Abstract
BackgroundUpland 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.Methodology/Principal FindingsTo 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/SignificanceA 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.
Highlights
Cotton is the leading agronomic fiber and oilseed crop in the world
These expressed sequence tag (EST) resources are suitable for gene discovery and molecular marker identification related to flower development of upland cotton
Of the 23 EST-simple sequence repeats (SSRs), 14 (60.9%) yielded microsatellite products from all 17 varieties, including 15 Gossypium species, whereas 9 (39.1%) amplified products from only a subset of the accessions, which ranged from 14 to 16 species. These results suggest that the EST-SSR markers derived from G. hirsutum produced a high rate of transferability across the Gossypium species
Summary
Gossypium hirsutum L. is a primary cultivated allotetraploid species (known as upland or American cotton) and has a tetraploid genome (AD; 2n = 46= 52) [1,2]. The products from this species include fibers and seeds that have a variety of uses. 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. Information about the flower development of this species is rare
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