Genome-wide transcriptome dissection of the rice root system: Implications for developmental and physiological functions

Plant Journal

Volumn 69, Issue 1, 2012, Pages 126-140

  Takehisa, Hinako ^a   Sato, Yutaka ^a   Igarashi, Motoko ^a,e   Abiko, Tomomi ^b,f   Antonio, Baltazar A ^a   Kamatsuki, Kaori ^c   Minami, Hiroshi ^c   Namiki, Nobukazu ^c   Inukai, Yoshiaki ^d   Nakazono, Mikio ^d   Nagamura, Yoshiaki ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c MITSUBISHI SPACE SOFTWARE CO LTD   (Japan)

^d NAGOYA UNIVERSITY   (Japan)

^e NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^f JAPAN INTERNATIONAL RESEARCH CENTER FOR AGRICULTURAL SCIENCES   (Japan)

Author keywords

database; laser microdissection; microarray; rice; root; transcriptome

Indexed keywords

DATABASE; LASER MICRODISSECTION; RICE; ROOT; TRANSCRIPTOMES;

BIOCHEMISTRY; CROPS; ETHYLENE; MICROARRAYS; NUTRIENTS; PLANTS (BOTANY); SOILS; TISSUE;

GENE EXPRESSION;

PHYTOHORMONE; VEGETABLE PROTEIN;

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICRODISSECTION; PHYSIOLOGY; PLANT GENOME; PLANT ROOT; PLANT ROOT CAP; RICE;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MICRODISSECTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT GROWTH REGULATORS; PLANT PROTEINS; PLANT ROOT CAP; PLANT ROOTS;

ORYZA SATIVA;

EID: 84355166594     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2011.04777.x     Document Type: Article

References (117)

1. Alonso, J.M., Stepanova, A.N., Leisse, T.J., et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301, 653-657. (Pubitemid 36927950)
2. Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H., and, Matsuoka, M., (2005) Cytokinin oxidase regulates rice grain production. Science, 309, 741-745. (Pubitemid 41077314)
3. Bao, F., Shen, J., Brady, S.R., Muday, G.K., Asami, T., and, Yang, Z., (2004) Brassinosteroids interact with auxin to promote lateral root development in Arabidopsis. Plant Physiol. 134, 1624-1631. (Pubitemid 38527370)
4. Barlow, P.W., (2003) The root cap: cell dynamics, cell differentiation and cap function. J. Plant Growth Regul. 21, 261-286.
5. Benková, E., and, Hejátko, J., (2009) Hormone interactions at the root apical meristem. Plant Mol. Biol. 69, 383-396.
6. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., and, Benfey, P.N., (2003) A gene expression map of the Arabidopsis root. Science, 302, 1956-1960. (Pubitemid 37523501)
7. Brady, S.M., Orlando, D.A., Lee, J.Y., Wang, J.Y., Koch, J., Dinneny, J.R., Mace, D., Ohler, U., and, Benfey, P.N., (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 318, 801-806. (Pubitemid 351411772)
8. Brady, S.M., Zhang, L., Megraw, M., et al. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7, 459-468.
9. Brown, D.M., Zeef, L.A.H., Ellis, J., Goodacre, R., and, Turner, S.R., (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell, 17, 2281-2295. (Pubitemid 41672947)
10. Buchner, P., Takahashi, H., and, Hawkesford, M.J., (2004) Plant sulphate transporters: co-ordination of uptake, intracellular and long-distance transport. J. Exp. Bot. 55, 1765-1773. (Pubitemid 39123310)
11. Cai, X., Chen, T., Zhou, Q., Xu, L., Qu, L., Hua, X., and, Lin, J., (2011) Development of casparian strip in rice cultivars. Plant Signal. Behav. 6, 59-65.
12. Casson, S., Spencer, M., Walker, K., and, Lindsey, K., (2005) Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. Plant J. 42, 111-123.
13. Chang, C., Kwok, S.F., Bleecker, A.B., and, Meyerowitz, E.M., (1993) Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. Science, 262, 539-544. (Pubitemid 23350666)
14. Chao, Q., Rothenberg, M., Solano, R., Roman, G., Terzaghi, W., and, Ecker, J.R., (1997) Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell, 89, 1133-1144. (Pubitemid 127678746)
15. Chung, Y., Maharjan, P.M., Lee, O., et al. (2011) Auxin stimulates DWARF4 expression and brassinosteroid biosynthesis in Arabidopsis. Plant J. 66, 564-578.
16. Clark, D.G., Gubrium, E.K., Barrett, J.E., Nell, T.A., and, Klee, H.J., (1999) Root formation in ethylene-insensitive plants. Plant Physiol. 121, 53-59. (Pubitemid 29451991)
17. De Smet, I., Tetsumura, T., De Rybel, B., et al. (2007) Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis. Development, 134, 681-690. (Pubitemid 46437910)
18. Dello Ioio, R., Linhares, F.S., Scacchi, E., Casamitjana-Martinez, E., Heidstra, R., Costantino, P., and, Sabatini, S., (2007) Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr. Biol. 17, 678-682. (Pubitemid 46552243)
19. Dello loio, R., Linhares, F.S., and, Sabatini, S., (2008) Emerging role of cytokinin as a regulator of cellular differentiation. Curr. Opin. Plant Biol. 11, 23-27. (Pubitemid 351172875)
20. Dembinsky, D., Woll, K., Saleem, M., et al. (2007) Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiol. 145, 575-588. (Pubitemid 350127593)
21. Driouich, A., Durand, C., and, Vicré-Gibouin, M., (2007) Formation and separation of root border cells. Trends Plant Sci. 12, 14-19. (Pubitemid 46096806)
22. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and, Su, Z., (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-W70.
23. Edgar, R., Domrachev, M., and, Lash, A.E., (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210. (Pubitemid 34679544)
24. Fan, C., Xing, Y., Mao, H., Lu, T., Han, B., Xu, C., Li, X., and, Zhang, Q., (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164-1171.
25. Ferguson, I.B., and, Clarkson, D.T., (1976) Simultaneous uptake and translocation of magnesium and calcium in barley (Hordeum vulgare L.) roots. Planta, 128, 267-269.
26. Fujimoto, S.Y., Ohta, M., Usui, A., Shinshi, H., and, Ohme-Takagi, M., (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell, 12, 393-404. (Pubitemid 30186308)
27. Fujita, M., Horiuchi, Y., Ueda, Y., et al. (2010) Rice expression atlas in reproductive development. Plant Cell Physiol. 51, 2060-2081.
28. Fukaki, H., and, Tasaka, M., (2009) Hormone interactions during lateral root formation. Plant Mol. Biol. 69, 437-449.
29. Fukaki, H., Tameda, S., Masuda, H., and, Tasaka, M., (2002) Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis. Plant J. 29, 153-168. (Pubitemid 34134693)
30. Furutani, I., Sukegawa, S., and, Kyozuka, J., (2006) Genome-wide analysis of spatial and temporal gene expression in rice panicle development. Plant J. 46, 503-511.
31. Gewin, V., (2010) An underground revolution. Nature, 466, 552-553.
32. Girke, T., Lauricha, J., Tran, H., Keegstra, K., and, Raikhel, N., (2004) The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol. 136, 3003-3008. (Pubitemid 41096301)
33. Harrison-Murray, R.S., and, Clarkson, D.T., (1973) Relationships between structural development and the absorption of ions by the root system of Cucurbita pepo. Planta, 114, 1-16.
34. + ratio in leaves during salinity stress. Plant Cell Environ. 33, 552-565.
35. Häussling, M., Jorns, C.A., Lehmbecker, G., Hecht-Buchholz, C., and, Marschner, H., (1988) Ion and water uptake in relation to root development in Norway spruce (Picea abies (L.) Karst.). J. Plant Physiol. 133, 486-491.
36. Hawes, M.C., Brigham, L.A., Wen, F., Woo, H.H., and, Zhu, Y., (1998) Function of root border cells in plant health: pioneers in the rhizosphere. Annu. Rev. Phytopathol. 36, 311-327. (Pubitemid 28456411)
37. Herder, G.D., Van Isterdael, G., Beeckman, T., and, De Smet, I., (2010) The roots of a new green revolution. Trends Plant Sci. 15, 600-607.
38. Hirano, K., Aya, K., Hobo, T., Sakakibara, H., Kojima, M., Shim, R.A., Hasegawa, Y., Ueguchi-Tanaka, M., and, Matsuoka, M., (2008) Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice. Plant Cell Physiol. 49, 1429-1450.
39. Hirota, A., Kato, T., Fukaki, H., Aida, M., and, Tasaka, M., (2007) The auxin-regulated AP2/EREBP gene PUCHI is required for morphogenesis in the early lateral root primordium of Arabidopsis. Plant Cell, 19, 2156-2168. (Pubitemid 47347459)
40. Hobo, T., Suwabe, K., Aya, K., et al. (2008) Various spatiotemporal expression profiles of anther-expressed genes in rice. Plant Cell Physiol. 49, 1417-1428.
41. Hochholdinger, F., Park, W.J., Sauer, M., and, Woll, K., (2004) From weeds to crops: genetic analysis of root development in cereals. Trends Plant Sci. 9, 42-48. (Pubitemid 38157645)
42. Hoecker, N., Keller, B., Piepho, H.P., and, Hochholdinger, F., (2006) Manifestation of heterosis during early maize (Zea mays L.) root development. Theor. Appl. Genet. 112, 421-429. (Pubitemid 43081585)
43. Hua, J., Chang, C., Sun, Q., and, Meyerowitz, E.M., (1995) Ethylene insensitivity conferred by Arabidopsis ERS gene. Science, 269, 1712-1714.
44. Hua, J., Sakai, H., Nourizadeh, S., Chen, Q.G., Bleecker, A.B., Ecker, J.R., and, Meyerowitz, E.M., (1998) EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. Plant Cell, 10, 1321-1332. (Pubitemid 28542167)
45. Hussain, A., Black, C.R., Taylor, I.B., and, Roberts, J.A., (1999) Soil compaction. A role for ethylene in regulating leaf expansion and shoot growth in tomato? Plant Physiol. 121, 1227-1237. (Pubitemid 30018508)
46. Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., Shibata, Y., Gomi, K., Umemura, I., Hasegawa, Y., Ashikari, M., Kitano, H., and, Matsuoka, M., (2005) Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling. Plant Cell, 17, 1387-1396. (Pubitemid 43138192)
47. 2+. Plant J. 45, 335-346. (Pubitemid 43373718)
48. Ito, Y., and, Kurata, N., (2006) Identification and characterization of cytokinin-signalling gene families in rice. Gene, 382, 57-65. (Pubitemid 44548254)
49. Iyer-Pascuzzi, A., Simpson, J., Herrera-Estrella, L., and, Benfey, P.N., (2009) Functional genomics of root growth and development in Arabidopsis. Curr. Opin. Plant Biol. 12, 165-171.
50. Jain, M., Kaur, N., Garg, R., Thakur, J.K., Tyagi, A.K., and, Khurana, J.P., (2006) Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct. Integr. Genomics, 6, 47-59. (Pubitemid 43013208)
51. Jiang, K., Zhang, S., Lee, S., Tsai, G., Kim, K., Huang, H., Chilcott, C., Zhu, T., and, Feldman, L.J., (2006) Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Mol. Biol. 60, 343-363. (Pubitemid 43327573)
52. Jiao, Y., Tausta, S.L., Gandotra, N., et al. (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat. Genet. 41, 258-263.
53. 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. (Pubitemid 32375908)
54. Kawata, S., and, Shibayama, H., (1965) On the lateral root primordial formation in the crown roots of rice plants. Proc. Crop Sci. Soc. Jpn. 33, 423-431.
55. Kieber, J.J., Rothenberg, M., Roman, G., Feldmann, K.A., and, Ecker, J.R., (1993) CTR1, a negative regulator of the ethylene response pathway in arabidopsis, encodes a member of the raf family of protein kinases. Cell, 72, 427-441. (Pubitemid 23059412)
56. Knee, E.M., Gong, F.C., Gao, M., Teplitski, M., Jones, A.R., Foxworthy, A., Mort, A.J., and, Bauer, W.D., (2001) Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source. Mol. Plant Microbe Interact. 14, 775-784. (Pubitemid 32464117)
57. Koike, S., Inoue, H., Mizuno, D., Takahashi, M., Nakanishi, H., Mori, S., and, Nishizawa, N.K., (2004) OsYSL2 is a rice metal-nicotianamine transporter that is regulated by iron and expressed in the phloem. Plant J. 39, 415-424. (Pubitemid 39040146)
58. Krichevsky, A., Zaltsman, A., Kozlovsky, S.V., Tian, G.W., and, Citovsky, V., (2009) Regulation of root elongation by histone acetylation in Arabidopsis. J. Mol. Biol. 385, 45-50.
59. Lee, H.W., Kim, N.Y., Lee, D.J., and, Kim, J., (2009) LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis. Plant Physiol. 151, 1377-1389.
60. Li, X., Qian, Q., Fu, Z., et al. (2003) Control of tillering in rice. Nature, 422, 618-621. (Pubitemid 36460415)
61. Li, L., Xu, J., Xu, Z.H., and, Xue, H.W., (2005) Brassinosteroids stimulate plant tropisms through modulation of polar auxin transport in Brassica and Arabidopsis. Plant Cell, 17, 2738-2753.
62. Lin, C.M., Koh, S., Stacey, G., Yu, S.M., Lin, T.Y., and, Tsay, Y.F., (2000) Cloning and functional characterization of a constitutively expressed nitrate transporter gene, OsNRT1, from rice. Plant Physiol. 122, 379-388. (Pubitemid 30153106)
63. Liu, H., Wang, S., Yu, X., Yu, J., He, X., Zhang, S., Shou, H., and, Wu, P., (2005) ARL1, a LOB-domain protein required for adventitious root formation in rice. Plant J. 43, 47-56. (Pubitemid 40962734)
64. Marin, E., Jouannet, V., Herz, A., Lokerse, A.S., Weijers, D., Vaucheret, H., Nussaume, L., Crespi, M.D., and, Maizel, A., (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell, 22, 1104-1117.
65. + transport in Arabidopsis. Plant Cell, 21, 2163-2178.
66. Morita, S., Lux, A., Enstone, D.E., Peterson, C.A., and, Abe, J., (1996) Reexamination of rice seminal root ontogeny using fluorescence microscopy. Jpn. J. Crop Sci. 65, 37-38.
67. Nakamoto, D., Ikeura, A., Asami, T., and, Yamamoto, K.T., (2006) Inhibition of brassinosteroid biosynthesis by either a dwarf4 mutation or a brassinosteroid biosynthesis inhibitor rescues defects in tropic responses of hypocotyls in the Arabidopsis mutant nonphototropic hypocotyl 4. Plant Physiol. 141, 456-464. (Pubitemid 43974540)
68. Nakamura, A., Higuchi, K., Goda, H., Fujiwara, M.T., Sawa, S., Koshiba, T., Shimada, Y., and, Yoshida, S., (2003) Brassinolide induces IAA5, IAA19, and DR5, a synthetic auxin response element in Arabidopsis, implying a cross talk point of brassinosteroid and auxin signaling. Plant Physiol. 133, 1843-1853. (Pubitemid 38047313)
69. Nakamura, A., Nakajima, N., Goda, H., Shimada, Y., Hayashi, K., Nozaki, H., Asami, T., Yoshida, S., and, Fujioka, S., (2006) Arabidopsis Aux/IAA genes are involved in brassinosteroid-mediated growth responses in a manner dependent on organ type. Plant J. 45, 193-205. (Pubitemid 43382054)
70. Nakazono, M., Qiu, F., Borsuk, L.A., and, Schnable, P.S., (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell, 15, 583-596. (Pubitemid 36339575)
71. Ohtsu, K., Takahashi, H., Schnable, P.S., and, Nakazono, M., (2007) Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant Cell Physiol. 48, 3-7. (Pubitemid 46181117)
72. Okushima, Y., Overvoorde, P.J., Arima, K., et al. (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell, 17, 444-463. (Pubitemid 41672967)
73. Okushima, Y., Fukaki, H., Onoda, M., Theologis, A., and, Tasaka, M., (2007) ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell, 19, 118-130. (Pubitemid 46852706)
74. Parizot, B., De Rybel, B., and, Beeckman, T., (2010) VisuaLRTC: a new view on lateral root initiation by combining specific transcriptome data sets. Plant Physiol. 153, 34-40.
75. Paszkowski, U., Kroken, S., Roux, C., and, Briggs, S.P., (2002) Rice phosphate transporters include an evolutionarily divergent gene specifically activated in arbuscular mycorrhizal symbiosis. Proc. Natl Acad. Sci. USA, 99, 13324-13329.
76. Pérez-Rodríguez, P., Riaño-Pachõn, D.M., Corrêa, L.G., Rensing, S.A., Kersten, B., and, Mueller-Roeber, B., (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38, D822-D827.
77. Petersson, S.V., Johansson, A.I., Kowalczyk, M., Makoveychuk, A., Wang, J.Y., Moritz, T., Grebe, M., Benfey, P.N., Sandberg, G., and, Ljung, K., (2009) An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell, 21, 1659-1668.
78. Plett, D., Toubia, J., Garnett, T., Tester, M., Kaiser, B.N., and, Baumann, U., (2010) Dichotomy in the NRT gene families of dicots and grass species. PLoS One, 5, e15289.
79. Rebouillat, J., Dievart, A., Verdeil, J.L., Escoute, J., Giese, G., Breitler, J.C., Gantet, P., Espeout, S., Guiderdoni, E., and, Périn, C., (2009) Molecular genetics of rice root development. Rice, 2, 15-34.
80. Rice Annotation Project (2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Res. 36, D1028-D1033.
81. Rogg, L.E., Lasswell, J., and, Bartel, B., (2001) A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell, 13, 465-480. (Pubitemid 32265369)
82. Sakai, H., Hua, J., Chen, Q.G., Chang, C., Medrano, L.J., Bleecker, A.B., and, Meyerowitz, E.M., (1998) ETR2 is an ETR1-like gene involved in ethylene signaling in Arabidopsis. Proc. Natl Acad. Sci. USA, 95, 5812-5817. (Pubitemid 28224179)
83. Sakurai, J., Ishikawa, F., Yamaguchi, T., Uemura, M., and, Maeshima, M., (2005) Identification of 33 rice aquaporin genes and analysis of their expression and function. Plant Cell Physiol. 46, 1568-1577. (Pubitemid 41436599)
84. Sakurai, J., Ahamed, A., Murai, M., Maeshima, M., and, Uemura, M., (2008) Tissue and cell-specific localization of rice aquaporins and their water transport activities. Plant Cell Physiol. 49, 30-39.
85. Sato, Y., Antonio, B., Namiki, N., et al. (2011a) Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol. 11, 10.
86. Sato, Y., Antonio, B.A., Namiki, N., Takehisa, H., Minami, H., Kamatsuki, K., Sugimoto, K., Shimizu, Y., Hirochika, H., and, Nagamura, Y., (2011b) RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res. 39, D1141-D1148.
87. Shen, C., Wang, S., Bai, Y., Wu, Y., Zhang, S., Chen, M., Guilfoyle, T.J., Wu, P., and, Qi, Y., (2010) Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.). J. Exp. Bot. 61, 3971-3981.
88. Shomura, A., Izawa, T., Ebana, K., Ebitani, T., Kanegae, H., Konishi, S., and, Yano, M., (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40, 1023-1028.
89. Smith, D.L., and, Fedoroff, N.V., (1995) LRP1, a gene expressed in lateral and adventitious root primordia of Arabidopsis. Plant Cell, 7, 735-745.
90. Solano, R., Stepanova, A., Chao, Q., and, Ecker, J.R., (1998) Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENEINSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 12, 3703-3714. (Pubitemid 29019651)
91. Sondergaard, T.E., Schulz, A., and, Palmgren, M.G., (2004) Energization of transport processes in plants. Roles of the plasma membrane H+-ATPase. Plant Physiol. 136, 2475-2482. (Pubitemid 41071291)
92. Song, X.J., Huang, W., Shi, M., Zhu, M.Z., and, Lin, H.X., (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39, 623-630. (Pubitemid 46676105)
93. Sonoda, Y., Ikeda, A., Saiki, S., von Wirén, N., Yamaya, T., and, Yamaguchi, J., (2003) Distinct expression and function of three ammonium transporter genes (OsAMT1;1-1;3) in rice. Plant Cell Physiol. 44, 726-734. (Pubitemid 36953627)
94. Stepanova, A.N., Hoyt, J.M., Hamilton, A.A., and, Alonso, J.M., (2005) A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Plant Cell, 17, 2230-2242. (Pubitemid 41672943)
95. Stepanova, A.N., Robertson-Hoyt, J., Yun, J., Benavente, L.M., Xie, D.Y., Doležal, K., Schlereth, A., Jürgens, G., and, Alonso, J.M., (2008) TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell, 133, 177-191. (Pubitemid 351442990)
96. Stephenson, M.B., and, Hawes, M.C., (1994) Correlation of pectin methylesterase activity in root caps of pea with root border cell separation. Plant Physiol. 106, 739-745.
97. Suenaga, A., Moriya, K., Sonoda, Y., Ikeda, A., von Wirén, N., Hayakawa, T., Yamaguchi, J., and, Yamaya, T., (2003) Constitutive expression of a novel-type ammonium transporter OsAMT2 in rice plants. Plant Cell Physiol. 44, 206-211. (Pubitemid 36289959)
98. Swarup, R., Perry, P., Hagenbeek, D., Van Der Straeten, D., Beemster, G.T., Sandberg, G., Bhalerao, R., Ljung, K., and, Bennett, M.J., (2007) Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell, 19, 2186-2196. (Pubitemid 47347461)
99. Takahashi, H., Kamakura, H., Sato, Y., Shiono, K., Abiko, T., Tsutsumi, N., Nagamura, Y., Nishizawa, N.K., and, Nakazono, M., (2010) A method for obtaining high quality RNA from paraffin sections of plant tissues by laser microdissection. J. Plant. Res. 123, 807-813.
100. Tatematsu, K., Kumagai, S., Muto, H., Sato, A., Watahiki, M.K., Harper, R.M., Liscum, E., and, Yamamoto, K.T., (2004) MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that functions together with the transcriptional activator NPH4/ARF7 to regulate differential growth responses of hypocotyl and formation of lateral roots in Arabidopsis thaliana. Plant Cell, 16, 379-393. (Pubitemid 38192697)
101. Tatsumi, J., (1982) Growth of crops and transport of nitrogen (3). Growth of crop roots and transport of nitrogen. Agric. Hortic. 57, 631-638.
102. Tian, Q., and, Reed, J.W., (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development, 126, 711-721. (Pubitemid 29106178)
103. Tsai, H.L., Lue, W.L., Lu, K.J., Hsieh, M.H., Wang, S.M., and, Chen, J., (2009) Starch synthesis in Arabidopsis is achieved by spatial cotranscription of core starch metabolism genes. Plant Physiol. 151, 1582-1595.
104. Uehara, T., Okushima, Y., Mimura, T., Tasaka, M., and, Fukaki, H., (2008) Domain II mutations in CRANE/IAA18 suppress lateral root formation and affect shoot development in Arabidopsis thaliana. Plant Cell Physiol. 49, 1025-1038. (Pubitemid 351989690)
105. Wang, K.L., Li, H., and, Ecker, J.R., (2002) Ethylene biosynthesis and signaling networks. Plant Cell, 14, 131-151.
106. Wang, D., Pei, K., Fu, Y., Sun, Z., Li, S., Liu, H., Tang, K., Han, B., and, Tao, Y., (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene, 394, 13-24. (Pubitemid 46601761)
107. Wang, E., Wang, J., Zhu, X., et al. (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat. Genet. 40, 1370-1374.
108. Wang, L., Xie, W., Chen, Y., et al. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 61, 752-766.
109. Weng, J., Gu, S., Wan, X., et al. (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res. 18, 1199-1209.
110. Wilmoth, J.C., Wang, S., Tiwari, S.B., Joshi, A.D., Hagen, G., Guilfoyle, T.J., Alonso, J.M., Ecker, J.R., and, Reed, J.W., (2005) NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Plant J. 43, 118-130. (Pubitemid 40962740)
111. Woll, K., Borsuk, L.A., Stransky, H., Nettleton, D., Schnable, P.S., and, Hochholdinger, F., (2005) Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. Plant Physiol. 139, 1255-1267. (Pubitemid 43786828)
112. Xing, Y., and, Zhang, Q., (2010) Genetic and molecular bases of rice yield. Annu. Rev. Plant Biol. 61, 421-442.
113. Yamaji, N., and, Ma, J.F., (2007) Spatial distribution and temporal variation of the rice silicon transporter Lsi1. Plant Physiol. 143, 1306-1313. (Pubitemid 46941548)
114. TIR1. Plant J. 40, 772-782. (Pubitemid 39623250)
115. Yazaki, J., Kishimoto, N., Nagata, Y., et al. (2003) Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. DNA Res. 10, 249-261. (Pubitemid 38249932)
116. Yoshida, S., Forno, D.A., Cook, J.H., and, Gomez, K.A., (1976) Routine procedures for growing rice plants in culture solution. In Laboratory Manual for Physiological Studies of Rice (, Yoshida, S., Forno, D.A., Cook, J.H., and, Gomez, K.A., eds). Philippines: IRRI, pp. 61-66.
117. +-ATPase of rice roots to low pH as related to ammonium nutrition. Plant Cell Environ. 32, 1428-1440.