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United States Department of Agriculture

Agricultural Research Service

Title: Toward Development of a Whole-Genome, Bac/bibac-Based Integrated Physical/genetic Map of the Cotton Genome Using the Upland Genetic Standard Tm-1:bac and Bibac Library Construction, Ssr Marker Development, and Physical/geneti

Authors
item Yu, John
item Kohel, Russell
item Zhang, Hong-Bin - TEXAS A&M UNIVERSITY
item Dong, Jianmin - TEXAS A&M UNIVERSITY
item Sun, Shuku - TEXAS A&M UNIVERSITY
item Steele, Nicole - TEXAS A&M UNIVERSITY

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Proceedings
Publication Acceptance Date: January 9, 2002
Publication Date: June 3, 2002
Citation: YU, J., KOHEL, R.J., ZHANG, H., DONG, J., SUN, S., STEELE, N. TOWARD DEVELOPMENT OF A WHOLE-GENOME, BAC/BIBAC-BASED INTEGRATED PHYSICAL/GENETIC MAP OF THE COTTON GENOME USING THE UPLAND GENETIC STANDARD TM-1: BAC AND BIBAC LIBRARY CONSTRUCTION, SSR MARKER DEVELOPMENT, AND PHYSICAL/GENETICS. PROCEEDINGS OF INTERNATIONAL COTTON GENOME INITIATIVE WORKSHOP. 2002. V. 14. P. 32.

Technical Abstract: Integrative physical mapping is the centerpiece of and essential for advanced genomics research. Upland cotton (Gossypium hirsutum L.) genetic standard line TM-1 is used as the reference genotype to develop a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton genome. From the TM-1 line we have constructed two BAC libraries with HindIII and EcoRI, respectively, and one plant-transformation-competent binary BAC (BIBAC) library with BamHI. Three large-insert BAC and BIBAC libraries constructed with different restriction enzymes not only reduce the number of clones needed, but also enhance the coverage of a genome-wide physical map. TM-1 is used for this effort because from this line extensive genetic mutants and cytogenetic stocks were developed. In addition, TM-1 is one of the two parents of our permanent recombinant inbred (RI) mapping population used in the integrated genetic/physical mapping of the cotton genome. Furthermore, seed stock of TM-1 for the libraries was maintained at 54th selfing generation by single-seed decent to ensure the plant homogeneity and homozygosity that are essential to a successful assembly of BAC contig maps by fingerprint analysis that truly reflect the genome structure of the Upland cotton. The three TM-1 BAC/BIBAC libraries contain 158,000 large-insert clones, have an average insert size of 130, 152 and 154 kb, respectively and cover >10x of the haploid (AD)1 genomes. They are now being used to construct the whole-genome BAC/BIBAC-based integrated genetic/physical map of Upland cotton and other aspects of genomic research. To have a large number of portable SSR markers for the cotton genetic map and facilitate physical/genetic map integration, we have been developing SSR markers from the TM-1 BAC libraries. The BAC-derived SSR markers have many advantages over those developed from small-insert DNA clones. The SSR marker-containing BACs provide direct bridges to physical contig maps with genetic linkage maps. They will not only streamline high-resolution mapping and positional cloning of QTLs and genes of interest, but also lead to the development of many different kinds of DNA markers that are well suited for marker-assisted breeding. An initial set of 1,000 such SSR primer pairs have been developed from the TM-1/HindIII BAC library. Approximately 60% of these BAC-SSR primer pairs amplify only single fragments, which are very useful for integration of physical/genetic maps and identification of the A- or D-subgenome specific BAC contigs. High-density filters and pools of the TM-1/HindIII BAC clones have been distributed to the international cotton research community for specific genomic studies. TM-1 BAC-derived SSR markers will be distributed to the cotton research community once we determine the value of polymorphism information content (PIC) on each SSR marker with a diverse cotton panel. The TM-1 x 3-79 genetic map has approximately 1,000 DNA markers and it is now being augmented with the 1,000 BAC-derived SSR markers and other 1,000 SSR markers currently funded by the Cotton Incorporated. Integration of genetic and physical maps with a large number of portable SSR markers on the BAC contigs will certainly benefit the cotton genome research including molecular breeding, germplasm evaluation, and functional analysis of thousands of cotton genes.

Last Modified: 4/23/2014
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