genomes/Genetics. 11(11). Article jkab276. https://doi.org/10.1093/g3journal/jkab276.
