Functional genomics of fuzzless-lintless mutant of Gossypium hirsutum L. cv. MCU5 reveal key genes and pathways involved in cotton fibre initiation and elongation

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Padmalatha, Kethireddy Venkata ^a   Patil, Deepak P ^b   Kumar, Krishan ^b   Dhandapani, Gurusamy ^a   Kanakachari, Mogilicherla ^a   Phanindra, Mullapudi L V ^a   Kumar, Saravanan ^b   Mohan, T C ^c   Jain, Neha ^a   Prakash, Arkalgud H ^d   Vamadevaiah, Hiremath ^c   Katageri, Ishwarappa S ^c   Leelavathi, Sadhu ^b   Reddy, Malireddy K ^b   Kumar, Polumetla Ananda ^a   Reddy, Vanga Siva ^b  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY ICGEB   (India)

^c UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

^d CENTRAL INSTITUTE FOR COTTON RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULOSE SYNTHASE; PHYTOHORMONE; SUCROSE SYNTHASE; SUCROSE SYNTHASE C; SYNTHETASE; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CARBOHYDRATE METABOLISM; CELL ELONGATION; CELL MEMBRANE PERMEABILITY; COTTON; ENERGY METABOLISM; FATTY ACID METABOLISM; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE IDENTIFICATION; GOSSYPIUM HIRSUTUM; MITOCHONDRIAL ENERGY TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CELL; PLANT DEVELOPMENT; PLANT GENE; PLANT GENETICS; PLANT STRUCTURES; SCANNING ELECTRON MICROSCOPY; SIGNAL TRANSDUCTION;

CALCIUM SIGNALING; CARBOHYDRATE METABOLISM; CELL WALL; COTTON FIBER; ELECTRON TRANSPORT; ENERGY METABOLISM; FATTY ACIDS; GENE EXPRESSION PROFILING; GENES, PLANT; GENOMICS; GOSSYPIUM; HOMEOSTASIS; MITOCHONDRIA; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OSMOSIS; PLANT GROWTH REGULATORS; PROTEIN STABILITY; RNA, MESSENGER; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

GOSSYPIUM HIRSUTUM;

EID: 84868681941     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-624     Document Type: Article

References (61)

1. Wilkins TA, Arpat AB. The cotton fiber transcriptome. Physiol Plant 2005, 124(3):295-300.
2. Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA. Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 2004, 54(6):911-929. 10.1007/s11103-004-0392-y, 15604659.
3. Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC, Zhu YX. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucleic Acids Res 2003, 31(10):2534-2543. 10.1093/nar/gkg358, 156040, 12736302.
4. Wu Y, Machado AC, White RG, Llewellyn DJ, Dennis ES. Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol 2006, 47(1):107-127.
5. Gou JY, Wang LJ, Chen SP, Hu WL, Chen XY. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res 2007, 17(5):422-434.
6. Zhao PM, Wang LL, Han LB, Wang J, Yao Y, Wang HY, Du XM, Luo YM, Xia GX. Proteomic identification of differentially expressed proteins in the Ligon lintless mutant of upland cotton (Gossypium hirsutum L.). J Proteome Res 2009, 9(2):1076-1087.
7. Pang CY, Wang H, Pang Y, Xu C, Jiao Y, Qin YM, Western TL, Yu SX, Zhu YX. Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fiber and Arabidopsis root hair elongation. Mol Cell Proteomics 2010, 9(9):2019-2033. 10.1074/mcp.M110.000349, 2938120, 20525998.
8. Liu K, Han M, Zhang C, Yao L, Sun J, Zhang T. Comparative proteomic analysis reveals the mechanisms governing cotton fiber differentiation and initiation. J Proteomics 2012, 75(3):845-856. 10.1016/j.jprot.2011.09.025, 22015716.
9. Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 2006, 18(3):651-664. 10.1105/tpc.105.040303, 1383640, 16461577.
10. Yang SS, Cheung F, Lee JJ, Ha M, Wei NE, Sze SH, Stelly DM, Thaxton P, Triplett B, Town CD, Chen ZJ. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J 2006, 47(5):761-775. 10.1111/j.1365-313X.2006.02829.x, 16889650.
11. Zhang M, Zheng X, Song S, Zeng Q, Hou L, Li D, Zhao J, Wei Y, Li X, Luo M, Xiao Y, Luo X, Zhang J, Xiang C, Pei Y. Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat Biotechnol 2011, 29(5):453-458. 10.1038/nbt.1843, 21478877.
12. Sun Y, Veerabomma S, Abdel-Mageed HA, Fokar M, Asami T, Yoshida S, Allen RD. Brassinosteroid regulates fiber development on cultured cotton ovules. Plant Cell Physiol 2005, 46(8):1384-1391. 10.1093/pcp/pci150, 15958497.
13. Luo M, Xiao Y, Li X, Lu X, Deng W, Li D, Hou L, Hu M, Li Y, Pei Y. GhDET2, a steroid 5α-reductase, plays an important role in cotton fiber cell initiation and elongation. Plant J 2007, 51(3):419-430. 10.1111/j.1365-313X.2007.03144.x, 17565582.
14. Machado A, Wu Y, Yang Y, Llewellyn DJ, Dennis ES. The MYB transcription factor GhMYB25 regulates early fibre and trichome development. Plant J 2009, 59(1):52-62. 10.1111/j.1365-313X.2009.03847.x, 19309462.
15. Guan X, Lee JJ, Pang M, Shi X, Stelly DM, Chen ZJ. Activation of Arabidopsis seed hair development by cotton fiber-related genes. PLoS One 2011, 6(7):e21301. 10.1371/journal.pone.0021301, 3136922, 21779324.
16. Walford SA, Wu Y, Llewellyn DJ, Dennis ES. GhMYB25-like: a key factor in early cotton fibre development. Plant J 2011, 65(5):785-797. 10.1111/j.1365-313X.2010.04464.x, 21235650.
17. Ruan YL, Llewellyn DJ, Furbank RT. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development. Plant Cell 2003, 15(4):952-964. 10.1105/tpc.010108, 152341, 12671090.
18. Wang L, Ruan YL. Unraveling mechanisms of cell expansion linking solute transport, metabolism, plasmodesmtal gating and cell wall dynamics. Plant Signal Behav 2010, 5(12):1561-1564. 10.4161/psb.5.12.13568, 3115103, 21139427.
19. Ruan YL, Xu SM, White R, Furbank RT. Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover. Plant Physiol 2004, 136(4):4104-4113. 10.1104/pp.104.051540, 535841, 15557097.
20. Yang YW, Bian SM, Yao Y, Liu JY. Comparative proteomic analysis provides new insights into the fiber elongating process in cotton. J Proteome Res 2008, 7(11):4623-4637. 10.1021/pr800550q, 18823139.
21. Pang Y, Wang H, Song WQ, Zhu YX. The cotton ATP synthase δ1 subunit is required to maintain a higher ATP/ADP ratio that facilitates rapid fibre cell elongation. Plant Biol 2010, 12(6):903-909. 10.1111/j.1438-8677.2009.00313.x, 21040305.
22. Lee J, Burns TH, Light G, Sun Y, Fokar M, Kasukabe Y, Fujisawa K, Maekawa Y, Allen RD. Xyloglucan endotransglycosylase/hydrolase genes in cotton and their role in fiber elongation. Planta 2010, 232(5):1191-1205. 10.1007/s00425-010-1246-2, 20711605.
23. Liu D, Tu L, Li Y, Wang L, Zhu L, Zhang X. Genes encoding fasciclin-like arabinogalactan proteins are specifically expressed during cotton fiber development. Plant Mol Biol Rep 2008, 26(2):98-113.
24. Harmer SE, Orford SJ, Timmis JN. Characterisation of six alpha-expansin genes in Gossypium hirsutum (upland cotton). Mol Genet Genomics 2002, 268(1):1-9. 10.1007/s00438-002-0721-2, 12242493.
25. Li XB, Cai L, Cheng NH, Liu JW. Molecular characterization of the cotton GhTUB1 gene that is preferentially expressed in fiber. Plant Physiol 2002, 130(2):666-674. 10.1104/pp.005538, 166596, 12376634.
26. Li XB, Fan XP, Wang XL, Cai L, Yang WC. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 2005, 17(3):859-875. 10.1105/tpc.104.029629, 1069704, 15722467.
27. Wang J, Wang HY, Zhao PM, Han LB, Jiao GL, Zheng YY, Huang SJ, Xia GX. Overexpression of a profilin (GhPFN2) promotes the progression of developmental phases in cotton fibers. Plant Cell Physiol 2010, 51(8):1276-1290. 10.1093/pcp/pcq086, 20558432.
28. Wang QQ, Liu F, Chen XS, Ma XJ, Zeng HQ, Yang ZM. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 2010, 96(6):369-376. 10.1016/j.ygeno.2010.08.009, 20828606.
29. Peter SD, Muralidharan V, Bhat MV. Fuzzless-lintless mutant of MCU 5 cotton. Cotton Dev 1984, 14:43.
30. Nadarajan N, Rangagasamy SRS. Breeding value of a fuzzless-lintless mutant in Gossypium hirsutum L. Indian J Genet 1997, 57(3):233-237.
31. Oh JE, Kwon Y, Kim JH, Noh H, Hong SW, Lee H. A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Mol Biol 2011, 77(1-2):91-103.
32. Suzuki N, Rizhsky L, Liang H, Shuman J, Shulaev V, Mittler R. Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c. Plant Physiol 2005, 139(3):1313-1322. 10.1104/pp.105.070110, 1283768, 16244138.
33. Gao P, Zhao PM, Wang J, Wang HY, Wu XM, Xia GX. Identification of genes preferentially expressed in cotton fibers: A possible role of calcium signaling in cotton fiber elongation. Plant Sci 2007, 173(1):61-69.
34. Huang QS, Wang HY, Gao P, Wang GY, Xia GX. Cloning and characterization of a calcium dependent protein kinase gene associated with cotton fiber development. Plant Cell Rep 2008, 27(12):1869-1875. 10.1007/s00299-008-0603-0, 18781305.
35. George L, Romanowsky SM, Harper JF, Sharrock RA. The ACA10 Ca2+-ATPase regulates adult vegetative development and inflorescence architecture in Arabidopsis. Plant Physiol 2008, 146(2):716-728. 2245845, 18065565.
36. Blakeslee JJ, Bandyopadhyay A, Lee OR, Mravec J, Titapiwatanakun B, Sauer M, Makam SN, Cheng Y, Bouchard R, Adamec J, Geisler M, Nagashima A, Sakai T, Martinoia E, Friml J, Peer WA, Murphy AS. Interactions among PIN-FORMED and P-Glycoprotein Auxin Transporters in Arabidopsis. Plant Cell 2007, 19(1):131-147. 10.1105/tpc.106.040782, 1820964, 17237354.
37. Molnar G, Bancos S, Nagy F, Szekeres M. Characterisation of BRH1, a brassinosteroid-responsive RING-H2 gene from Arabidopsis thaliana. Planta 2002, 215(1):127-133. 10.1007/s00425-001-0723-z, 12012249.
38. Brill E, van Thournout M, White RG, Llewellyn D, Campbell PM, Engelen S, Ruan YL, Arioli T, Furbank RT. A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber. Plant Physiol 2011, 157(1):40-54. 10.1104/pp.111.178574, 3165887, 21757635.
39. Yeo ET, Kwon HB, Han SE, Lee JT, Ryu JC, Byu MO. Genetic engineering of drought resistant potato plants by introduction of the trehalose-6-phosphate synthase (TPS1) gene from Saccharomyces cerevisiae. Mol Cells 2000, 10(3):263-268.
40. Padmalatha KV, Dhandapani G, Kanakachari M, Kumar S, Dass A, Patil DP, Rajamani V, Kumar K, Pathak R, Rawat B, Leelavathi S, Reddy PS, Jain N, Powar KN, Hiremath V, Katageri IS, Reddy MK, Solanke AU, Reddy VS, Kumar PA. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes. Plant Mol Biol 2012, 78(3):223-246. 10.1007/s11103-011-9857-y, 22143977.
41. Juszczuk IM, Szal B, Rychter AM. Oxidation-reduction and reactive oxygen species homeostasis in mutant plants with respiratory chain complex I dysfunction. Plant Cell Environ 2012, 35(2):296-307. 10.1111/j.1365-3040.2011.02314.x, 21414015.
42. Qin YM, Pujol FM, Shi YH, Feng JX, Liu YM, Kastaniotis AJ, Hiltunen JK, Zhu YX. Cloning and functional characterization of two cDNAs encoding NADPH-dependent 3-ketoacyl-CoA reductased from developing cotton fibers. Cell Res 2005, 15(6):465-473. 10.1038/sj.cr.7290315, 15987605.
43. Qin YM, Pujol FM, Hu CY, Feng JX, Kastaniotis AJ, Hiltunen JK, Zhu YX. Genetic and biochemical studies in yeast reveal that the cotton fibre-specific GhCER6 gene functions in fatty acid elongation. J Exp Bot 2007, 58(3):473-481.
44. Flugge UI, Hausler RE, Ludewig F, Gierth M. The role of transporters in supplying energy to plant plastids. J Exp Bot 2011, 62(7):2381-2392. 10.1093/jxb/erq361, 21511915.
45. Leung KC, Li HY, Mishra G, Chye ML. ACBP4 and ACBP5, novel Arabidopsis acyl-CoA-binding proteins with kelch motifs that bind oleoyl-CoA. Plant Mol Biol 2004, 55(2):297-309. 10.1007/s11103-004-0642-z, 15604682.
46. Anthony RG, Henriques R, Helfer A, Meszaros T, Rios G, Testerink C, Munnik T, Deak M, Koncz C, Bogre L. A protein kinase target of a PDK1 signalling pathway is involved in root hair growth in Arabidopsis. EMBO J 2004, 23(3):572-581. 10.1038/sj.emboj.7600068, 1271803, 14749726.
47. Bellevik S, Zhang J, Meijer J. Brassica napus soluble epoxide hydrolase (BNSEH1). Eur J Biochem 2002, 269(21):5295-5302. 10.1046/j.1432-1033.2002.03247.x, 12392563.
48. Bird DA. The role of ABC transporters in cuticular lipid secretion. Plant Sci 2008, 174(6):563-569.
49. Yeats TH, Rose JKC. The biochemistry and biology of extracellular plant lipid-transfer proteins (LTPs). Protein Sci 2008, 17(2):191-198. 10.1110/ps.073300108, 2222726, 18096636.
50. Zhu YQ, Xu KX, Luo B, Wang JW, Chen XY. An ATP-binding cassette transporter GhWBC1 from elongating cotton fibers. Plant Physiol 2003, 133(2):580-588. 10.1104/pp.103.027052, 219034, 12972649.
51. Luo B, Xue XY, Hu WL, Wang LJ, Chen XY. An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol 2007, 48(12):1790-1802. 10.1093/pcp/pcm152, 17989085.
52. DeBono A, Yeats TH, Rose JKC, Bird D, Jetter R, Kunst L, Samuels L. Arabidopsis LTPG is a glycosylphosphatidylinositol-anchored lipid transfer protein required for export of lipids to the plant surface. Plant Cell 2009, 21(4):1230-1238. 10.1105/tpc.108.064451, 2685631, 19366900.
53. Liu D, Tu L, Wang L, Li Y, Zhu L, Zhang X. Characterization and expression of plasma and tonoplast membrane aquaporins in elongating cotton fibers. Plant Cell Rep 2008, 27(8):1385-1394. 10.1007/s00299-008-0545-6, 18392624.
54. Park W, Scheffler BE, Bauer PJ, Campbell BT. Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 2010, 10:142. 10.1186/1471-2229-10-142, 3095289, 20626869.
55. Jou Y, Chiang CP, Jauh GY, Yen HE. Functional characterization of ice plant SKD1, an AAA-type ATPase associated with the endoplasmic reticulum-Golgi network, and its role in adaptation to salt stress. Plant Physiol 2006, 141(1):135-146. 10.1104/pp.106.076786, 1459316, 16581876.
56. Wang H, Guo Y, Lv F, Zhu H, Wu S, Jiang Y, Li F, Zhou B, Guo W, Zhang T. The essential role of GhPEL gene, encoding a pectate lyase, in cell wall loosening by depolymerization of the de-esterified pectin during fiber elongation in cotton. Plant Mol Biol 2010, 72(4-5):397-406.
57. Bischoff V, Nita S, Neumetzler L, Schindelasch D, Urbain A, Eshed R, Persson S, Delmer D, Scheible WR. TRICHOME BIREFRINGENCE and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis. Plant Physiol 2010, 153(2):590-602. 10.1104/pp.110.153320, 2879772, 20388664.
58. Mir IH, Channa A. A Scanning Electron Microscopic Examination of the Intestinal Tract of the Snow Trout, Schizothorax curvifrons Heckel. J Fish Aquat Sci 2010, 5(5):386-393.
59. Benjamini Y, Hochberg Y. On the adaptive control of the false discovery rate in multiple testing with independent statistics. J Educ Behav Stat 2000, 25(1):60-83.
60. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 1998, 95:14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
61. Artico S, Nardeli SM, Brilhante O, Grossi-de-Sa MF, Alves-Ferreira M. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data. BMC Plant Biol 2010, 10:49. 10.1186/1471-2229-10-49, 2923523, 20302670.