Abstract
Sea-island cotton (Gossypium barbadense L.) is one of the most valuable cotton species due to its silkiness, luster, long staples, and high strength, but its fiber development mechanism has not been surveyed comprehensively. We constructed a normalized fiber cDNA library (from −2 to 25 dpa) of G. barbadense cv. Pima 3-79 (the genetic standard line) by saturation hybridization with genomic DNA. We screened Pima 3-79 fiber RNA from five developmental stages using a cDNA array including 9,126 plasmids randomly selected from the library, and we selected and sequenced 929 clones that had different signal intensities between any two stages. The 887 high-quality expressed sequence tags obtained were assembled into 645 consensus sequences (582 singletons and 63 contigs), of which 455 were assigned to functional categories using gene ontology. Almost 50% of binned genes belonged to metabolism functional categories. Based on subarray analysis of the 887 high-quality expressed sequence tags with 0-, 5-, 10-, 15-, and 20-dpa RNA of Pima 3-79 fibers and a mixture of RNA of nonfiber tissues, seven types of expression profiles were elucidated. Furthermore our results showed that phytohormones may play an important role in the fiber development.
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Abe M, Takahashi T, Komeda Y (1999) Cloning and characterization of an L1 layer-specific gene in Arabidopsis thaliana. Plant Cell Physiol 40:571–580
Abe M, Takahashi T, 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
Andrawis A, Solomon M, Delmer DP (1993) Cotton fiber annexins: a potential role in the regulation of callose synthase. Plant J 3:763–772
Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 54:911–929
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Basra A, Malik CP (1984) Development of the cotton fiber. Int Rev Cytol 89:65–113
Beasley CA, Ting IP (1974) Effects of plant growth substances on in vitro fiber development from unfertilized cotton ovules. Am J Bot 61:188–194
Beasley CA, Ting IP, Linkins AE, Birnbaum EH, Delmer DP (1974) Cotton ovule culture: a review of progress and a preview of potential. In: Street HE (ed) Tissue culture and plant science. Academic, London, pp 169–192
Bonaldo MF, Lennon G, Soares MB (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6:791–806
Burgoyne RD, Geisow MJ (1989) The annexin family of calcium-binding proteins. Cell Calcium 10:1–10
Carpita N, McCann M (2000) The cell wall. In: Buchanan RB, Gruissem W, Jones RL (eds) Biochemistry and molecular biology of plants. American Society of Plant Biologists, Rockville, pp 52–108
Chee P, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005a) Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor Appl Genet 111:757–763
Chee PW, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005b) Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length. Theor Appl Genet 111:772–781
Chu ZH, Peng KM, Zhang LD, Zhou B, Wei J, Wang SP (2003) Construction and characterization of a normalized whole-life-cycle cDNA library of rice. Chin Sci Bull 48:229–235
Collinge CB, Kragh KM, Mikkelsen JD, Nielsen KK, Rasumussen U, Vad K (1993) Plant chitinases. Plant J 3:31–40
Cornelissen BJC, van Hooft Huijsduijnen RAM, Bol JF (1986) A tobacco mosaic virus-induced tobacco protein is homologous to the sweet-tasting protein thaumatin. Nature 321:531–532
Draye X, Chee P, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness. Theor Appl Genet 111:764–771
Hall AE, Findell JL, Schaller GE, Sisler EC, Bleecker AB (2000) Ethylene perception by the ers1 protein in Arabidopsis. Plant Physiol 123:1449–1457
Harmer SE, Orford SJ, Timmis JN (2002) Characterisation of six a-expansin genes in Gossypium hirsutum (upland cotton). Mol Genet Genomics 268:1–9
Hua J, Meyerowitz EM (1998) Ethylene responses are negatively regulated by a receptor gene family in Arabidopsis thaliana. Cell 94:261–271
Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC, Zhu YX (2003) Isolation and analyses of gene preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucleic Acids Res 31:2534–2543
John ME (1996) Structural characterization of genes corresponding to cotton fiber mRNA, E6:reduced E6 protein in transgenic plants by antisense gene. Plant Mol Biol 30:297–306
John ME, Crow LJ (1992) Gene expression in cotton (Gossypium hirsutum L.) fiber: cloning of the mRNAs. Proc Natl Acad Sci USA 89:5769–5773
Jung YC, Lee HJ, Yum SS, Soh WY, Cho DY, Auh CK, Lee TK, Soh HC, Kim YS, Lee SC (2005) Drought-inducible-but ABA-independent-thaumatin-like protein from carrot (Daucus carota L.). Plant Cell Rep 24:366–373
Kim HJ, Triplett BA (2004) Cotton fiber germin-like protein. I. Molecular cloning and gene expression. Planta 218:516–524
Kim HJ, Pesacreta TC, Triplett BA (2004) Cotton-fiber germin-like protein. II: Immunolocalization, purification, and functional analysis Planta 218:525–535
Kim MJ, Ham BK, Kim HR, Lee IJ, Kim YJ, Ryu KH, Park YI, Paek KH (2005) In vitro and in planta interaction evidence between Nicotiana tabacum thaumatin-like protein 1 (TLP1) and cucumber mosaic virus proteins. Plant Mol Biol 59:981–994
King GJ, Turner VA, Hussey CE, Wuterle ES, Lee SM (1988) Isolation and characterization of a tomato cDNA clone which codes for a salt-induced protein. Plant Mol Biol 10:401–412
Kosugi S, Ohashi Y (1997) PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 9:1607–1619
Kragh KM, Hendriks T, de Jong AJ, Schiavo FL, Bucherna N, Hojrup P, Mikkelsen JD, de Vries SC (1996) Characterization of chitinases able to rescue somatic embryos of the temperature-sensitive carrot variant ts11. Plant Mol Biol 31:631–645
Lee JJ, Hassan OS, Gao W, Wei NE, Kohel RJ, Chen XY, Payton P, Sze SH, Stelly DM, Chen ZJ (2006) Developmental and gene expression analyses of a cotton naked seed mutant. Planta 223:418–432
Li XB, Fan XP, Wang XL, Cai L, Yang WC (2005) The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17:859–875
McQueen-Mason SJ, Cosgrove DJ (1994) Disruption of hydrogen bonding between plant cell wall polymers by proteins that induce wall extension. Proc Natl Acad Sci USA 91:6574–6578
McQueen-Mason SJ, Cosgrove DJ (1995) Expansin mode of action on cell walls: analysis of wall hydrolysis, stress relaxation, and binding. Plant Physiol 107:87–100
McQueen-Mason SJ, Durachko DM, Cosgrove DJ (1992) Two endogenous proteins that induce cell wall extension in plants. Plant Cell 4:1425–1433
Mouille G, Robin S, Lecomte M, Pagant S, Hofte H (2003) Classification and identification of Arabidopsis cell wall mutants using Fourier-Transform InfraRed (FT-IR) microspectroscopy. Plant J 35:393–404
Ohmiya A, Tanaka Y, Kadowaki K, Hayashi T (1998) Cloning of genes encoding auxin-binding proteins (ABP19/20) from peach: significant peptide sequence similarity with germin-like proteins. Plant Cell Physiol 39:492–499
Okamoto H, Tanaka Y, Sakai S (1995) Molecular cloning and analysis of the cDNA for an auxin-regulated calmodulin gene. Plant Cell Physiol 36:1531–1539
Orford SJ, Timmis JN (1998) Specific expression of an expansin gene during elongation of cotton fibers. Biochim Biophys Acta 1398:342–346
Paterson AH, Brubaker CL, Wendell JF (1994) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122–127
Pear JR, Kawaoe Y, Schreckengost WE, Delmer DP, Stalker DM (1996) Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc Natl Acad Sci USA 93:12637–12642
Peterson LE (2002) Factor analysis of cluster-specific gene expression levels from cDNA microarrays. Comput Methods Programs Biomed 69:179–188
Richardson M, Valdes-Rodriguez S, Blanco-Labra A (1987) A possible function for thaumatin and a TMV-induced protein suggested by homology to a maize inhibitor. Nature 327:432–434
Rinehart JA, Petersen MW, John ME (1996) Tissue-specific and developmental regulation of cotton gene FbL2A. Plant Physiol 112:1331–1341
Ruan YL, Llewellyn DJ, Furbank RT (2003) Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development. Plant Cell 15:952–964
Sakamoto Y, Watanabe H, Nagai M, Nakade K, Takahashi M, Sato T (2006) Lentinula edodes tlg1 encodes a thaumatin-like protein that is involved in lentinan degradation and fruiting body senescence. Plant Physiol 141:793–801
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York
Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18:651–664
Shin H, Brown RM Jr (1999) GTPase activity and biochemical characterization of a recombinant cotton fiber annexin. Plant Physiol 119:925–934
Singh NK, Nelson DE, Kuhn D, Hasegawa PM, Bressan RA (1989) Molecular cloning of osmotin and regulation of its expression by ABA and adaptation to low water potential. Plant Physiol 90:1096–1101
Tahhan TJ, Randy DA (1999) Isolation of a novel cDNA encoding an auxin-induced basic helix-loop-helix transcription factor (accession no. AF165924) from cotton (Gossypium hirsutum L.). Plant Physiol 121:685
Tiwari SC, Wilkins TA (1995) Cotton (Gossypium hirsutum) seed trichomes expand via diffuse growing mechanism. Can J Bot 73:746–757
Van der Wel H, Van Soest TC, Royers EC (1975) Crystallization and crystal data of thaumatin I, a sweet-tasting protein from Thaumatococcus danielli Benth. FEBS Lett 6:316–317
Vreeburg RA, Benschop JJ, Peeters AJ, Colmer TD, Ammerlaan AH, Staal M, Elzenga TM, Staal RH, Darley CP, McQueen-Mason SJ, Voesenek LA (2005) Ethylene regulates fast apoplastic acidification and expansin A transcription during submergence-induced petiole elongation in Rumex palustris. Plant J 43:597–610
Wang S, Wang JW, Yu N, Li CH, Luo B, Gou JY, Wang LJ, Chen XY (2004) Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 16:2323–2334
Wang HY, Yu Y, Chen ZL, Xia GX (2005) Functional characterization of Gossypium hirsutum profilin 1 gene (GhPFN1) in tobacco suspension cells. Planta 222:594–603
Yang SS, Cheung F, Lee JJ, Ha M, Wei NE, Sze SH, Stelly DM, Thaxton P, Triplett B, Town CD, Chen ZJ (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
Zhang D, Hrmova M, Wan CH, Wu C, Balzen J, Cai W, Wang J, Densmore LD, Fincher GB, Zhang H, Haigler CH (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
Zhu YQ, Xu KX, Luo B, Wang JW, Chen XY (2003) An ATP binding cassette transporter GhWBC1 from elongating cotton fibers. Plant Physiol 133:580–588
Zhu LF, Tu LL, Zeng FC, Liu DQ, Zhang XL (2005) An improved simple protocol for isolation of high quality RNA from Gossypium spp. suitable for cDNA library construction. Acta Agron Sin 31:1657–1659
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This work was supported by a grant from the National Basic Research Program of China (2004CB117301) and National Natural Science Foundation of China.
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Communicated by Y. Lu.
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Tu, LL., Zhang, XL., Liang, SG. et al. Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber development. Plant Cell Rep 26, 1309–1320 (2007). https://doi.org/10.1007/s00299-007-0337-4
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DOI: https://doi.org/10.1007/s00299-007-0337-4