Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2006
Publication Date: 1/12/2007
Citation: Xu, Z., Yu, J., Cho, J., Coveleda, L., Dong, J., Song, G., Zhang, L., Atkins, M., Yu, J., Ding, K., Ulloa, M., Tomkins, J., Stelly, D.M., Zhang, H., Kohel, R.J. 2007. An integrated BAC/BIBAC-based physical and genetic map of the cotton genome [abstract]. In: Proceedings of Plant and Animal Genome XV Conference, January 13-17, 2007, San Diego, California. Paper No. W198.
Technical Abstract: Integrated genome-wide genetic and physical maps are crucial to many aspects of cotton genome research. We report a genome-wide BAC/BIBAC-based physical and genetic map of the upland cotton genome using a high-resolution and high-throughput capillary-based fingerprinting method. The map was constructed from 103,979 clones from three cotton BAC and BIBAC libraries representing five haploid genomes, and consisted of 6,031 BAC/BIBAC contigs, estimated to span 1,871 Mb in physical length with genome coverage of 88.3%. From the 6,031 contigs, 950 contigs were hit by 814 markers, which included 167 BAC-end derived SSR, 175 BAC sub-clone derived SSR, 79 small insert genomic library derived SSR, and 393 RFLP marekrs. Of the 950 contigs, 248 contigs were assigned to At sub-genome, 160 to Dt sub-genome unanimously, 260 contigs shared by At and Dt, and 242 contigs need more data to separate them to their chromosomes. By sequences comparison and overgo hybridization, 1,101 fiber EST unigenes and 425 non-fiber EST unigenes were located onto the contig map. The reliability of the map contigs were evaluated using different contig assembly strategies, independent contig building methods, DNA marker hybridization, FISH display, and the results showed that the contigs were assembled properly. This map represents the first genome-wide, BAC/BIBAC-based physical map of the allotetraploid cotton genome and would provide a platform for advanced genome research of cotton and other Gossypium species, and it is also the first physical map of allotetraploid plant that separates the sub-genomes by sub-genomic probes and locus-specific SSR markers. The inclusion of BIBACs in the map would streamline the utility of the map for positional cloning of genes and QTLs, and functional analysis of cotton genomic sequences.