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Open Access Highly Accessed Research article

Enrichment of a set of microRNAs during the cotton fiber development

Pieter Bas Kwak1, Qin Qin Wang1, Xu Sheng Chen2, Cheng Xiang Qiu1 and Zhi Min Yang1*

Author affiliations

1 Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, PR China

2 Laboratory of Cotton Breeding, Industrial Crop Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China

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Citation and License

BMC Genomics 2009, 10:457  doi:10.1186/1471-2164-10-457

Published: 29 September 2009

Abstract

Background

Cotton (Gossypium hirsutum) is one of the most important economic crops and provides excellent fibers for textile manufacture. In addition to its industrial and agricultural importance, the fiber cell (plant trichome) also is a biological model system for exploring gene expression and regulation. Small RNAs regulate many aspects of plant growth and development. However, whether small RNAs are involved in regulation of fiber cell development is unknown.

Results

We adopted a deep sequencing approach developed by Solexa (Illumina Inc.) to investigate global expression and complexity of small RNAs during cotton fiber initiation and development. We constructed two small RNA libraries prepared from wild type (WT) and fuzz/lintless (fl Mutant in the WT background) cotton ovules, respectively. Each library was sequenced individually and generated more than 6-7 million short sequences, resulting in a total of over 13 million sequence reads. At least 22 conserved candidate miRNA families including 111 members were identified. Seven families make up the vast majority of expressed miRNAs in developing cotton ovules. In total 120 unique target genes were predicted for most of conserved miRNAs. In addition, we identified 2 cell-type-specific novel miRNA candidates in cotton ovules. Our study has demonstrated significant differences in expression abundance of miRNAs between the wild-type and mutant, and suggests that these differentially expressed miRNAs potentially regulate transcripts distinctly involved in cotton fiber development.

Conclusion

The present study is the first to deep sequence the small RNA population of G. hirsutum ovules where cotton fibers initiate and develop. Millions of unique miRNA sequences ranging from 18~28 nt in length were detected. Our results support the importance of miRNAs in regulating the development of different cell types and indicate that identification of a comprehensive set of miRNAs in cotton fiber cells would facilitate our understanding of the regulatory mechanisms for fiber cell initiation and elongation.