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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 Cotton Genetic Standard Tm-1: Bac Fingerprinting and Physical Map Contig Construction.

item Zhang, Hong-Bin - TAMU SOIL & CROP
item Yu, John
item Kohel, Russell
item Stelly, David - TAMU
item Xu, Zhan-You - TAMU
item Covaleda, Lina - TAMU
item Ding, Ke-Jiao - TAMU
item Zhang, Liang-Tao - TAMU
item Wu, Cheng-Cang - TAMU
item Lee, Mi-Kyung - TAMU

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Abstract Only
Publication Acceptance Date: June 6, 2002
Publication Date: June 6, 2002
Citation: Zhang, H., Yu, J., Kohel, R.J., Stelly, D.M., Xu, Z., Covaleda, L., Ding, K., Zhang, L., Wu, C., Lee, M. 2002. Toward development of a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton genome using the upland cotton genetic standard TM-1: BAC fingerprinting and physical map contig construction [abstract]. International Cotton Genome Initiative Workshop. p. 33.

Technical Abstract: We are developing a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton (Gossypium hirsutum L.) genome using its genetic standard line TM-1 as the reference genotype. Whole-genome physical maps integrated with genetic maps will provide revolutionized tools and platforms for all kinds of genomics research, including large-scale gene mapping, cloning and target DNA marker development. Development of such an integrated physical map for cotton will accelerate its genomics research manifold. To ensure that the map is widely applicable to the cotton community, three large-insert TM-1 BAC and BIBAC libraries are used. We developed essential strategies, tools and techniques, and automated the procedure for genome physical mapping with BAC and BIBAC using a robotic workstation (Autogen 960), two capillary sequencers (ABI 3100) and several advanced computer programs. Experiments were conducted on the feasibility of development of the cotton physical map from the TM-1 BAC and BIBAC libraries using the strategies, techniques and procedures developed. The result showed that they allowed not only assembly of BAC/BIBAC contigs according to their origin of A or D genome, but also sorting of the contigs of A-genome from those of D genome. This result indicates that it is feasible to develop a robust physical map of the AD genome cotton using the techniques and strategies that we developed. Using the automated procedure, approximately 2000 BACs could daily be fingerprinted and analyzed, and the clones (about 150,000) covering 10 x cotton AD genomes could be analyzed within 3 - 4 months. These clones are sufficient to construct a whole-genome physical map of the cotton AD genome using our advanced computer programs. To effectively manipulate, disseminate, access and use integrated physical/genetic maps of agricultural genomes, we have established a core facility of bioinformatics and developed a web-based, integrated Genomic Information System (GIS). The GIS system allows users to access the results from many different areas of genome research, not only from integrated map to BAC/BIBAC contigs to BACs/BIBACs to gene/transcript/sequence map to gene expression map to protein sequence, structure and function, but also from genes/ESTs to BAC/BIBACs to BAC/BIBAC contigs to integrated physical/genetic map to association with traits. The system also allows users to access the macro- and micro-syntenies with others.

Last Modified: 4/19/2014
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