Plant Molecular Biology

, Volume 54, Issue 4, pp 471–487 | Cite as

Monitoring of Gene Expression Profiles and Isolation of Candidate Genes Involved in Pollination and Fertilization in Rice (Oryza Sativa L.) with a 10K cDNA Microarray

  • Lefu Lan
  • Wei Chen
  • Ying Lai
  • Jinfeng Suo
  • Zhaosheng Kong
  • Can Li
  • Ying Lu
  • Yujun Zhang
  • Xiangyu Zhao
  • Xiansheng Zhang
  • Yansheng Zhang
  • Bin Han
  • Jing Cheng
  • Yongbiao Xue
Article

Abstract

To monitor gene expression profiles during pollination and fertilization in rice at a genome scale, we generated 73 424 high-quality expressed sequence tags (ESTs) derived from the green/etiolated shoot and pistil (0–5 h after pollination, 5hP) of rice, which were subsequently used to construct a cDNA microarray containing ca. 10 000 unique rice genes. This microarray was used to analyze gene expression in pistil unpollinated (UP), 5hP and 5DAP(5 days after pollination), anther, shoot, root, 10-day-old embryo (10EM) and 10-day-old endosperm (10EN). Clustering analysis revealed that the anther has a gene-expression profile more similar to root than to pistil and most pistil-preferentially expressed genes respond to pollination and/or fertilization. There are 253 ESTs exhibiting differential expression (e±2-fold changes) during pollination and fertilization, and about 70% of them can be assigned a putative function. We also recovered 20 genes similar to pollination-related and/or fertility-related genes previously identified as well as genes that were not implicated previously. Microarray and real-time PCR analyses showed that the array sensitivity was estimated at 1–5 copies of mRNA per cell, and the differentially expressed genes showed a high correlation between the two methods. Our results indicated that this cDNA microarray constructed here is reliable and can be used for monitoring gene expression profiles in rice. In addition, the genes that differentially expressed during pollination represent candidate genes for dissecting molecular mechanism of this important biological process in rice.

cDNA microarray pollination and fertilization real-time PCR rice 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aarts, M.G., Hodge, R., Kalantidis, K., Florack, D., Wilson, Z.A., Mulligan, B.J., Stiekema, W.J., Scott, R. and Pereira, A. 1997. The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Plant J. 12: 615–623.CrossRefPubMedGoogle Scholar
  2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.CrossRefPubMedGoogle Scholar
  3. Ashikari, M., Wu, J., Yano, M., Sasaki, T. and Yoshimura, A. 1999. Rice gibberellin-insensitive dwarf mutant gene Dwarf1 encodes the alpha-subunit of GTP-binding protein. Proc. Natl. Acad. Sci. USA 96: 10284–10289.CrossRefPubMedGoogle Scholar
  4. Broekaert, W.F., Cammue, B., De Bolle, M., Thevissen, K. and De Samblanx, G. 1997. Antimicrobial peptides from plants. Crit. Rev. Plant Sci. 16: 297–323.Google Scholar
  5. Chen, F. and Foolad, M.R. 1997. Molecular organization of a gene in barley which encodes a protein similar to aspartic protease and its specific expression in nucellar cells during degeneration. Plant Mol. Biol. 35: 821–831.CrossRefPubMedGoogle Scholar
  6. Chen, Y.F., Matsubayashi, Y. and Sakagami, Y. 2000. Peptide growth factor phytosulfokine-a contributes to the pollen population effect. Planta 211: 752–755.CrossRefPubMedGoogle Scholar
  7. Chen, W., Tang, D., Suo, J., Zhang, Y. and Xue, Y. 2001. Expressional profiling of genes related to pollination and fertilization in rice. C.R. Acad. Sci. Paris, Sci. Vie 324: 1111–1116.Google Scholar
  8. Dickinson, H.G. and Elleman, C.J. 2000. Pollen coatings: chimeric genetics and new functions. Sex. Plant Reprod. 12: 302–309.CrossRefGoogle Scholar
  9. Dixit, R., Rizzo, C., Nasrallah, M. and Nasrallah, J. 2001. The brassica MIP-MOD gene encodes a functional water channel that is expressed in the stigma epidermis. Plant Mol. Biol. 45: 51–62.CrossRefPubMedGoogle Scholar
  10. 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.CrossRefPubMedGoogle Scholar
  11. Ewing, B., Hillier, L., Wendl, M.C. and Green, P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185.PubMedGoogle Scholar
  12. Favaro, R., Pinyopich, A., Battaglia, R., Kooiker, M., Borghi, L, Ditta, G., Yanofsky, M.F., Kater, M.M. and Colombo, L. 2003. MADS-box protein complexes control carpel and ovule development in Arabidopsis. Plant Cell 15: 2603–2611.CrossRefPubMedGoogle Scholar
  13. Feng, Q., Zhang, Y., Hao, P. et al. 2002. Sequence and analysis of rice chromosome 4. Nature 420: 316–320.CrossRefPubMedGoogle Scholar
  14. Franklin-Tong, V.E. 1999. Signaling and the modulation of pollen tube growth. Plzant Cell 11: 727–738.CrossRefGoogle Scholar
  15. Goff, S.A., Ricke, D., Lan, T.H. et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.CrossRefPubMedGoogle Scholar
  16. Goubet, F., Misrahi, A., Park, S.K., Zhang, Z., Twell, D. and Dupree P. 2003. AtCSLA7, a cellulose synthase-like putative glycosyltransferase, is important for pollen tube growth and embryogenesis in Arabidopsis. Plant Physiol. 131: 547–557.CrossRefPubMedGoogle Scholar
  17. Gu, T., Mazzurco, M., Sulaman, W., Matias, D.D. and Goring, D.R. 1998. Binding of an arm repeat protein to the kinase domain of the S-locus receptor kinase. Proc. Natl. Acad. Sci. USA 95: 382–387.CrossRefPubMedGoogle Scholar
  18. Guyon, V.N., Astwood, J.D., Garner, E.C., Dunker, A.K. and Taylor, L.P. 2000. Isolation and characterization of cDNAs expressed in the early stages of flavonol-induced pollen germination in petunia. Plant Physiol. 123: 699–710.CrossRefPubMedGoogle Scholar
  19. Gygi, S.P., Rochon, Y., Franza, B.R. and Aebersold, R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19: 1720–1730.PubMedGoogle Scholar
  20. Higuchi, K., Watanabe, S., Takahashi, M., Kawasaki, S., Nakanishi, H., Nishizawa, N.K. and Mori, S. 2001. Nicotianamine synthase gene expression differs in barley and rice under Fe-deficient conditions. Plant J. 25: 159–167.CrossRefPubMedGoogle Scholar
  21. Hsieh, H.M., Liu, W.K. and Huang, P.C. 1995. A novel stressinducible metallothionein-like gene from rice. Plant Mol. Biol. 28: 381–389.PubMedGoogle Scholar
  22. Huang, X. and Madan, A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9: 868–877.CrossRefPubMedGoogle Scholar
  23. Huang, Y.F., Jordan, W.R., Wing, R.A. and Morgan, P.W. 1998. Gene expression induced by physical impedance in maize roots. Plant Mol. Biol. 37: 921–930.CrossRefPubMedGoogle Scholar
  24. Hü lskamp, M., Kopczak, S.D., Horejsi, T.F., Kihl, B.K. and Pruitt, R.E. 1995. Identification of genes required for pollen-stigma recognition in Arabidopsis thaliana. Plant J. 8: 703–714.CrossRefPubMedGoogle Scholar
  25. Ikeda, S., Nasrallah, J.B., Dixit, R., Preiss, S. and Nasrallah, M.E. 1997. An aquaporin-like gene required for the Brassica self-incompatibility response. Science 276: 1564–1566.CrossRefPubMedGoogle Scholar
  26. Jack, T. 2001. Plant development going MADS. Plant Mol. Biol. 46: 515–520.CrossRefPubMedGoogle Scholar
  27. Jansen, M.A.K., Sessa, G., Malkin, S. and Fluhr, R. 1992. PEPC-mediated carbon fixation in transmitting tract cells reflects style-pollen tube interactions Plant J. 2: 507–515.Google Scholar
  28. Johns, C., Lu, M., Lyznik, A. and Mackenzie, S. 1992. A mitochondrial DNA sequence is associated with abnormal pollen development in cytoplasmic male sterile bean plants. Plant Cell 4: 435–449.CrossRefPubMedGoogle Scholar
  29. Kamalay, J.C. and Goldberg, R.B. 1980. Regulation of structural gene expression in tobacco. Cell 19: 935–946.CrossRefPubMedGoogle Scholar
  30. Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., Galbraith D. and Bohnert, H.J. 2001. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13: 889–905.CrossRefPubMedGoogle Scholar
  31. Li, H.Y., Guo, Z.F. and Zhu, Y.X. 1998. Molecular cloning and analysis of a pea cDNA that is expressed in darkness and very rapidly induced by gibberellic acid. Mol. Gen. Genet. 259: 393–397.CrossRefPubMedGoogle Scholar
  32. Li, H., Lin, Y., Heath, R.M., Zhu, M.X. and Yang, Z. 1999. Control of pollen tube tip growth by a Rop GTPasedependent pathway that leads to tip-localized calcium influx. Plant Cell 11: 1731–1742.CrossRefPubMedGoogle Scholar
  33. Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H. and Deng, X.W. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589–2607.CrossRefPubMedGoogle Scholar
  34. Mayfield, J.A., Fiebig, A., Johnstone, S.E. and Preuss, D. 2001. Gene families from the Arabidopsis thaliana pollen coat proteome. Science 292: 2482–2485.CrossRefPubMedGoogle Scholar
  35. Mou, Z., Wang, X., Fu, Z., Dai, Y., Han, C., Ouyang, J., Bao, F., Hu, Y. and Li, J. 2002. Silencing of phosphoethanolamine N-methyltransferase results in temperature-sensitive male sterility and salt hypersensitivity in Arabidopsis. Plant Cell 14: 2031–2143.CrossRefPubMedGoogle Scholar
  36. Muschietti, J., Eyal, Y. and McCormick, S. 1998. Pollen tube localization implies a role in pollen-pistil interactions for the tomato receptor-like protein kinases LePRK1 and LePRK2. Plant Cell 10: 319–330.CrossRefPubMedGoogle Scholar
  37. Ogihara, Y., Mochida, K., Nemoto, Y., Murai, K., Yamazaki, Y., Shin-I, T. and Kohara, Y. 2003. Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J. 33: 1001–1011.PubMedGoogle Scholar
  38. Oono, Y., Seki, M., Nanjo, T., Narusaka, M., Fujita, M., Satoh, R., Satou, M., Sakurai, T., Ishida, J., Akiyama, K., Iida, K., Maruyama, K., Satoh, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. 2003. Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca. 7000 full-length cDNA microarray. Plant J. 34: 868–887.CrossRefPubMedGoogle Scholar
  39. Palanivelu, R. and Preuss, D. 2000. Pollen tube targeting and axon guidance: parallels in tip growth mechanisms. Trends Cell Biol. 10: 517–524.CrossRefPubMedGoogle Scholar
  40. Palanivelu, R., Brass, L., Edlund, A.F. and Preuss, D. 2003. Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell 114: 47–59.CrossRefPubMedGoogle Scholar
  41. Park, S.Y., Jauh, G.Y., Mollet, J.C., Eckard, K.J., Nothnagel, E.A., Walling, L.L. and Lord, E.M. 2000. A lipid transferlike protein is necessary for lily pollen tube adhesion to an in vitro stylar matrix. Plant Cell 12: 151–164.CrossRefPubMedGoogle Scholar
  42. Potocky, M., Elias, M., Profotova, B., Novotna, Z., Valentova, O. and Zarsky V. 2003. Phosphatidic acid produced by phospholipase D is required for tobacco pollen tube growth. Planta 217: 122–130.PubMedGoogle Scholar
  43. Preuss, D., Lemieux, B., Yen, G. and Davis, R.W. 1993. A conditional sterile mutation eliminates surface components from Arabidopsis pollen and disrupts cell signaling during fertilization. Genes Dev. 7: 974–985.PubMedGoogle Scholar
  44. Ruan, Y., Gilmore, J. and Conner, T. 1998. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15: 821–833.CrossRefPubMedGoogle Scholar
  45. Rudd, J.J. and Franklin-Tong, V.E. 2003. Signals and targets of the self-incompatibility response in pollen of Papaverrhoeas. J. Exp. Bot. 54: 141–148.CrossRefPubMedGoogle Scholar
  46. Sakamoto, A., Ogawa, M., Masumura, T., Shibata, D., Takeba, G., Tanaka, K. and Fujii, S. 1989. Three cDNA sequences coding for glutamine synthetase polypeptides in Oryza sativa L. Plant Mol. Biol. 13: 611–614.PubMedGoogle Scholar
  47. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.PubMedGoogle Scholar
  48. Shi, L., Gast, R.T., Gopalraj, M. and Olszewski, N.E. 1992. Characterization of a shoot-specific, GA3-and ABA-regulated gene from tomato. Plant J. 2: 153–159.CrossRefPubMedGoogle Scholar
  49. Singh, D.P., Jermakow, A.M. and Swain, S.M. 2002. Gibberellins are required for seed development and pollen tube growth in Arabidopsis. Plant Cell 14: 3133–3147.CrossRefPubMedGoogle Scholar
  50. Steinebrunner, I., Wu, J., Sun, Y., Corbett, A. and Roux, S.J. 2003. Disruption of apyrases inhibits pollen germination in Arabidopsis. Plant Physiol. 131: 1638–1647.CrossRefPubMedGoogle Scholar
  51. van Eldik, G.J., Ruiter, R.K., Colla, P.H., van Herpen, M.M., Schrauwen, J.A. and Wullems GJ. 1997. Expression of an isoflavone reductase-like gene enhanced by pollen tube growth in pistils of Solanum tuberosum. Plant Mol. Biol. 33: 923–929.CrossRefPubMedGoogle Scholar
  52. Watanabe, H., Abe, K., Emori, Y., Hosoyama, H. and Arai, S. 1991. Molecular cloning and gibberellin-induced expression of multiple cysteine proteinases of rice seeds (oryzains). J. Biol. Chem. 266: 16897–16902.PubMedGoogle Scholar
  53. Wemmer, T., Kaufmann, H., Kirch, H.H., Schneider, K., Lottspeich, F. and Thompson, R.D. 1994. The most abundant soluble basic protein of the stylar transmitting tract in potato (Solanum tuberosum L.) is an endochitinase. Planta 194: 264–273.CrossRefPubMedGoogle Scholar
  54. Wolters-Arts, M., Lush, W.M. and Mariani, C. 1998. Lipids are required for directional pollen-tube growth. Nature 392: 818–821.CrossRefPubMedGoogle Scholar
  55. Wu, H., de Graaf, B., Mariani, C. and Cheung, A.Y. 2001. Hydroxyproline-rich glycoproteins in plant reproductive tissues: structure, functions and regulation. Cell. Mol. Life Sci. 58: 1418–1429.PubMedGoogle Scholar
  56. Yang, D., Chertov, O., Bykovskaia, S.N., Chen, Q., Buffo, M.J., Shogan, J., Anderson, M., SchrÖder, J.M., Wang, J.M., Howard, O.Z. and Oppenheim, J.J. 1999. b-Defensins: linking innate and adaptive immunity through dendritic and T cell CCR6. Science 286: 525–530.CrossRefPubMedGoogle Scholar
  57. Ylstra, B., Busscher, J., Franken, J., Hollman, P.C.H., Mol, J.N.M. and van Tunen, A.J. 1994. Flavonols and fertilization in Petunia hybrida: localization and mode of action during pollen tube growth. Plant J. 6: 201–212.CrossRefGoogle Scholar
  58. Yu, J., Hu, S., Wang, J., Wong, G.K. et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92.CrossRefPubMedGoogle Scholar
  59. Zinkl, G.M., Zwiebel, B.I., Grier, D.G. and Preuss, D. 1999. Pollen-stigma adhesion in Arabidopsis: a species-specific interaction mediated by lipophilic molecules in the pollen exine. Development 126: 5431–5440.PubMedGoogle Scholar
  60. Zonia, L., Cordeiro, S., Tupy, J. and Feijo, J.A. 2002. Oscillatory chloride efflux at the pollen tube apex has a role in growth and cell volume regulation and is targeted by inositol 3,4,5,6-tetrakisphosphate. Plant Cell 14: 2233–2249.CrossRefPubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Lefu Lan
    • 1
  • Wei Chen
    • 1
  • Ying Lai
    • 1
  • Jinfeng Suo
    • 1
  • Zhaosheng Kong
    • 1
  • Can Li
    • 2
  • Ying Lu
    • 2
  • Yujun Zhang
    • 2
  • Xiangyu Zhao
    • 3
  • Xiansheng Zhang
    • 3
  • Yansheng Zhang
    • 1
  • Bin Han
    • 2
  • Jing Cheng
    • 4
  • Yongbiao Xue
    • 1
  1. 1.Institute of Genetics and Development BiologyChinese Academy of Science and National Center for Plant Gene ResearchBeijingChina
  2. 2.National Center for Gene Research, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
  3. 3.College of Life SciencesShandong Agricultural UniversityTaianChina
  4. 4.Department of Biological Science and BiotechnologyTsinghua University and Beijing National Biochip Research and Engineering CenterBeijingChina

Personalised recommendations