植物的生长发育及逆境适应性是由遗传因子与环境因素共同决定，其中基因表达转录调控及激素交互作用途径尤为重要。深入研究植物生长及耐逆的调控机理，对提高作物产量及环境适应性具有重要的指导意义。在本研究中，通过筛选籼稻 9311 辐射诱变体库，获得了一个植株形态发生显著变异的突变体，并将其命名为 short internode1（shi1）。对 shi1 突变体的表型进行了详细鉴定，克隆了候选基因 OsSHI1，并对其参与水稻生长及耐逆调控的分子机制进行了深入分析，具体结果如下：
1. OsSHI1 对水稻株型发育调控机理研究
1.1. 种子萌发两周后，野生型幼苗逐渐形成分蘖芽并在基部开始发育。但是shi1突变体的分蘖芽发育迟缓，植株的分蘖数显著减少。与野生型植株相比，shi1 成熟植株的穗型也发生了以下显著变化：shi1 穗型直立紧凑，成熟后期逐渐呈现黑褐色，其一级枝梗、二级枝梗和小穗数均显著增加。此外，shi1 突变体的茎秆更为粗壮，抗倒伏能力显著加强。
1.2. 将shi1 与粳稻02428 杂交创建了F2 定位群体，通过图位克隆的方法将突变位点精细定位到了9 号染色体末端约50 kb 的区间内。测序发现，该区间内OsSHI1基因在shi1 突变体中缺失。转基因互补及敲除进一步确认了该基因在分蘖及穗分枝的调控作用。OsSHI1 编码与拟南芥SHI 家族同源的转录因子，具有高度保守的C3HC3H锌指结构域及家族特异的IGGH 结构域，在水稻中尚未报道。OsSHI1 定位于细胞核中，转录激活活性较微弱，并且主要在腋芽及幼穗中表达。
1.3. 经酵母双杂交筛库鉴定出了一互作蛋白，IPA1（即理想株型调控因子
OsSPL14）。通过体内BiFC 及体外Pull-down 等方法进一步验证了两者之间的互作。在IPA1 下游关键基因OsTB1 及OsDEP1 的启动子中分别发现了2 个和1 个OsSHI1的结合基序:T/GCTCTAC。酵母单杂交及EMSA 实验表明，OsSHI1 可以特异性的结合到这三个识别位点。采用OsSHI1 的特异性抗体进行ChIP 实验也进一步证实OsSHI1可以富集到OsTB1 及OsDEP1 启动子中T/GCTCTAC 基序附近。
1.4. RT-qPCR 结果表明，在突变体shi1 中OsTB1 及OsDEP1 的表达明显上调。通过LUC 酶活检测发现，IPA1 可以激活OsTB1 的转录，但是和OsSHI1 的共表达会显著抑制IPA1 的转录激活活性。进一步通过EMSA 实验证实，OsSHI1 可以降低IPA1对GTAC 元件的亲和性。Actin1:OsSHI1/35S:IPA1-Flag 转基因植株幼苗中进行ChIP发现OsSHI1 的过表达可以显著抑制IPA1-Flag 在OsTB1 启动子上的富集程度。以上
结果表明，OsSHI1 通过影响IPA1 的DNA 结合能力从而抑制其对下游靶基因的转录激活。与野生型Kitaake 相比，35S:IPA1-Flag 转基因植株的分蘖数显著减少，而Actin1:OsSHI1/35S:IPA1-Flag 转基因植株由于OsSHI1 蛋白的积累而部分恢复了分蘖数目。进一步在shi1 突变体中干扰IPA1，以便降低其表达水平。我们发现转基因干扰株系的株高降低，分蘖数显著增加并且穗分枝数急剧减少，同时OsTB1 及OsDEP1的表达水平也显著降低，表明IPA1 作用于OsSHI1 的下游。以上结果表明，OsSHI1位于IPA1 的上游并通过抑制IPA1 的功能来调控水稻株型发育。
2. OsSHI1 对水稻穗发育调控机理研究
2.1 shi1 突变体的穗及花器官发育发生显著的变异。与野生型相比，其穗部直立紧凑，枝梗及小花无序排布扭曲变形，生长后期逐渐褐化且顶部小穗存在严重的退化现象。此外，shi1 各轮花器官形态也显著改变。比如，其颍壳扭曲变小以至退化，内颍变小并且边缘部分扩大，外颍顶部发生弯曲。雌蕊顶端柱头部分组织发育受阻，雄蕊形态正常但体积变小，且花粉的育性也出现不同程度的降低。shi1 成熟时期的穗部结实率极低，籽粒变小，千粒重及品质性状相关指标等均显著下降。
2.2 OsSHI1 在各轮花器官组织中均表达。通过酵母双杂交筛选发现，OsSHI1 与调控发器官发育的E 类MADS 转录因子如OsMADS1、OsMADS5、OsMADS7、OsMADS8 及OsMADS34 等互作。Pull-down, BiFC 及LCI 等实验进一步对其互作关系进行了验证。酵母双杂交发现，OsSHI 与E 类MADS 转录因子的互作主要依赖于后者的DNA 结合结构域，即MADS 结构域。该结构域中保守氨基酸位点发生突变后，两者之间的互作显著降低。
2.3. OsSHI1 与OsMADS1 之间的互作并不影响后者的转录及蛋白稳定性。然而，LUC 活性检测及EMSA 实验发现，OsSHI1 显著抑制OsMADS1 的DNA 结合能力并进而影响其转录活性。OsMADS1 转基因过表达植株的花器官发育也发生显著变异，且其下游调控基因在过表达植株及shi1 突变体中均发生显著上调。
2.4. shi 突变体穗部退化表型与PCD 过程的调控可能存在一定关联。通过转录组测序发现，shi1 突变体穗部中大量与氧化还原过程相关的调控基因的表达水平发生明显改变。其中，编码多个编码过氧化物酶基因的表达显著降低。RT-qPCR 实验进一步验证此结果。shi1 突变体中的过氧化氢及丙二醛含量显著升高，而过氧化物酶活性则显著降低。
3. OsSHI1 对水稻生长及耐逆调控机理研究
3.1. 除以上表型分析外，shi1 突变体还表现为多种与植物激素相关的表型变异。比如， 与生长素相关的侧根数减少、重力响应迟缓及对生长素敏感性降低等，与油菜素内酯相关的株型紧凑、籽粒变小及对油菜素内酯不敏感等，与脱落酸相关的种子萌发降低、耐逆性增强及对脱落酸更为敏感等。
3.2. 激素含量测定结果表明，shi1 突变体中生长素及油菜素内酯相关物质的含量显著降低。Auxin 及BR 合成相关基因如OsYUCCAs 及D11 以及ABA 信号调控基因OsNAC2 在shi1 突变体中均显著下调。酵母单杂交、ChIP-qPCR 及EMSA 等实验证实OsSHI1 可以直接调控这些基因的表达。遗传分析结果表明，OsSHI1 位于D11 及OsNAC2 上游，进而调控水稻的生长及耐逆过程。
3.3. 外源激素处理结果表明，auxin 及ABA 促进而BR 则抑制OsSHI1 的表达。对OsSHI1 启动子序列进行分析发现，存在多种相关激素途径转录因子如ARF、ZIP及LIC 等的结合位点。酵母单杂交、ChIP-qPCR 及EMSA 等实验证实OsARF12、OsARF17、OsARF19、OsARF25、OsZIP26、OsZIP86 及LIC 等转录因子可以直接结合OsSHI1 的启动子，进而调控其表达。遗传分析结果证实，OsZIP86 及LIC 作用于
OsSHI1 上游发挥功能。表明OsSHI1 通过整合不同激素途径过程，协同调控水稻生长及耐逆过程。

Plant growth and adaptation to stresses are determined by genetic and environmental factors, among which the transcriptional regulation and plant hormone pathways play important roles. Therefore, the illumination of the regulatory mechanisms for plant growth and adaptation is of great values for our understanding of plant morphogenesis and the crop yield improvement. In this study, we obtained a rice mutant shi1 with dramatical phenotypic variations, cloned the candidate gene and demonstrated its roles in regulating plant growth and adaptation. The main contents and conclusions are as follows:

1. Regulation of plant architecture

1.1. The shi1 mutant was initially isolated by screening our 9311 60Co irradiation-mutation pool. Compared with the wild type, the tiller numbers of shi1 are significantly reduced. In addition, shi1 mutant has dense and erect panicles accompanied with substantially increased primary and secondary branch numbers, its culm diameters are significantly increased with enhanced lodging resistance and it has shortened and widened dark-green leaves with elevated chlorophyll contents.

1.2. Genetic analysis suggested that the shi1 mutant phenotype was controlled by one recessive nuclear locus. Map-based cloning anchored the mutant locus to a 50 kb region on the long arm of chromosome 9 with 4 ORFs. Sequencing, RT-PCR and western blot analysis revealed that ORF2 was deleted in the shi1 mutant. The genetic complementation and knockout transgenic plants confirmed that ORF2 was indeed responsible for the mutant phenotypes. Sequence analysis revealed that ORF2 encodes a homologous transcription factor of the Arabidopsis short internode (SHI) family with the same C3HC3H zinc finger domain and the SHI family-specific IGGH domain and is referred to as OsSHI1. Transient expression analysis in rice protoplasts showed that OsSHI1-GFP fusion protein was predominantly located in the nucleus. Yeast two-hybrid assays indicated that OsSHI1 exhibits quite weak transcriptional activation activity and can form homodimer via its C terminus. RT-qPCR and western blot analyses validated that both the OsSHI1 mRNA and OsSHI1 protein are mainly expressed in axillary bud and young panicle tissues.

1.3. Yeast two-hybrid screening assay identified IPA1 as an interaction protein of OsSHI1. Further, bimolecular fluorescence complementation (BiFC) and pull-down assays confirmed that OsSHI1 physically interacted with IPA1 both in vitro and in vivo. Two and one putative SHI-recognition T/GCTCTAC motifs were found in the promoter regions of OsTB1 and OsDEP1, respectively, two direct downstream targets of IPA1. Yeast one-hybrid assays and electrophoretic mobility shift assays (EMSA) suggested that OsSHI1 could bind specifically to these motifs. Followingly, Chromatin immunoprecipitation assay (ChIP) assay revealed that OsSHI1 could be specifically recruited to the P3 promoter regions of OsTB1 and OsDEP1.

1.4. RT-qPCR analysis revealed that the expression levels of OsTB1 and OsDEP1 were significantly upregulated in shi1 mutant compared to the wild-type. Transient expression assays in rice protoplasts showed that IPA1 greatly enhanced the transcriptional activity of OsTB1 promoter. However, when co-expressed with OsSHI1, the transcriptional activation activity of IPA1 was significantly repressed. EMSA assays revealed that the binding ability of IPA1 to target probes was repressed gradually by increasing amounts of OsSHI1 protein in the IPA1-DNA reactions. Furthermore, ChIP-qPCR assay with 35S:IPA1-Flag transgenic young seedlings indicated that IPA1-Flag was predominantly enriched to the P3 promoter region of OsTB1. However, due to the presence of excess OsSHI1 protein in Actin1:OsSHI1/35S:IPA1-Flag transgenic young seedlings, the enrichment of IPA1-Flag protein to the P3 promoter region was significantly reduced. Compared with WT, the tiller number of 35S:IPA1-Flag transgenic plants was dramatically reduced due to the excess accumulation of IPA1-Flag proteins which can evidently enhance the OsTB1 expression. In contrast to the repressed tillering of 35S:IPA1-Flag transgenic plants, the Actin1:OsSHI1/35S:IPA1-Flag transgenic plants display obviously reduced plant height and somewhat recovered tillering ability. The expression level of OsTB1 in Actin1:OsSHI1/35S:IPA1-Flag transgenic plants was significantly reduced compared with that in 35S:IPA1-Flag transgenic plants, even though still higher than that in the WT. Taken together, we concluded that OsSHI1 acts antagonistically on IPA1 to regulate plant morphogenesis in rice.

2. Regulation of panicle development

2.1 During the reproductive stage, shi1 exhibits conspicuously abnormal panicle morphology and spikelet development. Panicles of shi1 were erect and compact and in most cases, the apical parts of panicles were aborted before flowering. The arrangement of spikelet in shi1 was obviously disorganized, due to the twisted rachis branches. In addition, most spikelets of shi1 mutant were remarkably smaller and aberrant with crooked lemma and diminished palea, compared with the wild type. Glumes of shi1 were frequently twisted due to the highly compact organization of panicle. Scanning electron microscopy suggests that the development of palea of shi1 was dramatically repressed and the marginal region of palea was significantly enlarged in shi1. The stigmatic tissue of pistils of shi1 was greatly depressed. Stamens of shi1 were normal in appearance but with smaller size and the pollen sterility was significantly reduced. Due to the severe defects of panicle and grain development, the grain yield of shi1 was dramatically reduced. Compared with WT, the grain appearance and nutrition quality of shi1 was substantially compromised.

2.2. RT-qPCR， mmunoblot， histochemical staining and in situ mRNA hybridization assays showed that OsSHI1 is constitutively expressed in each whorl of floral organs. Yeast two-hybrid screening assay identified that OsSHI1 interacts with the class E MADS transcription factors. Further, BiFC and pull-down assays confirmed that OsSHI1 physically interacted with OsMADS1、OsMADS5、OsMADS7、OsMADS8 and OsMADS34 both in vitro and in vivo. We found that the conserved MADS-box domains specified the interactions between OsSHI1 and class E members and mutations of the MADS-box domains almost abolished the interactions between OsSHI1 and all the five class E members.

2.3. OsSHI1 does not affect the expression and protein accumulation levels of MADS transcription factors. However, OsSHI1 regulates the transcriptional activity of OsMADS1 by influent the DNA binding ability of OsMADS1. In addition, various floral organ defects are observed in OsMADS1 overexpression transgenic plants and the expression levels of OsMADS1 direct downstream target genes are increase in both OsMADS1 overexpression transgenic plants and shi1.

2.4 In addition to the variation of floral organ development, panicles of shi1 mutant displayed various degrees of apical panicle abortion from the booting stage, and up to half part of the panicle was aborted at the most severe level. Besides, panicles gradually turn brown towards the mature stage. These phenotypes remind us of the programmed cell death (PCD) caused by the excessive accumulation of reactive oxygen species (ROS). Indeed, RNA-sequencing (RNA-seq) analysis revealed that the most highly enriched gene ontology (GO) terms in the differentially expressed genes (DEG) were involved in oxidation-reduction processes. Expression levels of many peroxidase-encoding genes were dramatically reduced in shi1, which was also confirmed by RT-qPCR analysis. In agreement with RNA-seq result, the contents of endogenous H2O2 and malondialdehyde (MDA, an indicator of ROS production) were obviously increased in the panicle of the shi1 mutant, accompanied with the reduced peroxidase activity.

3. Regulation of plant growth and adaptation

3.1. Besides the above phenotypes, shi1 also exhibites typical hormone related morphological variations. For instance, the lateral root number, gravotropic response and auxin sensitivity of shi1 are reduced (auxin related phenotypes); shi1 displays erect plant architecture, small seeds and reduced BR sensitivity (BR related phenotypes); the germination rate and seedling growth of shi1 are sensitivity to ABA treatment and shi1 is more resistance to drought stress (ABA related phenotypes).

3.2. The auxin and BR contents are significantly reduced in shi1. RT-qPCR analysis showed the the expression levels of OsYUCCAs and D11, two group genes essential for the biosynthesis of auxin and BR, respectively, are decreased in shi1. However, the expression level of OsNAC2, a negative regulator of ABA signaling, is increased in shi1. Yeast one-hybrid, EMSA and ChIP-qPCR assays demonstrated that OsSHI1 binds directly to the promoter regions of these genes. Genetic evidences confirmed that OsSHI1 acts upstream of D11 and OsNAC2 to regulate plant growth and adaptation in rice.

3.3. Exougenous hormone treatment showed that auxin and ABA induce while BR represses the expression level of OsSHI1. Sequence analysis revealed the existence of multiple recognition motifs of ARF, ZIP and LIC transcription factors in the promoter region of OsSHI1. Yeast one-hybrid, EMSA and ChIP-qPCR analyses confirmed the direct binding of OsARF12, OsARF17, OsARF19, OsARF25, OsZIP26, OsZIP86 and LIC to the promoter of OsSHI1. The expression level of OsSHI1 is differentially altered in arf19, zip26, zip86 and lic mutants. Further genetic results validated that OsSHI1 functions downstream of OsZIP86 and LIC. These evidences suggest that OsSHI1 acts as an essential hub to integrate multiple hormone pathways to regulate plant growth and adaptation.

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