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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS

Location: Crop Germplasm Research

2011 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 2011, a total of 2072 molecular markers were characterized on a 6-species, 12-genotype cotton panel and determined to be suitable for construction and integration of physical and genetic maps of Upland cotton (G. hirsutum). Project scientists and collaborators finalized the mapping analysis of all 26 cotton chromosomes, creating a saturated map with the 2,072 molecular markers. This cotton genetic map with portable DNA markers provides useful resources for germplasm characterization, gene discovery, molecular breeding, and eventual assembly of the finished genome sequence for cotton. In other FY 2011 project work focused on characterization of the genetic diversity of the National Cotton Germplasm Collection, more than 2,000 accessions were genotyped using 105 core DNA markers. The genotyping of these lines will allow the Collection to be analyzed for patterns of genetic diversity, redundancy, purity, etc. The creation of a core marker set provides a common basis for systematic characterization of cotton germplasm collections in the U.S. and internationally. Project work in FY 2011 included the identification of 55 new putative molecular markers called SNPs (single nucleotide polymorphisms). This technology is considered to be the molecular marker system of the future, possessing superior capabilities and attributes as contrasted to current markers. A project to identify and localize genes involved in gossypol gland formation resulted in 36 SNP markers being developed and mapped, which tag 20 genes on the 15 chromosomes involved in gland morphogenesis. Because accumulation of toxic gossypol is closely related to the development of gland tissues, localization of DNA markers involved in gland formation on the cotton genome map is helpful for the discovery of candidate genes associated with gland and gossypol traits.


4.Accomplishments
1. A saturated molecular genetic map for cotton. Genetic mapping of molecular markers to the 26 chromosomes of cotton is essential to the identification and location of genes on the chromosomes, and to understanding the genetic complexity of this important fiber and food crop. ARS scientists at College Station, TX, working with other ARS cooperators at New Orleans, LA, Shafter, CA, and Starkville, MS; university cooperators at Texas A&M University; and with private researchers at Dow AgroSciences and Monsanto Company, have finalized work on a saturated genetic map having 2,072 loci. The work confirmed two major chromosomal exchanges and several DNA duplications among and within the cotton chromosomes. This map constitutes an important resource for cotton geneticists and breeders worldwide, who conduct studies on germplasm characterization, gene discovery, molecular breeding, and the eventual assembly of finished genome sequence for cottons. 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 production regions of the world.

2. Sequencing of Upland cotton chromosomes 12 and 26. Genetic improvements in Upland cotton yield and quality are needed to maintain cotton as one of the world’s most economically important crops. Understanding the genetic codes of various aspects of cotton development and production is necessary for significant further advancements. ARS researchers at College Station, TX, working with cooperators at the Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China, sequenced some 28 million base pairs of assembled nuclear DNA from chromosomes 12 and 26 of the complex Upland cotton genome. Detailed structural, functional, and comparative analyses of the DNA sequence data revealed the genome complexity and identified more than 1,000 genes of interest. This work provides a highly useful tool for cotton researchers throughout the world to use in their work to develop cottons with enhanced productivity and quality traits.


Review Publications
Xu, Z., Yu, J., Cho, J., Yu, J., Kohel, R.J., Percy, R.G. 2010. Polyploidization altered gene functions in cotton (Gossypium spp.). PLoS One. 5(12):e14351. doi:10.1371/journal.pone.0014351.

Cho, J., Lu, C., Kohel, R.J., Yu, J. 2011. Development and mapping of gene-tagged SNP markers for gland morphogenesis in cotton. Journal of Cotton Science. 15:22-32.

Reddy, U.K., Rong, J., Heller-Uszynska, K., Nimmakayala, P., Vajja, G., Rahman, M.A., Yu, J., Soliman, K.M., Kilian, A., Paterson, A.H. 2011. Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map. Genome. 54:349-359.

Last Modified: 9/20/2014
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