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Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling

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Abstract

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

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Acknowledgments

The authors thank the staff of the United States Department of Agriculture-Agricultural Research Service, Crop Genetics and Production Research Unit for their technical expertise in conducting the field work. We also thank Jeff Cary, Jay Shockey, Josh Udall, Jonathan Wendel, Sam Yang, and two anonymous reviewers for their helpful comments during the preparation of this manuscript. This research was funded by United States Department of Agriculture-Agricultural Research Service project 6435-21000-015-00 and by a grant from the National Science Foundation Plant Genome Research Project—Award Number 0624077.

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  1. Andrew W. Woodward

    Present address: Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street MS-140, Houston, TX, 77251-1892, USA

Authors and Affiliations

  1. USDA-ARS-SRRC, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA

    Doug J. Hinchliffe & Barbara A. Triplett

  2. USDA-ARS-MSA, Stoneville, MS, 38776, USA

    William R. Meredith

  3. USDA-ARS-SPA, College Station, TX, 77840, USA

    Kathleen M. Yeater

  4. Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, 70803, USA

    Hee Jin Kim

  5. Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, 1 University Station A6700, Austin, TX, 78712, USA

    Andrew W. Woodward & Z. Jeffrey Chen

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  1. Doug J. Hinchliffe
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Correspondence to Barbara A. Triplett.

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Communicated by H. T. Nguyen.

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Hinchliffe, D.J., Meredith, W.R., Yeater, K.M. et al. Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling. Theor Appl Genet 120, 1347–1366 (2010). https://doi.org/10.1007/s00122-010-1260-6

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