Genome Physical Mapping of Polyploids: Construction and Characterization of a BIBAC Physical Map of Cultivated Tetraploid Cotton, Gossypium hirsutum L

Polyploids are predominant in flowering plants, including many field, horticulture and forage crops, such as cotton, wheat, potatoes, canola, sugarcane, oats, peanut, tobacco, rose, coffee and banana. Cottons are the world-leading fiber and important oilseed crop, and a model species for study of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. This study has addressed the concerns of physical mapping of polyploids with BACs and/or BIBACs by constructing a plant-transformation-competent BIBAC physical map of the tetraploid Upland cotton, Gossypium hirsutum L. The physical map consists of 3,450 BIBAC contigs with an N50 contig size of 863 kb, collectively spanning 2,244 Mb in physical length. We sorted the map contigs according to their origin of subgenome, showing that we assembled physical maps for the two subgenomes, A- and D-subgenomes, of the tetraploid cotton, separately. We also identified the BIBACs in the map minimal tilling path (MTP), which consists of 15,277 clones. Moreover, we sequenced nearly 10,000 BIBAC ends (BESs), making one BES-STS (sequence-tagged site) in approximately 250 kb along the cotton genome. This physical map provides not only a strategy and a line of evidence for physical mapping of polyploids with BACs and/or BIBACs, but also a platform for advanced research of the Upland cotton genome, particularly cloning and characterization of genes and QTLs important to fibers, oilseeds and biotic/abiotic resistance, and sequencing and assembly of the Upland cotton genome using the next-gen sequencing technology. Meiping Zhang and Yang Zhang contributed to the study equally.