The Gossypium Transcriptome

  • Joshua A. Udall
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 3)


cDNA sequences representing the Gossypium transcriptome have been generated by numerous researchers within the cotton community. The bulk of these cDNA sequences are from cultivated Gossypium hirustum and its close diploid relatives G. arboreum and G. raimondii. Our current understanding of the Gossypium transcriptome is based on the assembly of these expressed sequences into unique, non-overlapping unigenes (putative gene models). With this compilation of expressed sequences, DNA microarrays have been constructed for gene expression experiments, evidence for recent genome duplication has been identified, and novel expression patterns in fiber development have been discovered. Future efforts to collect expressed sequences from domesticated cotton and its relatives will continue to enhance our understanding of the Gossypium transcriptome.


Gene Ontology Cotton Fiber Fiber Development Fiber Elongation Fiber Initiation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



A special thanks to Lex Flagel, Ran Hovav, Ryan Rapp, and Jonathan Wendel for proof-reading, assistance with figures, and insightful comments and discussion; and to Foo Cheung for creating the ESTinformatics assembly, proof-reading and helpful discussion.


  1. Adams, K.L. (2007) Evolution of duplicate gene expression in polyploid and hybrid plants. J. Hered. 98, 136–141.PubMedGoogle Scholar
  2. Adams, K.L., Cronn R., Percifield R., and Wendel J.F. (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. U.S.A. 100, 4649–4654.PubMedGoogle Scholar
  3. Adams, K.L., Percifield R., and Wendel J.F. (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168, 2217–2226.PubMedGoogle Scholar
  4. Adams, K.L. and Wendel J.F. (2005) Novel patterns of gene expression in polyploid plants. Trends Genet. 21, 539–543.PubMedGoogle Scholar
  5. Alba, R., Fei Z., Payton P., Liu Y., Moore S.L., Debbie P., Cohn J., D'Ascenzo M., Gordon J.S., Rose J.K.C., Martin G., Tanksley S.D., Bouzayen M., Jahn M.M., and Giovannoni J. (2004) ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J. 39, 697–714.PubMedGoogle Scholar
  6. Amarasinghe, B.H.R.R., Faivre-Nitschke E., Wu Y., Udall J.A., Dennis E.S., Constable G., and Llewellyn D.J. (2006) Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays. Plant Biotech. 23, 437–450.Google Scholar
  7. Applequist, W.L., Cronn R., and Wendel J.F. (2001) Comparative development of fiber in wild and cultivated cotton. Evol. Devel. 3, 3–17.Google Scholar
  8. Arpat, A., Waugh M., Sullivan J.P., Gonzales M., Frisch D., Main D., Wood T., Leslie A., Wing R., and Wilkins T. (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 54, 911–929.PubMedGoogle Scholar
  9. Barrett, T., Suzek T.O., Troup D.B., Wilhite S.E., Ngau W.-C., Ledoux P., Rudnev D., Lash A.E., Fujibuchi W., and Edgar R. (2005) NCBI GEO: mining millions of expression profiles--database and tools. Nuc. Acids Res. 33, D562–566.Google Scholar
  10. Basra, A.S. and Malik C.P. (1984) Development of the cotton fiber. In: K.W. Jeon (Eds.), International Review of Cytology. Elsevier Inc., New York, New York, pp. 65–113.Google Scholar
  11. Blanc, G. and Wolfe K.H. (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678.PubMedGoogle Scholar
  12. Bowers, J.E., Chapman B.A., Rong J., and Paterson A.H. (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438.PubMedGoogle Scholar
  13. Chen, Z.J. and Ni Z. (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28, 240–252.PubMedGoogle Scholar
  14. Comai, L. (2000) Genetic and epigenetic interactions in allopolyploid plants. Plant Mol. Biol. 43, 387–399.PubMedGoogle Scholar
  15. Conesa, A., Gotz S., Garcia-Gomez J.M., Terol J., Talon M., and Robles M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676.PubMedGoogle Scholar
  16. Cronn, R.C., Small R.L., Haselkorn T., and Wendel J.F. (2002) Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Bot. 89, 707–725.PubMedGoogle Scholar
  17. Cui, L., Wall P.K., Leebens-Mack J.H., Lindsay B.G., Soltis D.E., Doyle J.J., Soltis P.S., Carlson J.E., Arumuganathan K., Barakat A., Albert V.A., Ma H., and dePamphilis C.W. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res. 16, 738–749.PubMedGoogle Scholar
  18. Dowd, C., Wilson I.W., and McFadden H.G. (2004) Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum. Mol. Plant-Mic. Inter. 17, 654–667.Google Scholar
  19. Endrizzi, J.E., Turcotte E.L., and Kohel R.J. (1985) Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23, 271–375.Google Scholar
  20. Ewing, B. and Green P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194.Google Scholar
  21. Ewing, B., Hillier L., Wendl M.C., and Green P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.PubMedGoogle Scholar
  22. Ewing, R.M., Kahla A.B., Poirot O., Lopez F., Audic S., and Claverie J.-M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950–959.PubMedGoogle Scholar
  23. Fulton, T.M., Van der Hoeven R., Eannetta N.T., and Tanksley S.D. (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14, 1457–1467.PubMedGoogle Scholar
  24. Gaut, B.S. (1998) Molecular clocks and nucleotide substitution rate in higher plants. In: M.K. Hecht (Eds.), Evolutionary Biology. Plenum Press, New York, pp. 93–120.Google Scholar
  25. Glover, B.J., Bunnewell S., and Martin C. (2004) Convergent evolution within the genus Solanum: the specialised anther cone develops through alternative pathways. Gene 331, 1–7.PubMedGoogle Scholar
  26. Glover, B.J., Perez-Rodriguez M., and Martin C. (1998) Development of several epidermal cell types can be specified by the same MYB-related plant transcription factor. Devel. 125, 3497–508.Google Scholar
  27. Gou, J.-Y., Wang L.-J., Chen S.-P., Hu W.-L., and Chen X.-Y. (2007) Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res. 17, 422–434.PubMedGoogle Scholar
  28. Haigler, C.H., Zhang D., and Wilkerson C.G. (2005) Biotechnological improvement of cotton fibre maturity. Physiol. Plant 124, 285–294.Google Scholar
  29. Hasenfratz, M.P., Tsou C.L., and Wilkins T.A. (1995) Expression of two related vacuolar H+-ATPase 16-kilodalton proteolipid genes is differentially regulated in a tissue-specific manner. Plant Physiol. 108, 1395–1404.PubMedGoogle Scholar
  30. He, C., Yan J., Shen G., Fu L., Holaday A.S., Auld D., Blumwald E., and Zhang H. (2005) Expression of an arabidopsis vacuolar sodium/proton antiporter gene in cotton improves photosynthetic performance under salt conditions and increases fiber yield in the field. Plant Cell Physiol. 46, 1848–1854.PubMedGoogle Scholar
  31. He, P., Friebe B.R., Gill B.S., and Zhou J.-M. (2003) Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol. Biol. 52, 401–414.PubMedGoogle Scholar
  32. Hegarty, M.J., Jones J.M., Wilson I.D., Barker G.L., Coghill J.A., Sanchez-Baracaldo P., Liu G., Buggs R.J.A., Abbott R.J., Edwards K.J., and Hiscock S.J. (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol. Ecol. 14, 2493–2510.PubMedGoogle Scholar
  33. Hsu, C.-Y., Jenkins J.N., Saha S., and Ma D.-P. (2005) Transcriptional regulation of the lipid transfer protein gene LTP3 in cotton fibers by a novel MYB protein. Plant Sci. 168, 167–181.Google Scholar
  34. Huang, B. and Liu J.-Y. (2006) A cotton dehydration responsive element binding protein functions as a transcriptional repressor of DRE-mediated gene expression. Biochemical and Biophysical Research Communications 343, 1023–1031.PubMedGoogle Scholar
  35. Huang, X. and Madan A. (1999) CAP3: A DNA sequence assembly program. Genome Res. 9, 868–877.PubMedGoogle Scholar
  36. Hughes, A. and Friedman R. (2004) Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana. J. Mol. Evol. 60, 247–256.Google Scholar
  37. Hulskamp, M., Misra S., and Jurgens G. (1994) Genetic dissection of trichome cell development in Arabidopsis. Cell 76, 555–66.PubMedGoogle Scholar
  38. Humphries, J.A., Walker A.R., Timmis J.N., and Orford S.J. (2005) Two WD-repeat genes from cotton are functional homologues of the Arabidopsis thaliana TRANSPARENT TESTA GLABRA1 (TTG1) gene. Plant Mol. Biol. 57, 67–81.PubMedGoogle Scholar
  39. Ji, S.-J., Lu Y.-C., Feng J.-X., Wei G., Li J., Shi Y.-H., Fu Q., Liu D., Luo J.-C., and Zhu Y.-X. (2003) Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nuc. Acids Res. 31, 2534–2543.Google Scholar
  40. Jiang, C., Wright R.J., El-Zik K.M., and Paterson A.H. (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. U.S.A. 95, 4419–4424.PubMedGoogle Scholar
  41. John, M. and Crow L. (1992) Gene expression in cotton (Gossypium hirsutum L.) fiber: Cloning of the mRNAs. Proc. Natl. Acad. Sci. U.S.A. 89, 5769–5773.PubMedGoogle Scholar
  42. Kashkush, K., Feldman M., and Levy A.A. (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160, 1651–1659.PubMedGoogle Scholar
  43. Kim, H.J. and Triplett B.A. (2001) Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol. 127, 1361–1366.PubMedGoogle Scholar
  44. Kohel, R.J., Stelly D.M., and Yu J. (2002) Tests of six cotton (Gossypium hirsutum L.) mutants for association with aneuploids. J. Hered. 93, 130–132.PubMedGoogle Scholar
  45. Kosmas, S.A., Argyrokastritis A., Loukas M.G., Eliopoulos E., Tsakas S., and Kaltsikes P.J. (2006) Isolation and characterization of drought-related trehalose 6-phosphate-synthase gene from cultivated cotton (Gossypium hirsutum L.). Planta 23, 329–339.Google Scholar
  46. Lacape, J.-M., Nguyen T.-B., Courtois B., Belot J.-L., Giband M., Gourlot J.-P., Gawryziak G., Roques S., and Hau B. (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum x Gossypium barbadense backcross generations. Crop Sci. 45, 123–140.Google Scholar
  47. Lai, Z., Gross B.L., Zou Y., Andrews J., and Rieseberg L.H. (2006) Microarray analysis reveals differential gene expression in hybrid sunflower species. Mol. Ecol. 15, 1213–1227.PubMedGoogle Scholar
  48. Lee, J., Hassan O., Gao W., Wei N., Kohel R., Chen X.-Y., Payton P., Sze S.-H., Stelly D., and Chen Z. (2006) Developmental and gene expression analyses of a cotton naked seed mutant. Planta 223, 418–432.PubMedGoogle Scholar
  49. Li, C.-H., Zhu Y.-Q., Meng Y.-L., Wang J.-W., Xu K.-X., Zhang T.-Z., and Chen X.-Y. (2002) Isolation of genes preferentially expressed in cotton fibers by cDNA filter arrays and RT-PCR. Plant Sci. 163, 1113–1120.Google Scholar
  50. Li, W.-H., Yang J., and Gu X. (2005) Expression divergence between duplicate genes. Trends Genet. 21, 602–607.PubMedGoogle Scholar
  51. Li, X.-B., Fan X.-P., Wang X.-L., Cai L., and Yang W.-C. (2005) The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17, 859–875.PubMedGoogle Scholar
  52. Liang, P. and Pardee A. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967–971.PubMedGoogle Scholar
  53. Light, G.G., Mahan J.R., Roxas V.P., and Allen R.D. (2005) Transgenic cotton (Gossypium hirsutum L.) seedlings expressing a tobacco glutathione S-transferase fail to provide improved stress tolerance. Planta 222, 346–354.PubMedGoogle Scholar
  54. Liu, H.-C., Creech R.G., Jenkins J.N., and Ma D.-P. (2000) Cloning and promoter analysis of the cotton lipid transfer protein gene Ltp3. BBA - Mol. Cell Biol. Lipids 1487, 106–111.Google Scholar
  55. Loguercio, L.L., Zhang J.-Q., and Wilkins T.A. (1999) Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.). Mol. Genet. Gen. 261, 660–671.Google Scholar
  56. Madlung, A., Tyagi A.P., Watson B., Jiang H., Kagochi T., Doerge R.W., Martienssen R., and Comai L. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J. 41, 221–230.PubMedGoogle Scholar
  57. Meyers, B.C., Galbraith D.W., Nelson T., and Agrawal V. (2004) Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol. 135, 637–652.PubMedGoogle Scholar
  58. Noda, K., Glover B.J., Linstead P., and Martin C. (1994) Flower colour intensity depends on specialized cell shape controlled by a Myb-related transcription factor. Nature 369, 661–4.PubMedGoogle Scholar
  59. Oppenheimer, D.G., Herman P.L., Sivakumaran S., Esch J., and Marks M.D. (1991) A myb gene required for leaf trichome differentiation in Arabidopsis is expressed in stipules. Cell 67, 483–93.PubMedGoogle Scholar
  60. Osborn, T.C., Pires J.C., Birchler J.A., Auger D.L., Jeffery Chen Z., Lee H.-S., Comai L., Madlung A., Doerge R.W., Colot V., and Martienssen R.A. (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19, 141–147.PubMedGoogle Scholar
  61. Paterson, A.H., Saranga Y., Menz M., Jiang C.-X., and Wright R.J. (2003) QTL analysis of genotype x environment interactions affecting cotton fiber quality. Theor. Appl. Genet. 106, 384–396.PubMedGoogle Scholar
  62. Payne, T., Clement J., Arnold D., and Lloyd A. (1999) Heterologous myb genes distinct from GL1 enhance trichome production when overexpressed in Nicotiana tabacum. Devel. 126, 671–82.Google Scholar
  63. Perez-Rodriguez, M., Jaffe F.W., Butelli E., Glover B.J., and Martin C. (2005) Development of three different cell types is associated with the activity of a specific MYB transcription factor in the ventral petal of Antirrhinum majus flowers. Devel. 132, 359–70.Google Scholar
  64. Pertea, G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., and Quackenbush J. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651–652.PubMedGoogle Scholar
  65. Qiu, C.X., Xie F.L., Zhu Y.Y., Guo K., Huang S.Q., Nie L., and Yang Z.M. (2007) Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395, 49–61.PubMedGoogle Scholar
  66. Qu, Z.-L., Zhong N.-Q., Wang H.-Y., Chen A.-P., Jian G.-L., and Xia G.-X. (2006) Ectopic expression of the cotton non-symbiotic hemoglobin gene GhHbd1 triggers defense responses and increases disease tolerance in Arabidopsis. Plant Cell Physiol. 47, 1058–1068.PubMedGoogle Scholar
  67. Rabinowicz, P.D., Citek R., Budiman M.A., Numberg A., Bedell J.A., Lakey N., O'Shaughnessy A.L., Nacimiento L.U., McCombie W.R., and Martienssen R.A. (2005) Differential methylation of genes and repeats in land plants. Genome Res. 15, 1431–1440.PubMedGoogle Scholar
  68. Rensink, W.A. and Buell C.R. (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci. 10, 603–609.PubMedGoogle Scholar
  69. Ronning, C.M., Stegalkina S.S., Ascenzi R.A., Bougri O., Hart A.L., Utterbach T.R., Vanaken S.E., Riedmuller S.B., White J.A., Cho J., Pertea G.M., Lee Y., Karamycheva S., Sultana R., Tsai J., Quackenbush J., Griffiths H.M. , Restrepo S., Smart C.D., Fry W.E., van der Hoeven R., Tanksley S., Zhang P., Jin H., Yamamoto M.L., Baker B.J., and Buell C.R. (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131, 419–429.PubMedGoogle Scholar
  70. Ruan, Y. (2007) Rapid cell expansion and cellulose synthesis regulated by plasmodesmata and sugar: insights from the single-celled cotton fibre. Func. Plant Biol. 34, 1–10.Google Scholar
  71. Ruan, Y.-L. and Chourey P.S. (1998) A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds. Plant Physiol. 118, 399–406.PubMedGoogle Scholar
  72. Ruan, Y.-L., Llewellyn D.J., and Furbank R.T. (2001) The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin. Plant Cell 13, 47–60.PubMedGoogle Scholar
  73. Schlueter, J.A., Dixon P., Granger C., Grant D., Clark L., Doyle J., and Shoemaker R. (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome 47, 868–876.PubMedGoogle Scholar
  74. Senchina, D.S., Alvarez I., Cronn R.C., Liu B., Rong J., Noyes R.D., Paterson A.H., Wing R.A., Wilkins T.A., and Wendel J.F. (2003) Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Bio. Evol. 20, 633–643.Google Scholar
  75. Serna, L. and Martin C. (2006) Trichomes: different regulatory networks lead to convergent structures. Trends Plant Sci. 11, 274–280.PubMedGoogle Scholar
  76. Shi, Y.-H., Zhu S.-W., Mao X.-Z., Feng J.-X., Qin Y.-M., Zhang L., Cheng J., Wei L.-P., Wang Z.-Y., and Zhu Y.-X. (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18, 651–664.PubMedGoogle Scholar
  77. Smart, L.B., Vojdani F., Maeshima M., and Wilkins T.A. (1998) Genes involved in osmoregulation during turgor-driven cell expansion of developing cotton fibers are differentially regulated. Plant Physiol. 116, 1539–1549.PubMedGoogle Scholar
  78. Straus, D. and Ausubel F. (1990) Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc. Natl. Acad. Sci. U.S.A. 87, 1889–1893.PubMedGoogle Scholar
  79. Suo, J., Liang X., Pu L., Zhang Y., and Xue Y. (2003) Identification of GhMYB109 encoding a R2R3 MYB transcription factor that expressed specifically in fiber initails and elongating fibers of cotton (Gosspyium hirsutum L.). Biochem. Biophysica Acta 1630, 25–34.Google Scholar
  80. Taliercio, E. and Ray J.D. (2001) Identification of transcripts translated on free or membrane-bound polyribosomes by differential display. Plant Mol. Biol. Rep. 19, 269.Google Scholar
  81. Taliercio, E.W. and Boykin D. (2007) Analysis of gene expression in cotton fiber initials. BMC Plant Biology 7, 22.PubMedGoogle Scholar
  82. Tate, J.A., Ni Z., Scheen A.-C., Koh J., Gilbert C.A., Lefkowitz D., Chen Z.J., Soltis P.S., and Soltis D.E. (2006) Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173, 1599–1611.PubMedGoogle Scholar
  83. The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816.Google Scholar
  84. Udall, J.A., Flagel L.E., Cheung F., Woodward A., Hovav R., Rapp R.A., Swanson J.M., Lee J., Gingle A., Nettleton D., Town C.D., Chen Z.J., and Wendel J.F. (2007) Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8, 81 .PubMedGoogle Scholar
  85. Udall, J.A., Swanson J.M., Haller K., Rapp R.A., Sparks M.E., Hatfield J., Yu Y., Wu Y., Dowd C., Arpat A.B., Sickler B.A., Wilkins T.A., Guo J.Y., Chen X.Y., Scheffler J., Taliercio E., Turley R., McFadden H., Payton P., Klueva N., Allen R., Zhang D., Haigler C., Wilkerson C., Suo J., Schulze S.R., Pierce M.L., Essenberg M., Kim H., Llewellyn D.J., Dennis E.S., Kudrna D., Wing R., Paterson A.H., Soderlund C., and Wendel J.F. (2006) A global assembly of cotton ESTs. Genome Res. 16, 441-450.PubMedGoogle Scholar
  86. Udall, J.A., Swanson J.M., Nettleton D., Percifield R.J., and Wendel J.F. (2006) A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173, 1823–1827.PubMedGoogle Scholar
  87. Van't Hof, J. (1999) Increased nuclear DNA content in developing cotton fiber cells. Am. J. Bot. 86, 776–779.Google Scholar
  88. Wang, J., Tian L., Lee H.-S., Wei N.E., Jiang H., Watson B., Madlung A., Osborn T.C., Doerge R.W., Comai L., and Chen Z.J. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172, 507–517.PubMedGoogle Scholar
  89. Wang, J., Tian L., Madlung A., Lee H.-S., Chen M., Lee J.J., Watson B., Kagochi T., Comai L., and Chen Z.J. (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167, 1961–1973.PubMedGoogle Scholar
  90. Wang, S., Wang J.-W., Yu N., Li C.-H., Luo B., Gou J.-Y., Wang L.-J., and Chen X.-Y. (2004) Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 16, 2323–2334.PubMedGoogle Scholar
  91. Wendel, J.F. (2000) Cotton. In: J. Smartt (Eds.), Evolution of crop plants. Longman, London, pp. 358–366.Google Scholar
  92. Wendel, J.F. and Cronn R.C. (2003) Polyploidy and the evolutionary history of cotton. Adv. Agron. 78, 139–186.Google Scholar
  93. Wilkins, T.A. and Jernstedt J.A. (1999) Molecular genetics of developing cotton fibers. In: AS Basic (Eds.), Cotton Fibers. Haworth Press, New York, pp. 231–269.Google Scholar
  94. Wilkins, T.A. and Arpat A.B. (2005) The cotton fiber transcriptome. Physiol. Plant 124, 295–300.Google Scholar
  95. Wright, R.J., Thaxton P.M., El-Zik K.M., and Paterson A.H. (1998) D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics 149, 1987–1996.PubMedGoogle Scholar
  96. Wu, L.M., Ni Z.F., Meng F.R., Lin Z., and Sun Q.X. (2003) Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents. Mol. Genet. Gen. 270, 281–286.Google Scholar
  97. Wu, Y., Machado A.C., White R.G., Llewellyn D.J., and Dennis E.S. (2006) Expression profiling identifies genes e xpressed early during lint fibre initiation in cotton. Plant Cell Physiol. 47, 107–127.PubMedGoogle Scholar
  98. Wu, Y., Rozenfeld S., Defferrard A., Ruggiero K., Udall J., Kim H., Llewellyn D., and Dennis E. (2005) Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling. Mol. Genet. Gen. 274, 477–493.Google Scholar
  99. Xu, Y., Li H.-B., and Zhu Y.-X. (2007) Molecular biological and biochemical studies reveal new pathways important for cotton fiber development. Journal of Integrative Plant Biology 49, 69–74.Google Scholar
  100. Yang, S.S., Cheung F., Lee J.J., Ha M., Wei N.E., Sze S.-H., Stelly D.M., Thaxton P., Triplett B., Town C.D., and Chen Z.J. (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J. 47, 761–775.Google Scholar
  101. Zhang, D., Hrmova M., Wan C.-H., Wu C., Balzen J., Cai W., Wang J., Densmore L.D., Fincher G.B., Zhang H., and Haigler C.H. (2004) Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls. Plant Mol. Biol. 54, 353–372.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Joshua A. Udall

There are no affiliations available

Personalised recommendations