Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton

Plant Journal

Volumn 47, Issue 5, 2006, Pages 761-775

  Samuel Yang, S ^a   Cheung, Foo ^b   Lee, Jinsuk J ^c   Ha, Misook ^c   Wei, Ning E ^a   Sze, Sing Hoi ^a   Stelly, David M ^a   Thaxton, Peggy ^d   Triplett, Barbara ^e   Town, Christopher D ^b   Jeffrey Chen, Z ^a,c  

^a TEXAS A AND M UNIVERSITY   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d MISSISSIPPI STATE UNIVERSITY   (United States)

^e SOUTHERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

Cotton; Expressed sequence tags; Fiber; Gene expression; Phytohormone; Polyploidy

Indexed keywords

CELLS; COTTON; COTTON FIBERS; CROPS;

EXPRESSED SEQUENCE TAGS (EST); GENE EXPRESSION; PHYTOHORMONES; POLYPLOIDY;

GENETIC ENGINEERING;

ARABIDOPSIS PROTEIN; ATR1 PROTEIN, ARABIDOPSIS; CPC PROTEIN, ARABIDOPSIS; MYB PROTEIN, PLANT; PHYTOHORMONE; PROTEIN C MYB; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; BIOLOGY; CLUSTER ANALYSIS; COTTON; CYTOLOGY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYLOGENY; POLYPLOIDY; SIGNAL TRANSDUCTION;

ARABIDOPSIS PROTEINS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GOSSYPIUM; PHYLOGENY; PLANT GROWTH REGULATORS; PLANT PROTEINS; POLYPLOIDY; PROTO-ONCOGENE PROTEINS C-MYB; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

COTTON; FIBERS; HORMONES;

ARABIDOPSIS; GOSSYPIUM HIRSUTUM;

EID: 33747037492     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02829.x     Document Type: Article

References (80)

1. Abe, M., Takahashi, T. and Komeda, Y. (2001) Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein. Plant J. 26, 487-494.
2. Abo-el-Saad, M. and Wu, R. (1995) A rice membrane calcium-dependent protein kinase is induced by gibberellin. Plant Physiol. 108, 787-793.
3. 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. USA, 100, 4649-4654.
4. 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.
5. Applequist, W.L., Cronn, R. and Wendel, J.F. (2001) Comparative development of fiber in wild and cultivated cotton. Evol. Dev. 3, 3-17.
6. Arpat, A.B., Waugh, M., Sullivan, J.P., Gonzales, M., Frisch, D., Main, D., Wood, T., Leslie, A., Wing, R.A. and Wilkins, T.A. (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 54, 911-929.
7. Basra, A. and Malik, C.P. (1984) Development of the cotton fiber. Int. Rev. Cytol. 89, 65-113.
8. Beasley, J.O. (1940) The origin of American tetraploid Gossypium species. Am. Nat., 74, 285-286.
9. Beasley, C.A. and Ting, I.P. (1974) The effects of plant growth substances on in vitro fiber development from unfertilized cotton ovules. Am. J. Bot. 61, 188-194.
10. Berleth, T., Krogan, N.T. and Scarpella, E. (2004) Auxin signals - turning genes on and turning cells around. Curr. Opin. Plant Biol. 7, 553-563.
11. Cardle, L., Ramsay, L., Milbourne, D., Macaulay, M., Marshall, D. and Waugh, R. (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 156, 847-854.
12. Chang, S., Puryear, J. and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11, 113-116.
13. Chou, H.H. and Holmes, M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics, 17, 1093-1104.
14. Delmer, D.P., Pear, J., Andrawis, A. and Stalker, D. (1995) Genes encoding small GTP-binding proteins analogous to mammalian RAC are preferentially expressed in developing cotton fibers. Mol. Gen. Genet. 248, 43-51.
15. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
16. Endrizzi, J.E., Turcotte, E.L. and Kohel, R.J. (1984) Qualitative genetics, cytology and cytogenetics. In Agronomy: Cotton (Kohel, R.J. and Lewis, D.F., eds). Madison, WI: American Society of Agronomy, Inc., pp. 59-80.
17. Fleet, C.M. and Sun, T.P. (2005) A DELLAcate balance: the role of gibberellin in plantmorphogenesis. Curr. Opin. Plant Biol. 8, 77-85.
18. Frelichowski, J.E., Jr, Palmer, M.B., Main, D., Tomkins, J.P., Cantrell, R.G., Stelly, D.M., Yu, J., Kohel, R.J. and Ulloa, M. (2006) Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Mol. Genet. Genomics, 275, 479-491.
19. Gialvalis, S. and Seagull, R.W. (2001) Plant hormones alter fiber initiation in unfertilized cultured ovules of Gossypium hirsutum. J. Cotton Sci. 5, 252-258.
20. Glover, B.J. (2000) Differentiation in plant epidermal cells. J. Exp. Bot. 51, 497-505.
21. Haigler, C.H., Zhang, D.H. and Wilkerson, C.G. (2005) Biotechnological improvement of cotton fibre maturity. Physiol. Plant. 124, 285-294.
22. Hedden, P. and Kamiya, Y. (1997) GIBBERELLIN BIOSYNTHESIS: enzymes, genes and their regulation. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 431-460.
23. Hülskamp, M. (2004) Plant trichomes: a model for cell differentiation. Nat. Rev. Mol. Cell Biol. 5, 471-480.
24. 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.
25. 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. Nucleic Acids Res. 31, 2534-2543.
26. 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. Proc. Natl Acad. Sci. USA, 95, 4419-4424.
27. John, M.E. and Crow, L.J. (1992) Gene expression in cotton (Gossypium hirsutum L.) fiber: cloning of the mRNAs. Proc. Natl Acad. Sci. USA, 89, 5769-5773.
28. John, M.E. and Keller, G. (1995) Characterization of mRNA for a proline-rich protein of cotton fiber. Plant Physiol. 108, 669-676.
29. Johnson, C.S., Kolevski, B. and Smyth, D.R. (2002) TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell, 14, 1359-1375.
30. Kepinski, S. and Leyser, O. (2002) Ubiquitination and auxin signaling: a degrading story. Plant Cell, 14, S81-S95.
31. 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.
32. Kim, H.J. and Triplett, B.A. (2004) Cotton fiber germin-like protein. I. Molecular cloning and gene expression. Planta, 218, 516-524.
33. Kranz, H.D., Denekamp, M., Greco, R. et al. (1998) Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J. 16, 263-276.
34. Kuhl, J.C., Cheung, F., Yuan, Q. et al. (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell, 16, 114-125.
35. Kumar, S., Tamura, K. and Nei, M. (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 5, 150-163.
36. 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.
37. Lee, J.J., Hassan, O.S.S., Gao, W. et al. (2006) Developmental and gene expression analyses of a cotton naked seed mutant. Planta, 223, 418-432.
38. 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.
39. Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-time PCR and Z(-Delta Delta C(T)) method. Methods, 25, 402-408.
40. 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. Gen. Genet. 261, 660-671.
41. Ma, D.P., Liu, H.C., Tan, H., Creech, R.G., Jenkins, J.N. and Chang, Y.F. (1997) Cloning and characterization of a cotton lipid transfer protein gene specifically expressed in fiber cells. Biochim. Biophys. Acta 1344, 111-114.
42. Mei, M., Syed, N.H., Gao, W., Thaxton, P.M., Smith, C.W., Stelly, D.M. and Chen, Z.J. (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor. Appl. Genet. 108, 280-291.
43. 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, 661-664.
44. Orford, S.J. and Timmis, J.M. (1997) Abundant mRNAs specific to the developing cotton fibre. Theor. Appl. Genet. 94, 909-918.
45. Percival, A.E., Wendel, J.F. and Stewart, J.M. (1999) Taxonomy and germplasm resources. In Cotton: Origin, History, Technology, and Production (Smith, C.W. and Cothren, J.T., eds). New York: John Wiley & Sons, Inc., pp. 33-63.
46. 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. Development, 132, 359-370.
47. Pertea, G., Huang, X., Liang, F. et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19, 651-652.
48. Quackenbush, J. (2001) Computational analysis of microarray data. Nat. Rev. Genet. 2, 418-427.
49. Ramsay, N.A. and Glover, B.J. (2005) MYB-bHLH-WD40 protein complex and the evolution of cellular diversity. Trends Plant Sci. 10, 63-70.
50. Reinhart, J.A., Petersen, M.W. and John, M.E. (1996) Tissue-specific and developmental regulation of cotton gene fbl2a: demonstration of promoter activity in transgenic plants. Plant Physiol. 112, 1331-1341.
51. Rerie, W.G., Feldmann, K.A. and Marks, M.D. (1994) The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. Genes Dev. 8, 1388-1399.
52. Romualdi, C., Bortoluzzi, S. and Danieli, G.A. (2001) Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Hum. Mol. Genet. 10, 2133-2141.
53. Romualdi, C., Bortoluzzi, S., D'Alessi, F. and Danieli, G.A. (2003) IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol. Genomics, 12, 159-162.
54. Rosin, F.M., Hart, J.K., Horner, H.T., Davies, P.J. and Hannapel, D.J. (2003) Overexpression of a knotted-like homeobox gene of potato alters vegetative development by decreasing gibberellin accumulation. Plant Physiol. 132, 106-117.
55. Samora, P.J., Stelly, D.M. and Kohel, R.J. (1994) Localization and mapping of the Le1 and Gl2 of cotton (Gossypium hirsutum L.). J. Hered. 85, 152-157.
56. 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.
57. 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.
58. Stekel, D.J., Git, Y. and Falciani, F. (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res. 10, 2055-2061.
59. Sun, Y., Veerabomma, S., Abdel-Mageed, H.A., Fokar, M., Asami, T., Yoshida, S. and Allen, R.D. (2005) Brassinosteroid regulates fiber development on cultured cotton ovules. Plant Cell Physiol. 46, 1384-1391.
60. Suo, J., Liang, X., Pu, L., Zhang, Y. and Xue, Y. (2003) Identification of GhMYB109 encoding a R2R3 MYB transcription factor that is expressed specifically in fiber initials and elongating fibers of cotton (Gossypium hirsutum L.). Biochim. Biophys. Acta, 1630, 25-34.
61. Thiel, T., Michalek, W., Varshney, R.K. and Graner, A. (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411-422.
62. Tiwari, S.C. and Wilkins, T.A. (1995) Cotton (Gossypium hirsutum) seed trichomes expand via diffuse growing mechanism. Can. J. Bot. 73, 746-757.
63. Udall, J.A., Swanson, J.M., Haller, K. et al. (2006) A global assembly of cotton ESTs. Genome Res. 16, 441-450.
64. Ülker, B. and Somssich, I.E. (2004) WRKY transcription factors: from DNA binding towards biological function. Curr. Opin. Plant Biol. 7, 491-498.
65. Ulloa, M., Saha, S., Jenkins, J.N., Meredith, W.R., Jr, McCarty, J.C., Jr and Stelly, D.M. (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) Joinmap. J. Hered. 96, 132-144.
66. 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.
67. Wang, J., Tian, L., Lee, H.S. et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics, 172, 507-517.
68. Weijers, D. and Jurgens, G. (2005) Auxin and embryo axis formation: the ends in sight? Curr. Opin. Plant Biol. 8, 32-37.
69. Wendel, J.F. and Cronn, R.C. (2003) Polyploidy and the evolutionary history of cotton. Adv. Agron. 78, 139-186.
70. Wendel, J.F., Schnabel, A. and Seelanan, T. (1995) An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet Evol. 4, 298-313.
71. Whittaker, D.J. and Tripplett, B.A. (1999) Gene-specific changes in alpha-tubulin transcript accumulation in developing cotton fibers. Plant. Physiol. 121, 181-188.
72. Wilkins, T.a. and Arpat, A.B. (2005) The cotton fiber transcriptome. Physiol. Plant. 124, 295-300.
73. Wilkins, T.A. and Jernstedt, J.A. (1999) Molecular genetics of developing cotton fibers. In Cotton Fibers (Basra, A.M., ed.). New York: Hawthorne Press, pp. 231-267.
74. Woodward, A.W. and Bartel, B. (2005) Auxin: regulation, action, and interaction. Ann. Bot. 95, 707-735.
75. Wu, Y., Machado, A.C., White, R.G., Llewellyn, D.J. and Dennis, E.S. (2006) Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol. 47, 107-127.
76. Xie, Z., Zhang, Z.L., Zou, X., Huang, J., Ruas, P., Thompson, D. and Shen, Q.J. (2005) Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol. 137, 176-189.
77. Yang, G. and Komatsu, S. (2000) Involvement of calcium-dependent protein kinase in rice (Oryza sativa L.) lamina inclination caused by brassinolide. Plant Cell Physiol. 41, 1243-1250.
78. Yin, Y., Wang, Z.Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T. and Chory, J. (2002) BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell, 109, 181-191.
79. Zhang, T., Yuan, Y., Yu, J., Guo, W. and Kohel, R.J. (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor. Appl. Genet. 106, 262-268.
80. Zhang, Z.L., Xie, Z., Zou, X., Casaretto, J., Ho, T.H. and Shen, Q.J. (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol. 134, 1500-1513.