Therefore, it has been suggested that Os SPL14 alleles have great potential for breeding ( Jiao et al., 2010 Miura et al., 2010). WEALTHY FARMER'S PANICLE, another overexpression allele of Os SPL14, resulted from an epigenetic change in the Os SPL14 promoter and shows a similar phenotype ( Miura et al., 2010). IPA1 encodes the protein Os SPL14, and in the ipa1 mutant, one nucleotide substitution located in the recognition site for microRNA156 (miRNA156) perturbs IPA1 mRNA degradation, which results in accumulation of IPA1 and leads to the formation of ideal plant architecture with decreased tiller number and increased plant height and panicle branches ( Jiao et al., 2010). IDEAL PLANT ARCHITECTURE1 ( IPA1), a pleiotropic gene isolated through a map-based cloning approach, has been shown to be one of the key regulators that determine plant architecture ( Jiao et al., 2010). Features of ideal plant architecture include low tiller number, few unproductive tillers, more grains per panicle, stronger culms, and robust roots ( Khush, 1995 Virk et al., 2004). To meet the increasing demand for food, the concept of ideal plant architecture or new plant type has been proposed since the sixties of the last century ( Donald, 1968 Khush, 1995). However, the molecular mechanisms underlying plant architecture remain unclear. Recently, more genes involved in the regulation of rice architecture have been characterized, such as DEP3, RICE LEAFY HOMOLOG, MADS-BOX TRANSCRIPTION FACTOR57 ( MADS57), and SQUAMOSA PROMOTER BINDING-LIKE PROTEIN16 ( SPL16) ( Rao et al., 2008 Qiao et al., 2011 Wang et al., 2012 Guo et al., 2013). Rice varieties carrying the dep1 mutation, a dominant allele at the DEP1 locus, exhibit reduced length of inflorescence internodes, increased number of grains per panicle, and enhanced grain yield ( Huang et al., 2009). DENSE AND ERECT PANICLE1 ( DEP1) encodes a phosphatidylethanolamine binding protein–like domain protein.
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For the regulation of panicle morphology, LONELY GUY (LOG) and GRAIN NUMBER1a/CYTOKININ OXIDASE2, two components of the cytokinin metabolic pathway, play important roles in the development of panicle branches ( Ashikari et al., 2005 Kurakawa et al., 2007). TEOSINTE BRANCHED1 ( TB1), a member of the TEOSINTE BRANCHED1, CYCLOIDEA AND PCF TRANSCRIPTION FACTOR (TCP) gene family, functions as a negative regulator of lateral branching in rice that acts downstream of DWARF to repress the outgrowth of axillary buds ( Takeda et al., 2003 Minakuchi et al., 2010). The DWARF genes, including D3, D10, D14, D17, and D27, have been found to play critical roles in the strigolactone biosynthesis or signal transduction pathways influencing rice tiller number ( Ishikawa et al., 2005 Zou et al., 2005 Arite et al., 2007, 2009 Lin et al., 2009). Genes such as ELONGATED UPPERMOST INTERNODE1 ( EUI1), SEMI DWARF1, SLENDER RICE1 ( SLR1), GA-INSENSITIVE DWARF1 ( GID1), and GID2 are found to be important components of the gibberellic acid biosynthetic and signal transduction pathways regulating plant height ( Ikeda et al., 2001 Sasaki et al., 2002, 2003 Ueguchi-Tanaka et al., 2005 Zhu et al., 2006). Based on recent studies on rice mutants, many important genes involved in regulating plant architecture have been characterized. Rice ( Oryza sativa) plant architecture, including plant height, tiller number, tiller angle, and panicle morphology, is one of the major factors that determine grain productivity ( Wang and Li, 2008). The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.
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Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length.
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Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2.
IPA LIBRARY WILD FRONTIER GAME ACTIVATOR
To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 10 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. IDEAL PLANT ARCHITECTURE1 ( IPA1) is critical in regulating rice ( Oryza sativa) plant architecture and substantially enhances grain yield.