The Construction of a Gossypium AD-genome-wide Comprehensive Reference Map Based on Diverse Data Resources

Integration of two or more genomic maps provides a higher density of markers and greater genome coverage than can be obtained with the resources available for a single mapping study. Map integration is important in any species for which an annotated complete genome sequence is not available. For organisms currently being sequenced, a pre-sequence integrated map is essential to provide the "backbone" for assembly of the sequence. Map integration also facilitates the identification and resolution of discrepancies among different maps; mapping of QTLs, ESTs, and BACs; and positioning of candidate genes. However, the inconsistencies in markers and populations used in individual mapping studies limit our ability to fully integrate the available data. By concentrating on marker orders rather than marker distances, one can join together published map data to include a majority of markers with the best estimate of their order in the genome. In this study, a comprehensive reference map was constructed from 28 published cotton AD genome maps. The output reference map contains 7,424 markers and represents over 93% of the combined mapping information from the 28 individual AD genome genetic maps. This study applied the use of bioinformatics and computational biology in cotton genome mapping integration. The output will be stored and displayed through CottonDB (http://www.cottondb.org), a public cotton genome database.