Aichinger, E., Kornet, N., Friedrich, T., and Laux, T. (2012). Plant stem cell niches. Annu. Rev. Plant Biol. 63: 615-636.
Arber, A. (1934). The gramineae: a study of cereal, bamboo, and grasses. (Cambridge: University Press).
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.
Betsuyaku, S., Takahashi, F., Kinoshita, A., Miwa, H., Shinozaki, K., Fukuda, H., and Sawa, S. (2011). Mitogen-activated protein kinase regulated by the CLAVATA receptors contributes to shoot apical meristem homeostasis. Plant Cell Physiol. 52: 14-29.
Bleckmann, A., Weidtkamp-Peters, S., Seidel, C.A., and Simon, R. (2010). Stem cell signaling in Arabidopsis requires CRN to localize CLV2 to the plasma membrane. Plant Physiol. 152: 166-176.
Bommert, P., Je, B.I., Goldshmidt, A., and Jackson, D. (2013). The maize Ga gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size. Nature 502: 555-558.
Bommert, P., Lunde, C., Nardmann, J., Vollbrecht, E., Running, M., Jackson, D., Hake, S., and Werr, W. (2005). thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development 132: 1235-1245.
Brand, U., Fletcher, J.C., Hobe, M., Meyerowitz, E.M., and Simon, R. (2000). Dependence of stem cell fate in Arabidopsis on a feedback loop regulated by CLV3 activity. Science 289: 617-619.
Busch, W., Miotk, A., Ariel, F.D., Zhao, Z., Forner, J., Daum, G., Suzaki, T., Schuster, C., Schultheiss, S.J., Leibfried, A., Haubeiß, S., Ha, N., Chan, R.L., and Lohmann, J.U. (2010). Transcriptional control of a plant stem cell niche. Dev. Cell 18: 841-853.
Cai, Q., Yuan, Z., Chen, M., Yin, C., Luo, Z., Zhao, X., Liang, W., Hu, J., and Zhang, D. (2014). Jasmonic acid regulates spikelet development in rice. Nat. Commun. 5: 3476.
Causier, B., Ashworth, M., Guo, W., and Davies, B. (2012). The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol. 158: 423-438.
Chickarmane, V.S., Gordon, S.P., Tarr, P.T., Heisler, M.G., and Meyerowitz, E.M. (2012). Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem. Proc. Natl. Acad. Sci., USA 109: 4002-4007.
Clark, S.E., Running, M.P., and Meyerowitz, E.M. (1993). CLAVATA1, a regulator of meristem and flower development in Arabidopsis. Development 119: 397-418.
Clark, S.E., Running, M.P., and Meyerowitz, E.M. (1995). CLAVATA3 is a specific regulator of shoot and floral meristem development affecting the same processes as CLAVATA1. Development 121: 2057-2067.
Clark, S.E., Williams, R.W., and Meyerowitz, E.M. (1997). The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell 89: 575-585.
Coen, E.S., and Meyerowitz, E.M. (1991). The war of the whorls: genetic interactions controlling flower development. Nature 353: 31-37.
Daum, G., Medzihradszky, A., Suzaki, T., and Lohmann, J.U. (2014). A mechanistic framework for noncell autonomous stem cell induction in Arabidopsis. Proc. Natl. Acad. Sci., USA 111: 14619-14624.
Fletcher, J.C., Brand, U., Running, M.P., Simon, R., and Meyerowitz, E.M. (1999). Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283: 1911-1914.
Gallavotti, A., Long, J.A., Stanfield, S., Yang, X., Jackson, D., Vollbrecht, E., and Schmidt, R.J. (2010). The control of axillary meristem fate in the maize ramosa pathway. Development 137: 2849-2856.
Gordon, S.P., Chickarmane, V.S., Ohno, C., and Meyerowitz, E.M. (2009). Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem. Proc. Natl. Acad. Sci., USA 106: 16529-16534.
Ha, C.M., Jun, J.H., and Fletcher, J.C. (2010). Shoot apical meristem form and function. Curr. Top. Dev. Biol. 91: 103-140.
Haecker, A., Gross-Hardt, R., Geiges, B., Sarkar, A., Breuninger, H., Herrmann, M., and Laux, T. (2004). Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131: 657-668.
Hiei, Y., Ohta, S., Komari, T., and Kumashiro, T. (1994). Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6: 271-282.
Hirakawa, Y., Shinohara, H., Kondo, Y., Inoue, A., Nakanomyo, I., Ogawa, M., Sawa, S., Ohashi-Ito, K., Matsubayashi, Y., and Fukuda, H. (2008). Non-cell- autonomous control of vascular stem cell fate by a CLE peptide/receptor system. Proc. Natl. Acad. Sci., USA 105: 15208-15213.
Hirano, H.-Y., Tanaka, W., and Toriba, T. (2014). Grass flower development. In Flower development - Methods and protocols, J.L. Riechmann and F. Wellmer, eds (New York: Springer), pp. 57-84.
Hu, C., Zhu, Y., Cui, Y., Cheng, K., Liang, W., Wei, Z., Zhu, M., Yin, H., Zeng, L., Xiao, Y., Lv, M., Yi, J., Hou, S., He, K., Li, J., and Gou, X. (2018). A group of receptor kinases are essential for CLAVATA signalling to maintain stem cell homeostasis. Nat. Plants 4: 205-211.
Huang, X., Qian, Q., Liu, Z., Sun, H., He, S., Luo, D., Xia, G., Chu, C., Li, J., and Fu, X. (2009). Natural variation at the DEP1 locus enhances grain yield in rice. Nat. Genet. 41: 494-497.
Ikeda, K., Ito, M., Nagasawa, N., Kyozuka, J., and Nagato, Y. (2007). Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate. Plant J. 51: 1030-1040.
Ikeda, M., Mitsuda, N., and Ohme-Takagi, M. (2009). Arabidopsis WUSCHEL is a bifunctional transcription factor that acts as a repressor in stem cell regulation and as an activator in floral patterning. Plant Cell 21: 3493-3505.
Ikeda-Kawakatsu, K., Maekawa, M., Izawa, T., Itoh, J.-I., and Nagato, Y. (2012). ABERRANT PANICLE ORGANIZATION 2/RFL, the rice ortholog of Arabidopsis LEAFY, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1. Plant J. 69: 168-180.
Ishida, T., Tabata, R., Yamada, M., Aida, M., Mitsumasu, K., Fujiwara, M., Yamaguchi, K., Shigenobu, S., Higuchi, M., Tsuji, H., Shimamoto, K., Hasebe, M., Fukuda, H., and Sawa, S. (2014). Heterotrimeric G proteins control stem cell proliferation through CLAVATA signaling in Arabidopsis. EMBO rep. 15: 1202-1209.
Itoh, J.-I., Nonomura, K.-I., Ikeda, K., Yamaki, S., Inukai, Y., Yamagishi, H., Kitano, H., and Nagato, Y. (2005). Rice plant development: from zygote to spikelet. Plant Cell Physiol. 46: 23-47.
Jackson, D., and Hake, S. (1999). Control of phyllotaxy in maize by the abphyl1 gene. Development 126: 315-323.
Je, B.I., Xu, F., Wu, Q., Liu, L., Meeley, R., Gallagher, J.P., Corcilius, L., Payne, R.J., Bartlett, M.E., and Jackson, D. (2018). The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. eLife 7: e35673.
Je, B.I., Gruel, J., Lee, Y.K., Bommert, P., Arevalo, E.D., Eveland, A.L., Wu, Q., Goldshmidt, A., Meeley, R., Bartlett, M., Komatsu, M., Sakai, H., Jönsson, H., and Jackson, D. (2016). Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits. Nat. Genet. 48: 785-791.
Jeong, S., Trotochaud, A.E., and Clark, S.E. (1999). The Arabidopsis CLAVATA2 gene encodes a receptor-like protein required for the stability of the CLAVATA1 receptor-like kinase. Plant Cell 11: 1925-1934.
Jiao, Y., Wang, Y., Xue, D., Wang, J., Yan, M., Liu, G., Dong, G., Zeng, D., Lu, Z., Zhu, X., Qian, Q., and Li, J. (2010). Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet. 42: 541-544.
Jin, Y., Luo, Q., Tong, H., Wang, A., Cheng, Z., Tang, J., Li, D., Zhao, X., Li, X., Wan, J., Jiao, Y., Chu, C., and Zhu, L. (2011). An AT-hook gene is required for palea formation and floral organ number control in rice. Dev. Biol. 359: 277-288.
Kayes, J.M., and Clark, S.E. (1998). CLAVATA2, a regulator of meristem and organ development in Arabidopsis. Development 125: 3843-3851.
Kieber, J.J., and Schaller, G.E. (2018). Cytokinin signaling in plant development. Development 145.
Kieffer, M., Stern, Y., Cook, H., Clerici, E., Maulbetsch, C., Laux, T., and Davies, B. (2006). Analysis of the transcription factor WUSCHEL and its functional homologue in Antirrhinum reveals a potential mechanism for their roles in meristem maintenance. Plant Cell 18: 560-573.
Kinoshita, A., Betsuyaku, S., Osakabe, Y., Mizuno, S., Nagawa, S., Stahl, Y., Simon, R., Yamaguchi-Shinozaki, K., Fukuda, H., and Sawa, S. (2010). RPK2 is an essential receptor-like kinase that transmits the CLV3 signal in Arabidopsis. Development 137: 3911-3920.
Komatsu, K., Maekawa, M., Ujiie, S., Satake, Y., Furutani, I., Okamoto, H., Shimamoto, K., and Kyozuka, J. (2003). LAX and SPA: major regulators of shoot branching in rice. Proc. Natl. Acad. Sci., USA 100: 11765-11770.
Kondo, T., Sawa, S., Kinoshita, A., Mizuno, S., Kakimoto, T., Fukuda, H., and Sakagami, Y. (2006). A plant peptide encoded by CLV3 identified by in situ MALDI-TOF MS analysis. Science 313: 845-848.
Krogan, N.T., Hogan, K., and Long, J.A. (2012). APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. Development 139: 4180-4190.
Laux, T., Mayer, K.F.X., Berger, J., and Jürgens, G. (1996). The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development 122: 87-96.
Leibfried, A., To, J.P.C., Busch, W., Stehling, S., Kehle, A., Demar, M., Kieber, J.J., and Lohmann, J.U. (2005). WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators. Nature 438: 1172-1175.
Leyser, O., and Day, S. (2003). Mechanisms in plant development. (John Wiley & Sons).
Li, H., Xue, D., Gao, Z., Yan, M., Xu, W., Xing, Z., Huang, D., Qian, Q., and Xue, Y. (2009). A putative lipase gene EXTRA GLUME1 regulates both empty-glume fate and spikelet development in rice. Plant J. 57: 593-605.
Li, X., Sun, L., Tan, L., Liu, F., Zhu, Z., Fu, Y., Sun, X., Sun, X., Xie, D., and Sun, C. (2012). TH1, a DUF640 domain-like gene controls lemma and palea development in rice. Plant Mol. Biol. 78: 351-359.
Liu, P.-L., Du, L., Huang, Y., Gao, S.-M., and Yu, M. (2017). Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants. BMC Evol. Biol. 17: 47.
Liu, X., Galli, M., Camehl, I., and Gallavotti, A. (2019). RAMOSA1 ENHANCER LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture. Plant Physiol. 179: 348-363.
Long, J.A., Ohno, C., Smith, Z.R., and Meyerowitz, E.M. (2006). TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312: 1520-1523.
Long, J.A., Woody, S., Poethig, S., Meyerowitz, E.M., and Barton, M.K. (2002). Transformation of shoots into roots in Arabidopsis embryos mutant at the TOPLESS locus. Development 129: 2797-2806.
Lu, Z., Shao, G., Xiong, J., Jiao, Y., Wang, J., Liu, G., Meng, X., Liang, Y., Xiong, G., Wang, Y., and Li, J. (2015). MONOCULM 3, an ortholog of WUSCHEL in rice, is required for tiller bud formation. J. Genet. Genomics 42: 71-78.
Matsuoka, M., Ichikawa, H., Saito, A., Tada, Y., Fujimura, T., and Kanomurakami, Y. (1993). Expression of a rice homeobox gene causes altered morphology of transgenic plants. Plant Cell 5: 1039-1048.
Mayer, K.F., Schoof, H., Haecker, A., Lenhard, M., Jürgens, G., and Laux, T. (1998). Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95: 805-815. Mikami, M., Toki, S., and Endo, M. (2015). Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice. Plant Mol. Biol. 88: 561-572. Miura, K., Ikeda, M., Matsubara, A., Song, X.J., Ito, M., Asano, K., Matsuoka, M., Kitano, H., and Ashikari, M. (2010). OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet. 42: 545-549.
Miwa, H., Betsuyaku, S., Iwamoto, K., Kinoshita, A., Fukuda, H., and Sawa, S. (2008). The Receptor-Like Kinase SOL2 Mediates CLE Signaling in Arabidopsis. Plant Cell Physiol. 49: 1752-1757.
Morita, J., Kato, K., Nakane, T., Kondo, Y., Fukuda, H., Nishimasu, H., Ishitani, R., and Nureki, O. (2016). Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide. Nat. Commun. 7: 12383.
Müller, R., Bleckmann, A., and Simon, R. (2008). The receptor kinase CORYNE of Arabidopsis transmits the stem cell-limiting signal CLAVATA3 independently of CLAVATA1. Plant Cell 20: 934-946.
Müller, R., Borghi, L., Kwiatkowska, D., Laufs, P., and Simon, R. (2006). Dynamic and compensatory responses of Arabidopsis shoot and floral meristems to CLV3 signaling. Plant Cell 18: 1188-1198.
Nakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., Toyooka, K., Matsuoka, K., Jinbo, T., and Kimura, T. (2007). Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng. 104: 34-41.
Nardmann, J., Zimmermann, R., Durantini, D., Kranz, E., and Werr, W. (2007). WOX gene phylogeny in Poaceae: a comparative approach addressing leaf and embryo development. Mol. Biol. Evol. 24: 2474-2484.
Ogawa, M., Shinohara, H., Sakagami, Y., and Matsubayashi, Y. (2008). Arabidopsis CLV3 peptide directly binds CLV1 ectodomain. Science 319: 294.
Oh, E., Zhu, J.Y., Ryu, H., Hwang, I., and Wang, Z.Y. (2014). TOPLESS mediates brassinosteroid-induced transcriptional repression through interaction with BZR1. Nat. Commun. 5: 4140.
Ohmori, Y., Tanaka, W., Kojima, M., Sakakibara, H., and Hirano, H.-Y. (2013). WUSCHEL-RELATED HOMEOBOX4 is involved in meristem maintenance and is negatively regulated by the CLE gene FCP1 in rice. Plant Cell 25: 229-241.
Ohyama, K., Shinohara, H., Ogawa-Ohnishi, M., and Matsubayashi, Y. (2009). A glycopeptide regulating stem cell fate in Arabidopsis thaliana. Nat. Chem. Biol. 5: 578-580.
Ookawa, T., Hobo, T., Yano, M., Murata, K., Ando, T., Miura, H., Asano, K., Ochiai, Y., Ikeda, M., Nishitani, R., Ebitani, T., Ozaki, H., Angeles, E.R., Hirasawa, T., and Matsuoka, M. (2010). New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat. Commun. 1: 132.
Pauwels, L., Barbero, G.F., Geerinck, J., Tilleman, S., Grunewald, W., Pérez, A.C., Chico, J.M., Bossche, R.V., Sewell, J., Gil, E., García-Casado, G., Witters, E., Inzé, D., Long, J.A., De Jaeger, G., Solano, R., and Goossens, A. (2010). NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature 464: 788-791.
Pesquita, C., Faria, D., Falcão, A.O., Lord, P., and Couto, F.M. (2009). Semantic similarity in biomedical ontologies. PLOS Comput. Biol. 5: e1000443.
Pi, L., Aichinger, E., van der Graaff, E., Llavata-Peris, C.I., Weijers, D., Hennig, L., Groot, E., and Laux, T. (2015). Organizer-derived WOX5 signal maintains root columella stem cells through chromatin-mediated repression of CDF4 expression. Dev. Cell 33: 576-588.
Rao, N.N., Prasad, K., Kumar, P.R., and Vijayraghavan, U. (2008). Distinct regulatory role for RFL, the rice LFY homolog, in determining flowering time and plant architecture. Proc. Natl. Acad. Sci., USA 105: 3646-3651.
Reddy, G.V., and Meyerowitz, E.M. (2005). Stem-cell homeostasis and growth dynamics can be uncoupled in the Arabidopsis shoot apex. Science 310: 663-667.
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43: e47.
Ryu, H., Cho, H., Bae, W., and Hwang, I. (2014). Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3. Nat. Commun. 5: 4138.
Sato, D.-S., Ohmori, Y., Nagashima, H., Toriba, T., and Hirano, H.-Y. (2014). A role for TRIANGULAR HULL1 in fine-tuning spikelet morphogenesis in rice. Genes Genet. Syst. 89: 61-69.
Sato, Y., Hong, S.K., Tagiri, A., Kitano, H., Yamamoto, N., Nagato, Y., and Matsuoka, M. (1996). A rice homeobox gene, OSH1, is expressed before organ differentiation in a specific region during early embryogenesis. Proc. Natl. Acad. Sci., USA 93: 8117-8122.
Schoof, H., Lenhard, M., Haecker, A., Mayer, K.F.X., Jürgens, G., and Laux, T. (2000). The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100: 635– 644.
Shinohara, H., and Matsubayashi, Y. (2015). Reevaluation of the CLV3-receptor interaction in the shoot apical meristem: dissection of the CLV3 signaling pathway from a direct ligand-binding point of view. Plant J. 82: 328-336.
Somssich, M., Je, B.I., Simon, R., and Jackson, D. (2016). CLAVATA-WUSCHEL signaling in the shoot meristem. Development 143: 3238-3248.
Song, S.-K., Lee, M.M., and Clark, S.E. (2006). POL and PLL1 phosphatases are CLAVATA1 signaling intermediates required for Arabidopsis shoot and floral stem cells. Development 133: 4691-4698.
Steeves, T.A., and Sussex, I.M. (1989). Patterns in Plant Development. (Cambridge, UK: Cambridge University Press).
Supek, F., Bosnjak, M., Skunca, N., and Smuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PLOS one 6: e21800.
Suzaki, T., Yoshida, A., and Hirano, H.-Y. (2008). Functional diversification of CLAVATA3-related CLE proteins in meristem maintenance in rice. Plant Cell 20: 2049-2058.
Suzaki, T., Ohneda, M., Toriba, T., Yoshida, A., and Hirano, H.-Y. (2009). FON2 SPARE1 redundantly regulates floral meristem maintenance with FLORAL ORGAN NUMBER2 in rice. PLOS Genet. 5: e1000693.
Suzaki, T., Sato, M., Ashikari, M., Miyoshi, M., Nagato, Y., and Hirano, H.-Y. (2004). The gene FLORAL ORGAN NUMBER1 regulates floral meristem size in rice and encodes a leucine-rich repeat receptor kinase orthologous to Arabidopsis CLAVATA1. Development 131: 5649-5657.
Suzaki, T., Toriba, T., Fujimoto, M., Tsutsumi, N., Kitano, H., and Hirano, H.-Y. (2006). Conservation and diversification of meristem maintenance mechanism in Oryza sativa: function of the FLORAL ORGAN NUMBER2 gene Plant Cell Physiol. 47: 1591-1602.
Szemenyei, H., Hannon, M., and Long, J.A. (2008). TOPLESS mediates auxin- dependent transcriptional repression during Arabidopsis embryogenesis. Science 319: 1384-1386.
Tabuchi, H., Zhang, Y., Hattori, S., Omae, M., Shimizu-Sato, S., Oikawa, T., Qian, Q., Nishimura, M., Kitano, H., Xie, H., Fang, X., Yoshida, H., Kyozuka, J., Chen, F., and Sato, Y. (2011). LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems. Plant Cell 23: 3276- 3287.
Taguchi-Shiobara, F., Yuan, Z., Hake, S., and Jackson, D. (2001). The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize. Genes Dev. 15: 2755-2766.
Tanaka, W., Toriba, T., and Hirano, H.-Y. (2014). Flower development in rice. In The molecular genetics of floral transition and flower development, F. Fornara, ed (Amsterdam: Elsevier), pp. 221-262.
Tanaka, W., Toriba, T., and Hirano, H.-Y. (2017). Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice. New Phytol. 215: 825-839.
Tanaka, W., Pautler, M., Jackson, D., and Hirano, H.-Y. (2013). Grass meristems II: inflorescence architecture, flower development and meristem gate. Plant Cell Physiol. 54: 313-324.
Tanaka, W., Ohmori, Y., Ushijima, T., Matsusaka, H., Matsushita, T., Kumamaru, T., Kawano, S., and Hirano, H.-Y. (2015). Axillary meristem formation in rice requires the WUSCHEL ortholog TILLERS ABSENT1. Plant Cell 27: 1173-1184.
Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., Xu, W., and Su, Z. (2017). agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45: W122-W129.
Toriba, T., and Hirano, H.-Y. (2018). Two-color in situ hybridization: a technique for simultaneous detection of transcripts from different loci. In Plant Transcription Factors: Methods and Protocols, N. Yamaguchi, ed (New York, NY: Springer New York), pp. 269-287.
Tsai, Y.C., Weir, N.R., Hill, K., Zhang, W., Kim, H.J., Shiu, S.H., Schaller, G.E., and Kieber, J.J. (2012). Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiol. 158: 1666-1684.
Wickham, H. (2016). ggplot2: elegant graphics for data analysis. (Springer).
Williams, R.W., Wilson, J.M., and Meyerowitz, E.M. (1997). A possible role for kinase-associated protein phosphatase in the Arabidopsis CLAVATA1 signaling pathway. Proc. Natl. Acad. Sci., USA 94: 10467-10472.
Yadav, R.K., Perales, M., Gruel, J., Girke, T., Jönsson, H., and Reddy, G.V. (2011). WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex. Genes Dev. 25: 2025-2030.
Yamaguchi, T., Nagasawa, N., Kawasaki, S., Matsuoka, M., Nagato, Y., and Hirano, H.-Y. (2004). The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa. Plant Cell 16: 500-509.
Yamaguchi, Y.L., Ishida, T., and Sawa, S. (2016). CLE peptides and their signaling pathways in plant development. J. Exp. Bot. 67: 4813-4826.
Yamaki, S., Satoh, H., and Nagato, Y. (2005). Gypsy embryo specifies ovule curvature by regulating ovule/integument development in rice. Planta 222: 408-417.
Yang, F., Bui, H.T., Pautler, M., Llaca, V., Johnston, R., Lee, B.H., Kolbe, A., Sakai, H., and Jackson, D. (2015). A maize glutaredoxin gene, Abphyl2, regulates shoot meristem size and phyllotaxy. Plant Cell 27: 121-131.
Yasui, Y., Tanaka, W., Sakamoto, T., Kurata, T., and Hirano, H.-Y. (2017). Genetic enhancer analysis reveals that FLORAL ORGAN NUMBER2 and OsMADS3 co-operatively regulate maintenance and determinacy of the flower meristem in rice. Plant Cell Physiol. 58: 893-903.
Yasui, Y., Ohmori, Y., Takebayashi, Y., Sakakibara, H., and Hirano, H.-Y. (2018). WUSCHEL-RELATED HOMEOBOX4 acts as a key regulator in early leaf development in rice. PLOS Genet. 14: e1007365.
Yoshida, A., Suzaki, T., Tanaka, W., and Hirano, H.-Y. (2009). The homeotic gene LONG STERILE LEMMA (G1) specifies sterile lemma identity in the rice spikelet. Proc. Natl. Acad. Sci., USA 106: 20103-20108.
Yoshida, A., Ohmori, Y., Kitano, H., Taguchi-Shiobara, F., and Hirano, H.-Y. (2012). ABERRANT SPIKELET AND PANICLE1, encoding a TOPLESS-related transcriptional co-repressor, is involved in the regulation of meristem fate in rice. Plant J. 70: 327-339.
Yoshida, A., Sasao, M., Yasuno, N., Takagi, K., Daimon, Y., Chen, R., Yamazaki, R., Tokunaga, H., Kitaguchi, Y., Sato, Y., Nagamura, Y., Ushijima, T., Kumamaru, T., Iida, S., Maekawa, M., and Kyozuka, J. (2013). TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition. Proc. Natl. Acad. Sci., USA 110: 767-772.
Yu, L.P., Simon, E.J., Trotochaud, A.E., and Clark, S.E. (2000). POLTERGEIST functions to regulate meristem development downstream of the CLAVATA loci. Development 127: 1661-1670.
Zhang, H., Lin, X., Han, Z., Qu, L.J., and Chai, J. (2016). Crystal structure of PXY- TDIF complex reveals a conserved recognition mechanism among CLE peptide- receptor pairs. Cell Res. 26: 543-555.
Zhou, Y., Yan, A., Han, H., Li, T., Geng, Y., Liu, X., and Meyerowitz, E.M. (2018). HAIRY MERISTEM with WUSCHEL confines CLAVATA3 expression to the outer apical meristem layers. Science 361: 502-506.
Zhou, Y., Liu, X., Engstrom, E.M., Nimchuk, Z.L., Pruneda-Paz, J.L., Tarr, P.T., Yan, A., Kay, S.A., and Meyerowitz, E.M. (2015). Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 517: 377-380.