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United States Department of Agriculture

Agricultural Research Service

Title: Toward An Integrated Physical and Genetic Map of the Cultivated Cotton Genome: Physical Map Contig Assembling and Anchoring to Its Subgenomes

item Xu, Zhanyou - TEXAS A&M UNIVERSITY
item Yu, John
item Covaleda, Lina - TEXAS A&M UNIVERSITY
item Dong, Jiamin - TEXAS A&M UNIVERSITY
item Lee, Mi-Kyung - TEXAS A&M UNIVERSITY
item Ding, Kejiao - TEXAS A&M UNIVERSITY
item Kohel, Russell
item Zhang, Hongbin - TEXAS A&M UNIVERSITY

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Proceedings
Publication Acceptance Date: January 10, 2004
Publication Date: January 10, 2004
Citation: Xu, Z., Yu, J., Covaleda, L., Dong, J., Lee, M., Ding, K., Kohel, R.J., Zhang, H. 2004. Toward an integrated physical and genetic map of the cultivated cotton genome: Physical map contig assembling and anchoring to its subgenomes [abstract]. Plant and Animal Genome Conference XII. Paper No. P759.

Technical Abstract: We are developing an integrated physical and genetic map of the cultivated allotetraploid cotton (AD genomes) using three large-insert BAC and BIBAC libraries that were constructed from the genetic standard line TM-1 (G. hirsutum). An automated procedure previously developed and tested in both human and Arabidopsis genomes in our laboratories is being used, with a throughput of 1,536 BACs per day including clone fingerprint production, data editing and contig assembly. The clones (ca. 200,000) equivalent to 12 x cotton AD genomes can be fingerprinted and assembled into contigs within ten months. These clones are sufficient to construct a whole-genome physical map of the cotton AD genomes by use of our advanced computer programs. So far 100,000 clones equivalent to 6.1x cotton AD genomes from the TM-1 libraries have been fingerprinted, analyzed, and assembled into 5,646 contigs. These contigs are being anchored to the A and D sub-genomes of the cultivated cotton by using differential hybridization, subgenome-specific interspersed repeated sequences, representational difference analysis (RDA), and subgenome-specific DNA markers. Thirty-two contigs were selected and tested by the above methods. The results showed that clones from subgenomes A and D could be assembled into separate contigs, and the contigs could be sorted according to their origin of the sub-genomes, which is essential for physical mapping of the allotetraploid cotton.

Last Modified: 4/19/2015
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