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Title: Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.)

Author
item LEE, MI-KYUNG - Texas A&M University
item ZHANG, YANG - Texas A&M University
item ZHANG, MEIPING - Texas A&M University
item GOEBEL, MARK - Texas A&M University
item Kim, Hee-Jin
item Triplett, Barbara
item STELLY, DAVID - Texas A&M University
item ZHANG, HONG-BIN - Texas A&M University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2013
Publication Date: 3/28/2013
Citation: Lee, M., Zhang, Y., Zhang, M., Goebel, M., Kim, H.J., Triplett, B.A., Stelly, D.M., Zhang, H. 2013. Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics. doi:10.1186/1471-2164-14-208.

Interpretive Summary: Cotton is a world’s leading crop producing natural fibers. Despite the importance of cotton fibers, the genome for commercially important Upland cotton has not been sequenced. In an attempt of understanding and using the genome of Upland cotton, a binary bacterial artificial chromosome (BIBAC) library of Upland cotton (Gossypium hirsutum L. Texas Marker-1) has been constructed. The cotton BIBAC library can be directly used as a vector for transforming cotton gene in plants in addition for sequencing cotton genome sequences. The extensive analyses of the cotton BIBAC library have provided us with cotton genome sequence information and newly identified cotton genes involved in cotton fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. The information generated from the cotton BIBAC library will be used by cotton scientists for improving cotton fiber properties.

Technical Abstract: Cotton is a world’s leading crop important to the world’s textile and energy industries, and a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction and extensive analysis of a binary bacterial artificial chromosome (BIBAC) library of Upland cotton (Gossypium hirsutum L.) cv. Texas Marker-1 (TM-1). The BIBAC library can be used not only as a BAC library, but also as a vehicle of large DNA fragments for direct transformation in plants via both Agrobacterium and biolistic bombardment. The library contains 76,800 clones with an average insert size of 135 kb, equivalent to 4.1x Upland cotton haploid genomes, or providing a 98.4% probability of obtaining at least one positive clone from the library using a single-copy probe. The utility of the library was demonstrated by identification of BIBACs containing genes important to fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. We also sequenced nearly 10,000 BIBAC ends (BESs) from the library, making approximately one BES in every 250 kb along the Upland cotton genome. The BES analysis shows that the Gypsy/DIRS1 retroelements are predominant, accounting for 77.86% of all transposable elements in the Upland cotton genome. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Moreover, using the BESs we have investigated the relationships of the Upland cotton genome with the related D-genome diploid, G. raimondii. The result indicates that the Upland cotton genome is significantly diverged from the G. raimondii genome. Since the library represents the first BIBAC library in cotton and related species, it has been used in integrative physical and genetic mapping, large-scale sequencing and assembly, and large-scale functional analysis of the Upland cotton genome.