title: Generation of ESTs for flowering gene discovery and SSR marker development in upland cotton.
abstract: BACKGROUND
  Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare.
  
  
  RESULTS
  To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species.
  
  
  CONCLUSIONS
  A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis.
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.
authors.forename: Deyong
authors.initials: D
authors.lastname: Lai
authors.forename: Huaizhu
authors.initials: H
authors.lastname: Li
authors.forename: Shuli
authors.initials: S
authors.lastname: Fan
authors.forename: Meizhen
authors.initials: M
authors.lastname: Song
authors.forename: Chaoyou
authors.initials: C
authors.lastname: Pang
authors.forename: Hengling
authors.initials: H
authors.lastname: Wei
authors.forename: Junjie
authors.initials: J
authors.lastname: Liu
authors.forename: Dong
authors.initials: D
authors.lastname: Wu
authors.forename: Wenfang
authors.initials: W
authors.lastname: Gong
authors.forename: Shuxun
authors.initials: S
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D003001:Cloning, Molecular; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D035264:Flowers; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D005819:Genetic Markers / Q000235:genetics; D003368:Gossypium / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018749:RNA, Plant / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D005819:Genetic Markers; D018749:RNA, Plant