Location: Crop Germplasm Research2010 Annual Report
1a. Objectives (from AD-416)
Objective 1: Conserve and distribute a wide diversity of cotton genetic resources and associated information to researchers and breeders worldwide. Sub-objective 1.A: Strategically expand U.S. holdings of cotton genetic resources, especially wild relatives of cotton, through germplasm exchanges and plant explorations. Sub-objective 1.B: Maintain more than 10,000 cotton accessions in the active collection. Regenerate cotton accessions at the Cotton Winter Nursery (CWN) each year, with priorities determined by user input and by seed inventory and viability. Increase the proportion of the active collection backed-up at the National Center for Genetic Resources Preservation (NCGRP). Sub-objective 1.C: Distribute on request cotton accessions and information that meet the specific needs of researchers and breeders. Sub-objective 1.D: Collect and submit data to GRIN and CottonDB. Objective 2: Strategically evaluate (phenotype) cotton genetic resources for priority biotic and abiotic stress resistance, quality factors, and other priority agronomic traits. Sub-objective 2.A: Evaluate cotton accessions in the Cotton Winter Nursery for fiber properties (strength, length, micronaire, elongation). Sub-objective 2.B: Coordinate the cooperative evaluation of cotton genetic resources for other priority agronomic traits, such as resistance to various abiotic and biotic stresses. Sub-objective 2.C: Incorporate the evaluation data collected above into GRIN, CottonDB, and other genetic resource databases. Objective 3: Characterize the genetic variability in cotton genetic resources via genotyping with leading edge genetic marker technology. Sub-objective 3.A: Genotype priority cotton accessions with SSR genetic markers, and incorporate genotypic data into GRIN, CottonDB, and/or other databases. Sub-objective 3.B: With the genotypic information obtained above, measure genetic variation within and among cotton accessions. Sub-objective 3.C: Coordinate the cooperative DNA marker characterization of the cotton germplasm collection with a core subset of portable molecular markers developed by the sister project (6202-21000-030-00D).
1b. Approach (from AD-416)
To conserve and distribute a wide diversity of cotton genetic resources (Objective 1), 400-500 new accessions will be added to the collection – primarily through germplasm exchanges with national collections held in China, France, India, Russia, and Uzbekistan. Plant explorations will also be conducted as funds for this purpose are provided by the Plant Exchange Office section of the National Germplasm Resources Laboratory. Approximately 1,000 accessions (10% of the collection) will be regenerated each year, with priority for regeneration based upon age of seed and germination rate. We will distribute upwards of 4,000 accessions per year for a total worldwide distribution of approximately 20,000 accessions over the period of this project plan. To meet the goal of evaluating cotton genetic resources for priority biotic and abiotic stress resistance, quality factors, and other priority agronomic traits (Objective 2), basic descriptor data will be collected during the grow-outs for regeneration in the Cotton Winter Nursery or in our greenhouses and specific collaborations will be established to evaluate germplasm for responses to biotic and abiotic stresses. To facilitate incorporation of evaluation data into GRIN, CottonDB, and other genetic resource databases, methods of electronic data collection and downloading into appropriate databases will be developed and cooperative efforts with managers at the Database Management Unit will be established to create new and appropriate fields within the GRIN database. More detailed or complex data will be stored in the local database until GRIN establishes the proper formats for public display. Efforts to characterize the genetic variability of the collection via genotyping with genetic marker technology (Objective 3) are being pursued in cooperation with the sister project (6202-21000-030-00D), and are focused on developing a comprehensive set of 208 core DNA markers for evaluation. To evaluate the suitability of the markers, a standard panel of the U.S. Cotton Germplasm Collection is being used. When appropriate markers have been identified, the DNA marker profile of a preselected set of 384 accessions representing a subset of the U.S. Cotton Germplasm Collection will be scored. Genetic diversity and phylogenetic relationships will be evaluated using population genetic software such as NT-SYS and Arlequin. The 384 samples will be clustered using the computer package PAUP and/or the neighboring-joining method. Once a core set of DNA markers is established and validated on the selected subset of the U.S. Cotton Germplasm Collection, the markers will be made available to cooperators, and coordination will be provided to accomplish the work in an efficient manner to prevent duplication of effort. Standard use of the core DNA markers will enable all characterizations and evaluations of Gossypium germplasm to be pooled into a common, publicly available database for analysis and interpretation across different gene pools or germplasm sources.
3. Progress Report
Significant progress was made during FY 2010 in seed increases for the cotton germplasm collection, distribution of seed to users of the collection, and improvement in data management and germplasm operations. Seed of nearly 1300 accessions of the National Cotton Germplasm Collection were increased, with the majority from the Cotton Winter Nursery (1020), and the remainder from the field (130) or greenhouses (110) in College Station, Texas. Descriptor information, fiber samples, and digital photographs were collected to the fullest extent possible for characterization, identity confirmation, and updating the Germplasm Resources INformation (GRIN) database and local databases. Many of the accessions harvested in FY 2010 from the Cotton Winter Nursery (750) and at College Station (50) were analyzed for fiber quality by Cotton Incorporated personnel. Approximately 28 accessions were added to the collection, either from prior collecting expeditions (4), from germplasm exchanges (5), or from elite germplasm whose Plant Variety Protection status had expired (19). Seed requests increased in FY 2010, with 1838 accessions being distributed in response to requests from 83 individuals and institutions. The collection as well as seed increase samples were barcoded for efficient processing and real time inventory. A new project to characterize the genetic diversity of the germplasm collection using molecular markers was initiated in FY 2010. DNA has been harvested from over 2300 accessions representing 33 species of the collection. In a pilot project, 105 mapped, validated, SSR markers representative of all the chromosomes contained within the genome of cultivated Upland cotton were used to assay diversity in a subset of 96 accessions representing four tetraploid species and four wild diploid species. Evidence of genetic diversity within the marker set was good, and the project continues. Work to define the genetic diversity of Upland cotton (Gossypium hirsutum) cultivars within the national Germplasm Collection continued in FY 2010. In collaboration with Texas A&M University scientists, replicated evaluations of a set of 62 cultivars were conducted in College Station and Lubbock, Texas. Agronomic, fiber, and descriptor data for cultivar accessions from North Africa, South Africa, China, and the U.S. were obtained, and genotyping samples to generate a molecular fingerprint of the cultivars is 50% complete. In a collaborative project with ARS scientists at Florence, South Carolina, to create high and low oil content cotton germplasm pools, first-year replicated trials were grown in both states to evaluate seed oil index, fiber quality, and agronomic properties. A breeding program was initiated in FY 2010 to improve the fiber length of key cotton germplasm.
1. New genetic breeding populations available for cotton improvement. There is need to improve the performance, productivity, and fiber quality of cotton to meet changing environmental challenges and global market standards. Resources that are available for cotton improvement in the U.S. Cotton Germplasm Collection and in public breeding programs are often under-utilized because they are poorly adapted to specific environments or occur in poor agronomic backgrounds. To make the genetic variability for desirable agronomic and fiber traits more available to researchers and breeders, ARS researchers at College Station, Texas, created four genetically diverse breeding populations using random mating of multiple cotton parents that had different physical characteristics, physiological traits, and geographic/climatic adaptation. The resulting four cotton populations each contain a wide diversity of potentially valuable genetic traits in a more "accessible" form to breeders, as contrasted to focusing on a large number of specific accessions to identify traits for breeding purposes. Availability of these new genetic populations will enhance and in a real sense simplify the work of cotton breeders to improve the crop.
2. Coordinated international analysis of the contents, diversity, and health of cotton germplasm collections worldwide. The genetic variation contained within the genus Gossypium (cotton) represents the raw material available to cotton geneticists and breeders in their ongoing work to improve cultivated cotton as a fiber and seed crop. However, the status and potential of cotton germplasm resources contained in collections worldwide is poorly understood. Further, there has historically been only minimal coordination and sharing of information and resources among these collections. ARS researchers at College Station, Texas, working with key individuals associated with seven other global cotton germplasm collections, conducted an intensive analysis of collection content, status, and long-term viability. The work constitutes a critical first step in a multi-national commitment to efficiently preserve, manage, and develop the full range of cotton genetic resources so as to improve the crop agronomically, and also to facilitate preservation, in perpetuity, of the totality of the world's Gossypium genetic resources.Campbell, B.T., Saha, S., Jenkins, J.N., Park, W., Percy, R.G., Frelichowski, J.E., Mayee, C., Gotmare, V., Dessauw, D., Giband, M., Du, X., Jia, Y., Constable, G., Dillon, S., Abdurakhmonov, I.Y., Abdukarimov, A., Rizaeva, S.M., Adullaev, A.A., Barroso, P.V., Padua, J.G., Hoffman, L.V., Podolnaya, L. 2010. Status of the global cotton germplasm resources. Crop Science. 50:1161-1179.