Plant Molecular Biology

, Volume 54, Issue 6, pp 911–929 | Cite as

Functional genomics of cell elongation in developing cotton fibers

  • A. Arpat
  • Mark Waugh
  • John P. Sullivan
  • Michael Gonzales
  • David Frisch
  • Dorrie Main
  • Todd Wood
  • Anna Leslie
  • Rod Wing
  • Thea Wilkins


Cotton fibers are single-celled seed trichomes of major economic importance. Factors that regulate the rate and duration of cell expansion control fiber morphology and important agronomic traits. For genetic characterization of rapid cell elongation in cotton fibers, ∼ 14,000 unique genes were assembled from 46,603 expressed sequence tags (ESTs) from developmentally staged fiber cDNAs of a cultivated diploid species (Gossypium arboreumL.). Conservatively, the fiber transcriptome represents 35–40% of the genes in the cotton genome. In silico expression analysis revealed that rapidly elongating fiber cells exhibit significant metabolic activity, with the bulk of gene transcripts, represented by three major functional groups – cell wall structure and biogenesis, the cytoskeleton and energy/carbohydrate metabolism. Oligonucleotide microarrays revealed dynamic changes in gene expression between primary and secondary cell wall biogenesis showing that fiber genes in the dbEST are highly stage-specific for cell expansion – a conclusion supported by the absence of known secondary cell wall-specific genes from our fiber dbEST. During the developmental switch from primary to secondary cell wall syntheses, 2553 “expansion-associated” fiber genes are significantly down regulated. Genes (81) significantly up-regulated during secondary cell wall synthesis are involved in cell wall biogenesis and energy/carbohydrate metabolism, which is consistent with the stage of cellulose synthesis during secondary cell wall modification in developing fibers. This work provides the first in-depth view of the genetic complexity of the transcriptome of an expanding cell, and lays the groundwork for studying fundamental biological processes in plant biology with applications in agricultural biotechnology.

cell expansion ESTs oligonucleotide microarrays primary cell wall secondary cell wall 


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Supplementary material

PLAN883-rSupplementary Table 1.doc (162 kb)
PLAN883-rSupplementary Table 1.doc
PLAN883-rSupplementary Table 2.doc (60 kb)
PLAN883-rSupplementary Table 2.doc
PLAN883-rSupplementary Table 3.doc (44 kb)
PLAN883-rSupplementary Table 3.doc
PLAN883-Supplementary Figure 1.tif (121 kb)
PLAN883-Supplementary Figure 1.tif
PLAN883-Supplementary Figure 2.tif (79 kb)
PLAN883-Supplementary Figure 2.tif
PLAN883-Supplementary Table 4.xls (300 kb)
PLAN883-Supplementary Table 4.xls


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Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • A. Arpat
    • 1
  • Mark Waugh
    • 2
  • John P. Sullivan
    • 2
  • Michael Gonzales
    • 2
  • David Frisch
    • 3
    • 4
  • Dorrie Main
    • 3
  • Todd Wood
    • 3
    • 5
  • Anna Leslie
    • 1
    • 6
  • Rod Wing
    • 3
    • 7
  • Thea Wilkins
    • 1
  1. 1.Department of Agronomy and Range ScienceUniversity of CaliforniaUSA
  2. 2.National Center for Genome ResourcesUSA
  3. 3.Computer Science DepartmentUniversity of MassachusettsUSA
  4. 4.Genome Center of WisconsinUniversity of WisconsinUSA
  5. 5.Center for Origins Research and EducationBryan CollegeUSA
  6. 6.College of Agriculture and Environmental Sciences Genomics FacilityUniversity of CaliforniaUSA
  7. 7.Arizona Genomics Institute, Department of Plant SciencesUniversity of ArizonaUSA

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