Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2003
Publication Date: 1/18/2004
Citation: Yu, J., Kohel, R.J., Zhang, H., Stelly, D.M., Xu, Z., Dong, J., Covaleda, L., Lee, M., Cui, P., Lazo, G.R., Gupta, P., Ding, K. 2004. Toward an integrated physical and genetic map of the cultivated allotetraploid cotton genome [abstract]. Plant and Animal Genome Conference XII. Paper No. W147.
Technical Abstract: Integrated infrastructure and genomic tools are needed by the research community to advance basic and applied research in cotton and other polyploid crops. We are developing an integrated physical and genetic map of the cultivated allotetraploid cotton (AD1 genome) by use of three complementary large-insert BAC and BIBAC libraries that were constructed from TM-1, the genetic standard of Upland cottons and a recombinant inbred (RI) population of TM-1 and 3-79, the genetic standard of extra long staple cottons. Approximately 100,000 TM-1 BAC/BIBAC clones have been fingerprinted and the fingerprints are assembled into 5,646 physical contigs. In addition, approximately 2,000 cotton SSR loci have been isolated from the above TM-1 BAC clones/contigs. Forward and reverse primers have been designed from the flanking sequence of the SSR loci and they are used to screen for polymorphism information content (PIC) values on a standardized cotton panel that consists of 12 diverse genotypes. BAC-derived SSR markers that show a polymorphism between TM-1 and 3-79 are being mapped on the permanent RI population. Such markers facilitate an integration of physical and genetic mapping information. Molecular cytogenetic markers are also being developed from the TM-1 BAC clones/contigs to assist in the map integration. Subgenomic origins (A or D) of the cotton contigs are derived with sub-genome based hybridization; representational difference analysis (RDA); and sub-genome specific DNA markers. Cotton BAC clones, SSR primers, and related information have been delivered to the cotton research community through CottonDB that is incorporating new bioinformatic tools. An integrated physical and genetic map of the cultivated allotetraploid cotton will accelerate gene discovery and utilization from cotton germplasm, and facilitate studies of gene duplication, distribution, and interaction in many polyploid crop genomes.