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Identification of differentially expressed genes associated with cotton fiber development in a chromosomal substitution line (CS-B22sh)

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Abstract

One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development. Availability of chromosome arm substitution line CS-B22sh (chromosome 22 short arm substitution from 3–79 (Gossypium barbadense) into a TM-1 (Gossypium hirsutum) background) provides a novel opportunity to study fiber-associated genes because previous studies revealed this line was associated with some superior fiber quality traits compared to TM-1. We used an integrated approach of suppression subtractive hybridization (SSH), microarray, and real-time reverse transcription-polymerase chain reaction (RT-PCR) technologies to identify the potential genes associated with fiber development. Utilizing mRNAs from 15 days post-anthesis (dpa) fibers, we constructed a SSH cDNA library with chromosome substitution line CS-B22sh as the tester and TM-1 as the driver. The SSH cDNA library was screened using microarrays. Microarray analysis showed that 36 genes were differentially expressed in CS-B22sh 15-dpa fiber compared to TM-1 as confirmed by real time RT-PCR. These genes include two beta-tubulins, an actin, a putative kinesin light chain, a cellulose synthase, glycosyl hydrolase family 3 protein, pyruvate decarboxylase, glycoside hydrolase family 5, GDP-mannose pyrophosphorylase, dynamin-like protein, annexin, and a number of genes involved in signal transduction, and protein, nucleic acid, and lipid metabolisms. To our knowledge, this is the first report on identification of differentially expressed fiber-associated genes in a cotton chromosomal substitution line.

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Acknowledgement

The authors would like to recognize the late Dr. Allan E. Zipf’s suggestions when writing the proposal for this project. We also thank Dr. Govind C. Sharma for his valuable suggestions when composing this manuscript. This research was a collaborative effort by the Agricultural Experiment Station, Alabama A&M University, and USDA-ARS Crop Science Research Lab scientists. We thank Dr. Michael Crowley, Genomics Core Facility at University of Alabama at Birmingham, for his assistance on microarray analysis in this project. We acknowledge the contribution of Dr. D.M. Stelly, Texas A&M University for developing CS-B22sh line. Contributed by the Agricultural Experiment Station, Alabama A&M University, Journal No. 615. This research was supported in part by the United States Department of Agriculture—Cooperative State Research, Education and Extension Service (USDA-CSREES) Capacity Building Grant#2003-38814-13932.

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Authors and Affiliations

  1. Department of Natural Resources and Environmental Sciences, Alabama A&M University, Normal, AL, 35762, USA

    Zhengdao Wu, Khairy M. Soliman & James J. Bolton

  2. USDA/ARS, Crop Science Research Laboratory, P. O. Box 5367, Mississippi State, MS, 39762, USA

    Sukumar Saha & Johnie N. Jenkins

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  1. Zhengdao Wu
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  2. Khairy M. Soliman
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  3. James J. Bolton
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  4. Sukumar Saha
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Correspondence to Khairy M. Soliman.

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This paper is dedicated to the memory of the late Dr. Allan Zipf. Mention of trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture or Alabama A&M University and does not imply its approval to the exclusion of other products that may also be suitable.

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Wu, Z., Soliman, K.M., Bolton, J.J. et al. Identification of differentially expressed genes associated with cotton fiber development in a chromosomal substitution line (CS-B22sh). Funct Integr Genomics 8, 165–174 (2008). https://doi.org/10.1007/s10142-007-0064-5

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  • DOI: https://doi.org/10.1007/s10142-007-0064-5

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