Submitted to: American Society of Agronomy
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2004
Publication Date: 10/31/2004
Citation: Yu, J., Kohel, R.J., Zhang, H.B., Xu, Z., Dong, J., Lee, M., Cui, P., Covaleda, L. 2004. Integrative physical mapping of the cotton genome and its synteny with Arabidopsis [abstract]. American Society of Agronomy. 2004 CDROM.
Technical Abstract: Shortage of genomic tools hinders continued genetic improvement of cotton. We are developing such genomic tools that are immediately needed by the cotton research community. Our first objective is to construct an integrated physical map of Upland cotton genetic standard (TM-1). The physical map consisted of 5,466 contigs assembled from 101,376 TM-1 BACs and BIBACs, 675 fiber ESTs anchored to the BAC contigs, and nearly 1,000 SSRs isolated from the BACs. Once mapped genetically, the BAC-derived SSRs will enable integration of cotton physical and genetic maps, and will locate mapped genes and QTLs to BACs, BIBACs and/or their contigs for detailed analysis. Secondly we are leveraging cotton genomic resources by use of its synteny with the model plant Arabidopsis that has the closest relationship among the angiosperm. Approximately 1,200 base pairs of DNA sequences were determined at both ends of 576 clones from 52 cotton BAC contigs selected for syntenic analysis. A high level of synteny between cotton and Arabidopsis was observed by comparison with Arabidopsis conserved ortholog set (COS) sequences identified at Cornell. Single- or low-copy numbers in cotton counterparts indicated potential cross-utilization of genomic tools and resources between the two species and they could shed light on evolutionary events associated with the divergence of their seemingly disparate genomes.