Toward Development of Robust Integrated Physical and Genetic Maps for Individual Chromosomes of Upland Cotton for Accurately Sequencing Its Genome

Structural Genomics

oral

Zhang, Yang; Zhang, Meiping; Liu, Yun-Hua ; Smith, Wayne; Hague, Steve; Stelly, David ; Zhang, Hong-Bin

Zhang, Yang

Zhang, Hong-Bin

Whole-genome sequences provide tools significant for many studies in genomics, genetics and breeding. Next-generation high-throughput sequencing technologies have provided an unprecedented opportunity of sequencing the cotton genomes because of their million-fold increased throughput and million-fold decreased cost. However, robust integrated physical and genetic maps for individual chromosomes of Upland cotton, which yields >90% of the world’s cotton fibers, are needed for accurate assembly of its genome sequence due to the complexity of each of its A- and D-subgenomes, and the polyploidy nature of its genome. Toward this end, we developed a BIBAC physical map for Upland cotton. It consists of 3,450 BIBAC contigs with an N50 contig size of 863 kb, collectively spanning 2,244 Mb in physical length. Analysis of the source BIBACs showed that the physical map contigs were assembled within the A- or D-subgenome, i.e., without combining BIBACs derived from homeologous segments. We also identified the minimal tilling path (MTP) BIBACs of the map and assembled the MTP BIBAC library, consisting of 15,277 clones. Moreover, we sequenced 10,000 BIBAC ends (BESs) randomly selected from the physical map, making one BES in approximately every 250 kb. Currently, we are integrating the BIBAC physical map with a super high-density cotton genetic map and developing robust physical maps for every chromosome of the Upland cotton A- and D-subgenomes, with one to a few BIBAC contigs per chromosome. The physical maps will provide a platform for advanced research of the Upland cotton genome in many aspects, particularly accurately sequencing and assembling the cotton genome using the next-generation sequencing technology, cloning its agronomic genes and QTLs, and systems functional analysis of the cotton genome.