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United States Department of Agriculture

Agricultural Research Service

Research Project: CHARACTERIZE, EVALUATE, AND ENHANCE COTTON GERMPLASM, AND ENLARGE, IMPROVE, AND MAINTAIN GERMPLASM DATABASES

Location: Crop Germplasm Research

2011 Annual Report


1a.Objectives (from AD-416)
The objectives of this project are to characterize, evaluate, and enhance cotton germplasm, and augment, improve, and maintain germplasm databases. Evaluation and enhancement efforts will focus on agronomic, fiber quality, and biotic and abiotic stress tolerance traits important to the cotton industry and to the improvement of cotton as a crop. Specifically, this project will investigate the genetic diversity and agronomic potential of improved global cultivars in order to:.
1)determine the genetic diversity and relationships among cultivars from cotton-growing regions of the world, including Africa, Brazil, China, Greece, India, Pakistan, Russia, Turkey, the U.S., and Uzbekistan;.
2)identify within these global cultivars agronomic traits with potential for enhancing the breeding programs for cotton grown in Texas; and.
3)more fully characterize a portion of the U.S. Cotton Germplasm Collection. Efforts to characterize and evaluate germplasm will be complemented and augmented by molecular mapping efforts on the cotton genome and database improvement and maintenance efforts.


1b.Approach (from AD-416)
Cotton germplasm will be characterized and evaluated for agronomic traits, fiber quality, and biotic and abiotic stress tolerance. Molecular marker profiles will be used to establish genetic relationships between germplasm lines and to characterize genetic diversity within germplasm sets. Molecular mapping techniques will be employed in characterizing genome structure. Data collected from phenotypic characterizations and evaluations, and from molecular characterization and mapping will be maintained in the CottonDB and GRIN databases. An initial project, occurring during the first three years of the project, will involve the phenotypic evaluation and molecular characterization of global cultivars and elite germplasm. Phenotypic evaluations will focus on agronomic, yield, and fiber quality traits of cultivars. Morphological descriptor data will also be taken. Phenotypic evaluations will occur in replicated tests on cooperator facilities at College Station, TX, using seed provided by the ARS. Phenotypic evaluation will be a joint effort. Molecular characterization of the cultivars/elite lines will take place in ARS facilities by ARS personnel. Molecular diversity will be assessed using a set of 208 simple sequence repeat (SSR) markers. Data from the molecular diversity assessment will be used to calculate genetic similarity coefficients. This coefficient will be further used in a cluster analysis to construct a dendrogram showing relationships between cultivars and a principal component analysis to observe how individual cultivars form groups based on SSR similarities. An analysis of molecular variance (AMOVA) based on the SSR data will measure genetic structure between and among the twelve groups of cotton cultivars. The project may be extended to other germplasm and beyond the initial three years. Complementary efforts to supplement characterization of germplasm through physical mapping of the cotton genome and database development will occur.


3.Progress Report

The goals of this project are to characterize and evaluate the genetic variation in the National Cotton Germplasm Collection, and to maintain and upgrade important cotton databases. In FY 2011, selected lines from a project to evaluate genetic diversity in cultivars from North Africa, South Africa, China, and the U.S. were crossed to determine their general combining ability--a measure of how well two parents combine to produce superior offspring. Anaylsis of the genetic diversity of the parent cultivars using molecular markers was completed. Efforts at improving the cotton database, CottonDB, and to improve its accessibility continued. A new feature, a "breeders' toolbox" was added to the database. The cotton database is in the process of being incorporated into an integrated database being established through a cooperative agreement with Cotton Incorporated. The database aspect of the current agreement will cease with the successful establishment of the cooperative agreement with Cotton Inc.; this will occur no later than early FY 2012. Work by this project has developed, and will continue to develop essential information on the genetic diversity of the National Cotton Germplasm Collection, and will identify useful genetic traits for exploitation by breeders to develop improved cotton cultivars for U.S. farmers. The ADODR of this project and the cooperator are located in close physical proximity and are in contact with one another on an ongoing basis. There are regular personal interactions between the ADODR and the cooperator, or key personnel working directly under the cooperator, to discuss the direction and progress of the work.


Last Modified: 4/20/2014
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