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Location: Crop Germplasm Research

2012 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:
In FY 2012, seed of nearly 2,100 lines of cotton were increased to maintain the National Cotton Germplasm Collection. Of the lines increased, about 90% were increased in the Cotton Winter Nursery (CWN) in Mexico, and the remainder was increased in field and greenhouse facilities at College Station, Texas. Data was taken on descriptive traits, and fiber quality was analyzed in a great majority of these lines. For a second consecutive year, digital photographic records were made of many of the lines. Thirty-five lines were added to the collection in FY 2012 from elite cultivars whose plant variety protection status has expired. The collection filled requests for 4383 lines in response to requests from 92 individuals and institutions. A project to determine the genetic diversity, and therefore increase the usefulness of the National Cotton Germplasm Collection in improvement efforts, was continued in FY 2012. Data collection was completed and data analyses begun. In this project, data was collected on 2,300 lines from the Collection using 105 molecular markers. An investigation of the diversity of the species Gossypium arboreum was begun. The ancestor of Gossypium arboreum is thought to be one of the parents of modern commercial cotton. A set of 188 markers have been selected for the investigation, and DNA has been extracted from 760 G. arboreum lines. Data collection on another project to characterize the physical diversity of improved cultivars from the U.S., China, northern Africa, and southern Africa was accomplished in FY 2012. Data were collected on agronomic, fiber quality, and seed quality traits in replicated trials grown in College Station and Lubbock, Texas.

4. Accomplishments
1. Regeneration and characterization of cotton lines held in the National Cotton Germplasm Collection. Seed of almost 10,000 cotton accessions must be renewed on a 10-year cycle to maintain the genetic diversity present in the National Cotton Germplasm Collection and to continue to provide cotton researchers worldwide with critical germplasm for research and crop improvement efforts. ARS scientists at College Station, Texas, using plantings in the Cotton Winter Nursery in Mexico, and fields and greenhouses at College Station, increased almost 25% of the entire collection in FY 2012. Descriptors were taken on all of the accessions, and approximately 3980 accessions, or 40% of the collection, was documented via digital photography. The Cotton Winter Nursery remains as one of the most critical support operations for the worldwide cotton research and development communities.

2. Molecular diversity of improved cotton cultivars. To effectively exploit the diversity of the National Cotton Germplasm Collection for cotton improvement, it must first be established where in the Collection diversity can be found. ARS scientists at College Station, Texas, working with Texas AgriLife Research colleagues, measured genetic diversity and relatedness among cotton cultivars in the Collection to determine how cultivars differ at the molecular level based on the country where they were developed. Country of origin was shown to be an inadequate criterion for selecting cultivars with diverse molecular genetic backgrounds. In the past, users of the Cotton Collection have judged country of origin to be a significant indicator for determining genetic diversity when selecting parents for a breeding program. This work clearly shows that country of origin is a poor criterion. This knowledge will be of major value in guiding cotton breeders in their efforts to develop improved varieties for the producer.

Review Publications
Zhang, H., Hinze, L.L., Lan, Y., Westbrook, J.K., Hoffmann, W.C. 2012. Discriminating among cotton cultivars with varying leaf characteristics using hyperspectral radiometry. Transactions of the ASABE. 55(1):275-280.

Hinze, L.L., Dever, J.K., Percy, R.G. 2012. Molecular variation among and within improved cultivars in the U.S. cotton germplasm collection. Crop Science. 52:222-230.