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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS

Location: Crop Germplasm Research

2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Identify a core set of molecular markers tailored for systematic characterization of the genetic diversity within and among Gossypium germplasm accessions that will be maintained under the sister project 6202-21000-032-00D. Objective 2: Maintain and enhance CottonDB as a user-friendly tool for the cotton research community. Sub-objective 2.A: Maintain and enhance CottonDB, including development of user friendly public interfaces. Sub-objective 2.B: Develop bioinformatic software and tools to assist both users and curators of CottonDB. Objective 3: Collaborate with other public sector researchers to construct and integrate physical and genetic maps of G. hirsutum. Sub-objective 3.A: Develop cotton genetic maps that contain PCR-based DNA markers. Sub-objective 3.B: Develop cotton physical maps that contain large-insert BAC clones. Sub-objective 3.C: Integrate cotton genetic and physical maps with EST unigene information. Objective 4: Identify key genes and genomic regions of cotton for use in developing cotton germplasm resources that exhibit desirable/improved agronomic and fiber traits. Sub-objective 4.A: Apply genomic and bioinformatic tools to identify and characterize QTLs or alleles from cotton genetic resources, maintained under the sister project 6202-21000-032-00D, that govern key agronomic or fiber traits. Sub-objective 4.B: Apply the preceding information to identify superior parents for developing breeding populations with novel sources of variability for traits of interest. Sub-objective 4.C: Recombine and select the preceding breeding populations to accumulate desirable QTLs and alleles in enhanced cotton breeding lines.


1b.Approach (from AD-416)
To develop a portable core set of markers for cotton (Objective 1), new SSR and SNP markers will be developed from cotton BAC libraries and other genomic DNA templates. From the markers created, a core set of 208 markers will be carefully selected from the saturated genome map of tetraploid cotton (TM-1 x 3-79) with 8 markers from each of 26 chromosomes. Each of these core markers will have a high polymorphism information content (PIC) value to be determined on a standardized core germplasm panel consisting of 12 diverse Gossypium genotypes. These markers will be evenly distributed on the cotton genome, with every chromosome arm having 4 core markers at approximately 15-cM intervals. Data from marker development will be stored and made available in the CottonDB database. CottonDB, a tool for the research community, will be enhanced through continued migration of its information content to a relational structure, improved display pages, and direct record-to-record links between internet databases to integrate information into a larger virtual database (Objective 2). To enrich the delivered content and streamline users' searches for specific information, work will integrate related data from multiple databases. Solutions developed by other genome databases will be adapted and implemented to this project's databases where appropriate. To construct and integrate physical and genetic maps, genetic mapping of TM-1 BAC-derived and other markers will be conducted using the TM-1 x 3-79 RI population. Diagnostic DNA markers will be identified that are capable of detecting polymorphism in intraspecific populations, and these markers will be used to genotype the entire TM-1 x 3-79 RI mapping population. A score matrix will be generated from the genotyping experiments and merged with the existing mapping database to perform linkage analysis via MapMaker and/or JOINMAP software programs. Recombination frequencies will be converted into map distances (cM). Approximately 500 SSR and 500 SNP markers will be added to the existing genetic map that contains 1,200 SSR markers to obtain an average resolution of 1-2 cM per marker. Integration of cotton genetic and physical maps will be achieved by anchoring framework genetic markers to TM-1 BAC contigs, and locating BAC-derived markers to the TM-1 x 3-79 RI map (Objective 3). Comparisons of genetic and physical map tools (CMap and IntegratedMap) will allow for consolidation of all structural and physical genomic information. In order to utilize the growing numbers of QTLs reported in cotton, work will validate those QTL by aligning genomic locations and comparing genetic effects (Objective 4). Information for QTLs of interest will be related among comparable studies in cotton and will be obtained from a variety of sources, including published accounts and database records. Once specific chromosomal regions containing genes that make a significant contribution to the expression of a complex phenotype of interest are identified, fine-mapping of the most promising genomic regions will be used to identify polymorphisms in coding and/or regulatory regions.


3.Progress Report
In FY 2010, we completed developing and testing a set of 105 genetic tools (known as portable DNA markers) for use in studying the genetic diversity of cotton. These markers will provide a common basis for systematic characterization of cotton germplasm collections in the U.S. and throughout the world; and as a core marker set they can be used by cotton geneticists and breeders to better detect and track important genetic traits in different cotton germplasm types in efforts to improve the crop. The marker set is being expanded as new DNA markers are developed, characterized, and sited in the cotton genome. The database CottonDB, developed more than a decade ago by precursors of this project, was significantly improved in structure and content in FY 2010, with new information added on markers, genomic maps, and germplasm. In FY 2010, project scientists utilized available information from almost 30 cotton genomic maps developed by others throughout the world to develop a comprehensive reference map. The map includes a majority of known cotton genetic markers (7,424 markers) and represents more than 90% of the mapping information developed thus far on cotton. In a study of 535 cotton fiber genes, we learned that more fiber development genes occur on a particular genomic component (known as the At subgenome) than on the Dt subgenome. In contrast, genetic components known as transcription factors were found more on the Dt subgenome as compared to the At subgenome. The fiber gene map developed by project work will be of major benefit to cotton researchers in their work to genetically improve fiber quality in commercial cottons. Project scientists working in collaboration with cooperators also made progress in sequencing the DNA of chromosomes 12 and 26 of the complex cotton genome. Genetic comparisons made between cotton and poplar, grape, rice, corn, and the model plant Arabidopsis established that cotton is more closely related to poplar than to any of the other plants. Project work in FY 2010 continued to make significant progress to identify cotton genes and/or genic regions known as quantitative trait loci (QTL) that are associated with fiber and seed quality, as well as other important traits affecting cotton growth and development. Using updated mapping information, 84 QTLs were re-evaluated for fiber properties and yield components. Many new QTLs were identified that showed specific effects on or contributions to fiber quality and lint yield. This work continues to more clearly define the genetic mechanisms of fiber development and is critical in guiding the focus and direction of cotton improvement programs being conducted worldwide. Work also began on characterizing two QTL mapping populations to identify genomic regions involved in cottonseed oil synthesis and composition. Altering the quantity and quality of cottonseed oil will create new product opportunities for cotton and will address major human health and nutrition issues.


4.Accomplishments
1. Core genetic markers for cotton. The lack of a uniformly recognized and utilized set of DNA markers to characterize cotton lines maintained in national and international germplasm collections has limited our understanding of the genetic variability in cotton and has retarded progress in effectively using that variability to develop better commercial cottons. ARS researchers at College Station, Texas, working with many other federal, state, and private researchers, developed a set of 105 portable DNA markers that are appropriate for identifying genetic diversity among the thousands of different cotton types that have been preserved worldwide and maintained in many different collections. These core DNA markers provide a common basis for systematic characterization of cotton germplasm collections for gene discovery in the U.S. and throughout the world. The marker set will in the years to come have major positive impact on the cotton research and breeding communities in their efforts to develop better cotton varieties for productive and profitable use by farmers worldwide.

2. Successful integration of genetic maps for cotton. The range and multiplicity of genetic populations and molecular markers used in mapping has hindered the integration of their data into a single integrated genetic map for applications in cotton improvement. By focusing on marker order rather than distances between markers, ARS researchers at College Station, Texas, working with Texas A&M University colleagues, exploited the information contained in more than two dozen different mapping datasets to create a single integrated "comprehensive reference map" that retained a large proportion of the data available in the individual maps. The new genetic map contains more than 7,000 DNA markers and incorporates some 93% of all the relevant information and data available from publicly accessible sources worldwide. This new map is an important resource for cotton geneticists and breeders because by consolidating and integrating multiple genetic maps it provides a single high density map, which enhances efforts to identify genes or genetic regions (QTLs) for superior traits such as fiber and yield improvement factors. It also provides a basic structure or reference for assembling sequences when sequencing the DNA of cotton. Effective utilization of the map will accelerate the development of new and improved cotton types that will enhance the productivity and profitability of cotton grown by farmers in all cotton-producing regions of the world.

3. A cotton fiber genetic map. Improvements in both fiber production (quantity) and fiber quality (length, strength, fineness, etc.) are needed to maintain cotton as the most important natural fiber for international commerce. Understanding the genetic control of various aspects of fiber generation by the plant is necessary for significant further advancements. ARS researchers at College Station, Texas, conducted detailed analysis of the genetic components involved in cotton fiber development, and developed what is known as a genetic map that provides the highest clarity available to date on the organization and distribution of fiber-related genes as they occur on different subdivisions (known as subgenomes) of the larger, total cotton genome. The fiber map developed by this work provides cotton researchers with a highly useful tool for application in ongoing work to develop cottons with enhanced fiber traits (both in quantity and quality). Success in fiber improvement will ensure that cotton remains the world’' most economically important natural fiber crop.


Review Publications
Van Deynze, A., Stoffel, K., Lee, M., Wilkins, T.A., Kozik, A., Cantrell, R.G., Yu, J., Kohel, R.J., Stelly, D.M. 2009. Sampling nucleotide diversity in cotton. BMC Plant Biology. 9:Article 125.

Yu, J., Kohel, R.J., Smith, C. 2010. The construction of a tetraploid cotton genome wide comprehensive reference map. Genomics. 95:230-240.

Last Modified: 8/30/2014
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