IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. 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. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. 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. 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.
IPA1在調(diào)控水稻株型方面非常重要，它能顯著增加水稻產(chǎn)量。為了深入了解其分子機制，我們首次確認(rèn)IPA1是一個有功能的轉(zhuǎn)錄激活因子，通過全基因染色質(zhì)免疫沉淀測序分析（Chip-Seq）發(fā)現(xiàn)，在水稻莖尖SAs和幼穗組織YPs中發(fā)現(xiàn)有1067和2185基因與IPA1結(jié)合位點有關(guān)。SBP-box（SQUAMOSA啟動子結(jié)合蛋白框）直接結(jié)合核心基序GTAC在IPA1結(jié)合峰中高度富集，有趣的是，之前報道的未知的間接結(jié)合基序TGGGCC/T也通過IPA1與增殖細胞核抗原啟動子結(jié)合因子（PCF1）和（PCF2）的互作顯著富集。通過RNA重測序?qū)θ蚪M表達譜進一步分析顯示IPA1參與調(diào)控多個生長發(fā)育過程。而且，我們結(jié)果表明IPA1能與控制水稻分蘗側(cè)芽生長的負(fù)調(diào)控因子OsTB1的啟動子直接結(jié)合，抑制水稻分蘗發(fā)生，還通過直接正調(diào)控水稻株型重要基因DEP1，調(diào)節(jié)水稻株高和穗長。通過對IPA1全基因組的靶基因的闡釋，有助于我們對水稻株型的分子機制認(rèn)識并且有利于培育優(yōu)良品種的選育。