http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=April+Cui 2026-08-27T17:45:24Z User contributions MediaWiki 1.30.0 https://ngdc.cncb.ac.cn/ricewiki/index.php?title=IPA1&diff=175425 2014-06-01T06:57:21Z

<p>April Cui: </p> <hr /> <div><br /> 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.<br /> <br /> ==Annotated Information==<br /> <br /> [[File: IPA1 figure 1.png|left|thumb|200px|'''Figure 1''' Figure 1. IPA1 Directly and Positively Regulates the Expression of Os TB1.<br /> (A) IPA1 binding profile in the promoter of Os TB1. The open arrowhead refers to the GTAC around the peak summit and the solid arrowhead to the GTAC around the subsummit. The red vertical line denotes the peak summit. The primer pair Os TB1 Pro (see Supplemental Table 1 online) was used for amplifying the Os TB1 promoter.<br /> (B) Validation of IPA1 direct binding sites in the Os TB1 promoter by ChIP-qPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) EMSA showing that GST-IPA1 could directly bind to the promoter of Os TB1. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition.<br /> (D) Comparison of Os TB1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (E) Suppression of tiller number by tb1/fc1 in RIL-ipa1/tb1 lines. Bar = 20 cm. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File:IPA1 figure 2.png|left|thumb|200px|'''Figure 2'''Figure 2. IPA1 Directly Binds to the DEP1 Promoter.<br /> (A) IPA1 binding profile in the promoter of DEP1. The open arrowhead refers to the GTAC around the peak summit, solid arrowheads to other GTAC sequences around subsummits, and red vertical lines to peak summits. Primer pairs DEP1-Pro1 and DEP1-Pro2 were used for amplifying DEP1 Pro-1 and DEP1 pro-2,respectively.<br /> (B) Validation of IPA1 direct binding sites in the DEP1 promoter by ChIPqPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significance difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) Direct binding of IPA1 to the DEP1 promoter in EMSA. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File:IPA1 figure 3.png|left|thumb|200px|'''Figure 3''' Figure 3. DEP1 Is Positively Regulated by IPA1.<br /> (A) Suppression of plant height by dep1 in RIL-ipa1/dep1 lines. Bar = 20 cm.<br /> (B) Statistical analysis of (A). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences between different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (C) Suppression of panicle length by dep1 in RIL-ipa1/dep1 lines. Bar = 5 cm.<br /> (D) Statistical analysis of (C). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences among different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (E) Expression patterns of IPA1 and DEP1 in different tissues revealed by qPCR analyses. R, roots; C, culms; B, leaf blades; S, leaf sheathes; A, SAs; Y, YPs; M, mature panicles. Rice Ubiquitin was used as reference. Values are means 6 SE (n = 3).<br /> (F) Comparison of DEP1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> ===Function===<br /> ==== IPA1 Suppresses Rice Tillering Mainly through Positive Regulation of Os TB1 ====<br /> <br /> Os TB1 acts as a negative regulator of rice tillering (Takeda et al., 2003; Minakuchi et al.,<br /> 2010) and that Os TB1 is a potential direct target of IPA1. The peak summits for IPA1 binding sites were located 96 and 187 bp upstream of the Os TB1 TSS in the two YP replicates, respectively.However, the Os TB1 promoter was significantly enriched in both SAs and YPs by the ChIP-qPCR analysis, indicating that Os TB1 is probably under the control of IPA1 in both tissues (Figure 1B). Further analysis of binding peaks revealed that the GTAC motif, rather than the TGGGCC/T motif, existed in the Os TB1 promoter. To test whether IPA1 can directly bind to the GTAC motif in the Os TB1 promoter, we performed an EMSA assay and found that GST-IPA1 could bind to a 59-bp probe from the Os TB1 promoter (Figure 1C). The mutation of GTAC to ATAC abolished its binding<br /> affinity, demonstrating that the binding was dependent on the GTAC motif. As a negative regulator in rice tiller development, Os TB1 is expressed in axillary buds, and its deficiency results in a semidwarf phenotype with a significant increase in tiller number (Takeda et al., 2003; Minakuchi et al., 2010). This suggests that the reduced tiller phenotype of ipa1 plants may result from the direct activation of Os TB1 by IPA1. The RNA level of Os TB1 was significantly upregulated in SAs in NIL-ipa1, but much less significantly in YPs (Figure 1 D). Furthermore, the double mutant analysis showed that the mutation of Os TB1 could suppress the tillering phenotype of ipa1 (Figure 1E). Since Os TB1 is homologous to PCF1 and PCF2, we tested whether Os TB1 could also interact with IPA1. A weak interaction was detected in the yeast two-hybrid assay , and EMSA further showed that Os TB1 could directly bind the TGGGCC/T motif,<br /> indicating that Os TB1 also functions as an adaptor for the interaction between IPA1 and the TGGGCC/T motif. Considering that Os TB1 is not only a target of IPA1, but also can interact with IPA1, we propose that Os TB1 is probably involved in the feedback regulation of IPA1 transcriptional activity.<br /> <br /> ====Increased Plant Height and Panicle Branches ====<br /> <br /> DEP1 is another important regulatory gene that affects rice architecture, especially panicle morphology. A truncated mutation of DEP1 enhances panicle meristematic activity, resulting in reduced length of inflorescence internodes, increased number of grains per panicle, and a consequent increase in grain yield (Huang et al., 2009). IPA1 ChIP-seq analysis revealed that DEP1<br /> was also a direct target of IPA1 . The peak summits of IPA1 binding were located 566, 514, 440, and 500 bp upstream of the DEP1 TSS in SA rep 1, SA rep 2, YP rep 1, and YP rep 2, respectively (Figure 2A). Within the peaks in the DEP1 promoter, besides the highest peak summit, there are other two subsummits showing local max sequencing reads (Figure 2A). Through analyzing the DEP1 promoter sequence, several GTAC motifs were found, and three sites around the peak summits and subsummits were considered to be responsible for the binding of IPA1. To confirm this, ChIP-qPCR was performed. As shown in Figure 2B, the two specific regions were significantly enriched. We then tested whether IPA1 could directly bind to the promoter of DEP1 by EMSA with three 59-bp sequences around the peak summit and subsummits as probes and found that IPA1 could bind to all the three probes but could not bind to a probe containing the mutated binding core motif (Figure 2C). These results demonstrate that IPA1 can directly bind to the promoter of DEP1 at different sites and the GTAC core motifs are responsible for IPA1 binding, suggesting that DEP1 is a direct target of IPA1. To further understand the biological functions of DEP1 as a direct target of IPA1, we generated recombinant inbred lines by crossing Ri22, an ipa1-carrying cultivar (Jiao et al., 2010), with LJ5, a rice variety carrying the dep1 mutation (Huang et al.2009). As shown in Figures 3A and3B, the plant height of the RIL-ipa1/dep1 lines was reduced to a similar level to the RIL-IPA1/dep1 lines. Consistent with the previous result that dep1 does not affect rice tillering, the tiller number of RIL-ipa1/dep1 lines exhibited no significant difference from RIL-ipa1/DEP1 lines. We also noticed that the panicle morphology of the RIL-ipa1/dep1 lines was dense and erect (Figures 3C and 3D). Compared with the RIL-ipa1/DEP1 lines, the panicle length of RIL-ipa1/dep1 lines was significantly reduced, but no obvious change in panicle branches was found. Like IPA1, DEP1 was also strongly expressed in culms, SAs, and YPs, but weakly in roots (Figure 3E), suggesting that IPA1 may regulate the expression of DEP1. We further examined the expression of DEP1 in NIL-ipa1 lines and found that DEP1 transcripts were significantly increased in the SA of NIL-ipa1 lines, but only slightly in YP (Figure 3F). Therefore, it is likely that IPA1 functions as a positive regulator of DEP1 in regulating plant height and panicle length in rice. <br /> <br /> ===Protein===<br /> 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 (from reference&lt;ref name=&quot;ref2&quot; /&gt;).<br /> <br /> 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). Therefore, it has been suggested that Os SPL14 alleles have great potential for breeding (Jiao et al., 2010; Miura et al., 2010).<br /> <br /> ==Labs working on this gene==<br /> State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Zefu Lu, Hong Yu, Yonghong Wang, Jiayang Li)<br /> State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China(Xingming Hu, Qian Qian)<br /> State Key Laboratory of Plant Cell and Chromosome Engineering and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Xiangdong Fu)<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li .Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture. The Plant Cell, 2013, 25(10): 3743-3759&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Yongqing Jiao, Yonghong Wang, Dawei Xue, Jing Wang, Meixian Yan, Guifu Liu, Guojun Dong, Dali Zeng, Zefu Lu, Xudong Zhu, Qian Qian, Jiayang Li. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice .Nature Genetics, 2010, 42(6): 541-544&lt;/ref&gt;<br /> <br /> ==Structured Information==<br /> <br /> LOCUS GU136674 7229 bp DNA linear PLN 29-JUN-2010<br /> DEFINITION Oryza sativa Japonica Group IPA1 (IPA1) gene, complete cds.<br /> ACCESSION GU136674<br /> VERSION GU136674.1 GI:299482811<br /> KEYWORDS .<br /> SOURCE Oryza sativa (rice)<br /> ORGANISM Oryza sativa<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> REFERENCE 1 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Xue,D., Wang,J., Yan,M., Liu,G., Dong,G.,<br /> Zeng,D., Lu,Z., Zhu,X., Qian,Q. and Li,J.<br /> TITLE Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture<br /> in rice<br /> JOURNAL Nat. Genet. 42 (6), 541-544 (2010)<br /> PUBMED 20495565<br /> REFERENCE 2 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Qian,Q. and Li,J.<br /> TITLE Direct Submission<br /> JOURNAL Submitted (22-OCT-2009) State Key Laboratory of Plant Genomics and<br /> National Center for Plant Gene Research, Institute of Genetics and<br /> Developmental Biology, Chinese Academy of Sciences, No.1 West<br /> Beichen Road, Chaoyang District, Beijing 100101, China<br /> FEATURES Location/Qualifiers<br /> source 1..7229<br /> /organism=&quot;Oryza sativa&quot;<br /> /mol_type=&quot;genomic DNA&quot;<br /> /db_xref=&quot;taxon:4530&quot;<br /> /chromosome=&quot;8&quot;<br /> /map=&quot;RM149-RM1345&quot;<br /> gene 995..5150<br /> /gene=&quot;IPA1&quot;<br /> mRNA join(995..1566,3997..4130,4233..5150)<br /> /gene=&quot;IPA1&quot;<br /> /product=&quot;IPA1&quot;<br /> CDS join(1118..1566,3997..4130,4233..4903)<br /> /gene=&quot;IPA1&quot;<br /> /note=&quot;transcription factor&quot;<br /> /codon_start=1<br /> /product=&quot;IPA1&quot;<br /> /protein_id=&quot;ADJ19220.1&quot;<br /> /db_xref=&quot;GI:299482812&quot;<br /> /translation=&quot;MEMASGGGAAAAAGGGVGGSGGGGGGGDEHRQLHGLKFGKKIYF<br /> EDAAAAAGGGGTGSGSGSASAAPPSSSSKAAGGGRGGGGKNKGKGVAAAAPPPPPPPP<br /> RCQVEGCGADLSGIKNYYCRHKVCFMHSKAPRVVVAGLEQRFCQQCSRFHLLPEFDQG<br /> KRSCRRRLAGHNERRRRPQTPLASRYGRLAASVGEHRRFRSFTLDFSYPRVPSSVRNA<br /> WPAIQPGDRISGGIQWHRNVAPHGHSSAVAGYGANTYSGQGSSSSGPPVFAGPNLPPG<br /> GCLAGVGAATDSSCALSLLSTQPWDTTTHSAAASHNQAAAMSTTTSFDGNPVAPSAMA<br /> GSYMAPSPWTGSRGHEGGGRSVAHQLPHEVSLDEVHPGPSHHAHFSGELELALQGNGP<br /> APAPRIDPGSGSTFDQTSNTMDWSL&quot;<br /> ORIGIN <br /> 1 gcaatgtaga gccacgtagg caagtcgctt gcgtggagga gagaggggag tggggaccgt<br /> 61 tcccaaccca gcttcgtgtg accaagtttg gccacacggg ccaaacgaac ctcagcaact<br /> 121 tttgtcagaa agaaaagaac ctccgcgaga aacaagaaag cgagagaggg agagaaagga<br /> 181 ggctcgtcgg agtaggggcg ctcggggtat ggggctcggc ggaggctcgc tggagtaggg<br /> 241 gccgccactg cgtggggctc gccggagtag gggcgctcgg ggagcctccc gagatccgcc<br /> 301 gctcagcggc gccgccgtct tccgggcaga gctctcgaag ctcgccctcc tcgcgcgccg<br /> 361 gtggcgttgg cggggcccgc gtgtggctac gcagctccgg tgctgcgcct ccaccgtcga<br /> 421 cgacagcgcc gcttggcgct gccgccgtct tccgccgcgc cgctggacgc cgccagatct<br /> 481 gctgctcgtc gccgcgtggg ccgctccacc cggttggagg aggagaggcg gcgccgcgct<br /> 541 tgggctgccc caccgccgag ctctgccgcg ccgttcgccg gtgctgccga gctccgccgc<br /> 601 gcctgccgga gcacgctgcc atggccgccc tggagaagac acgagagaat taggtggagg<br /> 661 gtgggggaag ggtgagattt tttatattat ctatgggtcc cattataaat tttctaaacc<br /> 721 acacttatac tgtgggtgca gtgtcattta gagttcccaa accacctatg ttgcagctgt<br /> 781 ggtataacaa tttgctagga cgcattgcta ctgcccttgt accctgctat aagaagataa<br /> 841 ccaatgacat ctccactcga ttttctcggc gcgcgtgtga gggtgtgagg ataattttta<br /> 901 ttttaagtgg tttttaaggg cggagagaga gagagagaga gggcaccgca ctacttctac<br /> 961 ttgtgtgtgt gtcgctcgct gggcttcgcc acctttccgt ctctttcctc tctcttctct<br /> 1021 ctccccctct cctggaggag agagaggaga agaggagggg gggccgcgcc aagagccacg<br /> 1081 cgcgctacag tctccttccc acccgcgacc gcgagcaatg gagatggcca gtggaggagg<br /> 1141 cgccgccgcc gccgccggcg gcggagtagg cggcagcggc ggcggtggtg gtggagggga<br /> 1201 cgagcaccgc cagctgcacg gtctcaagtt cggcaagaag atctacttcg aggacgccgc<br /> 1261 cgcggcagca ggcggcggcg gcactggcag tggcagtggc agcgcgagcg ccgcgccgcc<br /> 1321 gtcctcgtct tccaaggcgg cgggtggtgg acgcggcgga gggggcaaga acaaggggaa<br /> 1381 gggcgtggcc gcggcggcgc caccgccgcc gccgccgccg ccgcggtgcc aggtggaggg<br /> 1441 gtgcggcgcg gatctgagcg ggatcaagaa ctactactgc cgccacaagg tgtgcttcat<br /> 1501 gcattccaag gctccccgcg tcgtcgtcgc cggcctcgag cagcgcttct gccagcagtg<br /> 1561 cagcaggtca ctctctcact cacctcgcca ttgctgatgt caccactgct tttgctttgc<br /> 1621 tttgcttgct ctccctcctc tttcacctat ctctcttgtt tatttgcttc ttgttcttgt<br /> 1681 ttagtgctag tacatgtgtt gttattgttg tgccgttttg tcttttgggt tattgtgttg<br /> 1741 ttgttactac tcgttttact ataggttttt aaggtttatg agcacggcca ccacattaga<br /> 1801 tgcactgtca agtggtgtgt gtgggacctt tcctgctaaa acaagctgat ttcaactctc<br /> 1861 tgaaacttcc tgcatttcat ctatttttat ctttgattgt gttgggagta ctacactagt<br /> 1921 agtgttaata ttttgactgg tgcttatgag atttttaagt tggtaggttg atgaggaaaa<br /> 1981 tactccttta tatggttgag tgatgtgact tgcctgtctg cctgcctgcc tgccgctttg<br /> 2041 cataagattc ctctgtgtta gtaagagcca ctgtttattt gtactggtgc ttactctact<br /> 2101 tagttaatta gccattagct ataaaattcc gttgatgttg caagcttagc aatggccacg<br /> 2161 gtaagaatgg gagagagaag ttggctaaag ctgttgcttt gtagtttgta ctatatatgt<br /> 2221 gtctttgtgt tgcaagatat gcaactccta ctatgctgtg acttgagctc aaggttttca<br /> 2281 gttatctata gatccttact actactgagc atactaccac ttctgtatgg tagcatatgg<br /> 2341 tagcatagtc caagttccaa cgcctcgcca gttgttcata atctatacta ccacttctgt<br /> 2401 gcatttgtta cttttattta atagtttgtc tcattagctg acaagcatat gcctgttttg<br /> 2461 atatctgccc ctcttgtaat agtctatgga tagcttggac tgtttgatgc tttaattttt<br /> 2521 tactagcaac acttagggcc cctttgaaat ggaggattag caaaggaatt ttggaggatt<br /> 2581 cattttccta aggatttttt cctatagagc cctttgattc atagaaagag gataggaaaa<br /> 2641 cttccgtagg attgcattcc tatgatcaat tccataggaa aataagcaag aggttagacc<br /> 2701 tcttgtgaaa ctttcctttg ttgagtgtat cttgtggtat aatcaaaggg ctcttctctc<br /> 2761 catttcatgt gttttcaatt cctgtaggat tggaaaaaca tacaacttca attcctacgt<br /> 2821 ttttcctatt cctatgtttt tcctatcctg cgtttcaaag gggcccttaa ggatgaaggg<br /> 2881 aagtaagaga aacatactag agaatatgta gtagtatttc tacattccat atttgtagca<br /> 2941 ctagcccaca aatatctttg ccttgtactt acttcatacc agttcccccc ttttcagagc<br /> 3001 aaaccaacaa tttctgttgc cttatatatc tagtgtcttc gtactaatat atctgttcca<br /> 3061 aaatgtacct gtccaaattc atagctagaa atagctttat ttaggacgga agtaataact<br /> 3121 gttgttagag acttggttca gacttttggt tatgttgagg ctactatcat ttcctttacg<br /> 3181 ggccaaatta ctacaaatga gaattcataa aaatgtcaag attttatgat tgttgtagct<br /> 3241 ttatttagga cggaggtagt aattgttgtt agagacttgg ttcagacttt tggttacgtt<br /> 3301 gaagctacta tcatttcctt tatggtcaaa ttactaacaa tgagtattca taaaaatgtc<br /> 3361 aagattttat aattgagctg tgccagtgct aagtgtgtca ctatctgatg ccataatgca<br /> 3421 tcattataaa agccagatgg accattagct tttatgtgta ggacacctgc cgtccaatta<br /> 3481 gatggataac catctagtgt ttgtgtactg ttattttaag cccgacatct cacaactcca<br /> 3541 tgaatgatta cagtcttcct ttcacatggt gtccttttgt tgtgttagga atagcatttt<br /> 3601 ttatttatgg gtgtaattat gaaaggcact aggagagttg ctgctttatc ttgatgggat<br /> 3661 ttgtagtaat accatcttta ggatgacaag aaatcttgtt ctgagttagc atgggctgcc<br /> 3721 ttttgacctg agctacggtt tgctatgttt ggcttgcatc atgcagatct attaggataa<br /> 3781 taagcatata aaagttgctt gcattgtgca ttgcttgttt taccttgatt catgtaggag<br /> 3841 taatttgctc gccatgcctc gttttgcttt ctgagtcaac agccaaattt agatgatgta<br /> 3901 ccttctgttg cttcaaaaac tcagtcactg cacagcagca gtggatagga ttcagaatca<br /> 3961 atctatccat gattctctgt tcacataata tgacaggttc cacctgctgc ctgaatttga<br /> 4021 ccaaggaaaa cgcagctgcc gcagacgcct tgcaggtcat aatgagcgcc ggaggaggcc<br /> 4081 gcaaacccct ttggcatcac gctacggtcg actagctgca tctgttggtg gtatcatcag<br /> 4141 aggctcttgt tttctttgca tcttgtgtgt ttgttggtaa ctactggttg cattcgctga<br /> 4201 tgtgttgttt gttgcgattc ttgatccaga agagcatcgc aggttcagaa gctttacgtt<br /> 4261 ggatttctcc tacccaaggg ttccaagcag cgtaaggaat gcatggccag caattcaacc<br /> 4321 aggcgatcgg atctccggtg gtatccagtg gcacaggaac gtagctcctc atggtcactc<br /> 4381 tagtgcagtg gcgggatatg gtgccaacac atacagcggc caaggtagct cttcttcagg<br /> 4441 gccaccggtg ttcgctggcc caaatctccc tccaggtgga tgtctcgcag gggtcggtgc<br /> 4501 cgccaccgac tcgagctgtg ctctctctct tctgtcaacc cagccatggg atactactac<br /> 4561 ccacagtgcc gctgccagcc acaaccaggc tgcagccatg tccactacca ccagctttga<br /> 4621 tggcaatcct gtggcaccct ccgccatggc gggtagctac atggcaccaa gcccctggac<br /> 4681 aggttctcgg ggccatgagg gtggtggtcg gagcgtggcg caccagctac cacatgaagt<br /> 4741 ctcacttgat gaggtgcacc ctggtcctag ccatcatgcc cacttctccg gtgagcttga<br /> 4801 gcttgctctg caggggaacg gtccagcccc agcaccacgc atcgatcctg ggtccggcag<br /> 4861 caccttcgac caaaccagca acacgatgga ttggtctctg tagaggctgt tccagctgcc<br /> 4921 atcgatctgt cgtcccgcaa ggcgagtcat ggaactgaag aacctcatgc tgcctgccct<br /> 4981 tattttgtgt tcaaattttc ctttccagta tggaaaggaa attctaaggt gactggcgat<br /> 5041 taatctccct gtgatgaata ataatgcgcg cccttgaact caattaattg ctgtgccgca<br /> 5101 tccatctatg taactctcca tgaattttta agtatcagtg ttaatgctgt attgtcgagg<br /> 5161 acttctgctc gatatgttat ttctcttatg ttgttcatca tgaatctttt tctgcttatt<br /> 5221 attctggtgc cgggttgtcc ttaccacaga agattcagtt tcggttggcg agagtaaaca<br /> 5281 ccttccctgg ttgtgacaaa agctccaacc ttttcacttc tcggcctgta tttgatcttc<br /> 5341 cccttctgac gctgttatac tacttttaag cctgtatgtt tccagccttc caggtgaagg<br /> 5401 gccatactga agagaaaaca tgctttcagg gtttgatgca ttgtgtactt tacaagtgta<br /> 5461 cttaagattt tgtacaattt atatatgtac ctgctctgct gctgagtatt gtaggaaaga<br /> 5521 atcagttcga agggcgtgtg ttcatgtaaa gtgagaccac atgcacagcg tggatttgca<br /> 5581 gcatgctctc tgcaccagtg gtgttctgtt gatgcctttg atgggctggc tgaggtgaga<br /> 5641 ggaggatgat ccatgttggc agcttcttca ctctgaaaaa taaaagagaa gaaatgttca<br /> 5701 gatttgcaga caagtggaga gcagtgatat attctacaat aaaacattac caccttgctt<br /> 5761 ttctgtgatg atagatactc catggaattt tgcatcaagc atctcttgtt ttccagccac<br /> 5821 tgtttgctgg gttgttgctt caatttcgtc ccaattgatt ggtcaccttt ggttgtgact<br /> 5881 tgagagcact gagcactgaa acttttgctg tcagcaggca atgcacctca tccatgtcac<br /> 5941 gacagaggga gagagcccac ataaatggcc aaagaggaca catacagtgg cactgatgca<br /> 6001 gtcattgcaa cataattgac atcatgctaa acagtggtgt aaccatatgt tagctagcct<br /> 6061 gtgatcagca aacagtgatt atggatctta atgtcacatg caagatttga cacagttgta<br /> 6121 aaaccatcat tgcattgaag atagatccca gcaacaggtg tatgatgtat tgctagaatg<br /> 6181 aatcaaaaat atcagtgcca tcctaaacac agtactacca acttgaacag ttatcaccgt<br /> 6241 gattggaaaa cagaaatgta taattgcttt ggcgccatct gcttatcatt atcatatgtc<br /> 6301 gcagatcact tgttccattg acacgactct ttttcactgt gaggagaggc accttgattt<br /> 6361 ggacttttca agagctgtag caagggctcc tttgaagcct tctacatgga ggagcagagc<br /> 6421 ataccatatg cagaactgta aactcttcct gaagctttcc agttccaccc ttgtagcttt<br /> 6481 aagctgccgc aagagaatta tcatttctaa cattgagatg tgatactgaa atgtgaaagg<br /> 6541 tgattcgcag tataggtccc aaaatatcgt ttacagcaac ttgcaaatcc tgcatgatac<br /> 6601 agttaattca tcaaaatatt agaccattag tactacagtc tacaaatacc ccttaactga<br /> 6661 acatgtatga taaggacaag attctgaagc tccagtgcat caggaatcca acgcagtatg<br /> 6721 caaatcatta ctgaacaaga ttcctgcact tacagaatca tcacctgttg taacaaggac<br /> 6781 cattctttgt tgccccagac acagcgaatt aatggtcatc ttcatttggc ccaggacatt<br /> 6841 catttgccaa tgcttctgct gattcatact gaaaagggga caatgcgtcc aattttaaaa<br /> 6901 gcatggaaga tgctataaaa gatcacccta tttaaaatgc agagaaaacc aaagatccaa<br /> 6961 catgatatgg taatcacaga ttcccaacag taatgccgtc cagtaggcag taggggcatg<br /> 7021 cacataaaca ctagtactat gtagagctga agcttatttc cagaatgaag ctgaccttgc<br /> 7081 aaccgcaata aaggcaatag tagtgttcat cgcgcagctt agccaatata ttttgcaaat<br /> 7141 cctgcaagaa taaacacagg tcaatctcgt cctttcagca aaatttgcag tcttgcataa<br /> 7201 gatttctcag ataaaaaagg aagtctaga<br /> //</div>

April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=IPA1&diff=175412 2014-06-01T06:48:24Z

<p>April Cui: </p> <hr /> <div><br /> 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.<br /> <br /> ==Annotated Information==<br /> <br /> [[File: IPA1 figure 1.png|left|thumb|200px|'''Figure 1''' Figure 1. IPA1 Directly and Positively Regulates the Expression of Os TB1.<br /> (A) IPA1 binding profile in the promoter of Os TB1. The open arrowhead refers to the GTAC around the peak summit and the solid arrowhead to the GTAC around the subsummit. The red vertical line denotes the peak summit. The primer pair Os TB1 Pro (see Supplemental Table 1 online) was used for amplifying the Os TB1 promoter.<br /> (B) Validation of IPA1 direct binding sites in the Os TB1 promoter by ChIP-qPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) EMSA showing that GST-IPA1 could directly bind to the promoter of Os TB1. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition.<br /> (D) Comparison of Os TB1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (E) Suppression of tiller number by tb1/fc1 in RIL-ipa1/tb1 lines. Bar = 20 cm. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File:IPA1 figure 2.png|left|thumb|200px|'''Figure 2'''Figure 2. IPA1 Directly Binds to the DEP1 Promoter.<br /> (A) IPA1 binding profile in the promoter of DEP1. The open arrowhead refers to the GTAC around the peak summit, solid arrowheads to other GTAC sequences around subsummits, and red vertical lines to peak summits. Primer pairs DEP1-Pro1 and DEP1-Pro2 were used for amplifying DEP1 Pro-1 and DEP1 pro-2,respectively.<br /> (B) Validation of IPA1 direct binding sites in the DEP1 promoter by ChIPqPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significance difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) Direct binding of IPA1 to the DEP1 promoter in EMSA. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File:IPA1 figure 3.png|left|thumb|200px|'''Figure 3''' Figure 3. DEP1 Is Positively Regulated by IPA1.<br /> (A) Suppression of plant height by dep1 in RIL-ipa1/dep1 lines. Bar = 20 cm.<br /> (B) Statistical analysis of (A). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences between different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (C) Suppression of panicle length by dep1 in RIL-ipa1/dep1 lines. Bar = 5 cm.<br /> (D) Statistical analysis of (C). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences among different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (E) Expression patterns of IPA1 and DEP1 in different tissues revealed by qPCR analyses. R, roots; C, culms; B, leaf blades; S, leaf sheathes; A, SAs; Y, YPs; M, mature panicles. Rice Ubiquitin was used as reference. Values are means 6 SE (n = 3).<br /> (F) Comparison of DEP1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> ===Function===<br /> ==== IPA1 Suppresses Rice Tillering Mainly through Positive Regulation of Os TB1 ====<br /> <br /> Os TB1 acts as a negative regulator of rice tillering (Takeda et al., 2003; Minakuchi et al.,<br /> 2010) and that Os TB1 is a potential direct target of IPA1. The peak summits for IPA1 binding sites were located 96 and 187 bp upstream of the Os TB1 TSS in the two YP replicates, respectively.However, the Os TB1 promoter was significantly enriched in both SAs and YPs by the ChIP-qPCR analysis, indicating that Os TB1 is probably under the control of IPA1 in both tissues (Figure 1B). Further analysis of binding peaks revealed that the GTAC motif, rather than the TGGGCC/T motif, existed in the Os TB1 promoter. To test whether IPA1 can directly bind to the GTAC motif in the Os TB1 promoter, we performed an EMSA assay and found that GST-IPA1 could bind to a 59-bp probe from the Os TB1 promoter (Figure 1C). The mutation of GTAC to ATAC abolished its binding<br /> affinity, demonstrating that the binding was dependent on the GTAC motif. As a negative regulator in rice tiller development, Os TB1 is expressed in axillary buds, and its deficiency results in a semidwarf phenotype with a significant increase in tiller number (Takeda et al., 2003; Minakuchi et al., 2010). This suggests that the reduced tiller phenotype of ipa1 plants may result from the direct activation of Os TB1 by IPA1. The RNA level of Os TB1 was significantly upregulated in SAs in NIL-ipa1, but much less significantly in YPs (Figure 1 D). Furthermore, the double mutant analysis showed that the mutation of Os TB1 could suppress the tillering phenotype of ipa1 (Figure 1E). Since Os TB1 is homologous to PCF1 and PCF2, we tested whether Os TB1 could also interact with IPA1. A weak interaction was detected in the yeast two-hybrid assay , and EMSA further showed that Os TB1 could directly bind the TGGGCC/T motif,<br /> indicating that Os TB1 also functions as an adaptor for the interaction between IPA1 and the TGGGCC/T motif. Considering that Os TB1 is not only a target of IPA1, but also can interact with IPA1, we propose that Os TB1 is probably involved in the feedback regulation of IPA1 transcriptional activity.<br /> <br /> ====Increased Plant Height and Panicle Branches ====<br /> <br /> DEP1 is another important regulatory gene that affects rice architecture, especially panicle morphology. A truncated mutation of DEP1 enhances panicle meristematic activity, resulting in reduced length of inflorescence internodes, increased number of grains per panicle, and a consequent increase in grain yield (Huang et al., 2009). IPA1 ChIP-seq analysis revealed that DEP1<br /> was also a direct target of IPA1 . The peak summits of IPA1 binding were located 566, 514, 440, and 500 bp upstream of the DEP1 TSS in SA rep 1, SA rep 2, YP rep 1, and YP rep 2, respectively (Figure 2A). Within the peaks in the DEP1 promoter, besides the highest peak summit, there are other two subsummits showing local max sequencing reads (Figure 2A). Through analyzing the DEP1 promoter sequence, several GTAC motifs were found, and three sites around the peak summits and subsummits were considered to be responsible for the binding of IPA1. To confirm this, ChIP-qPCR was performed. As shown in Figure 2B, the two specific regions were significantly enriched. We then tested whether IPA1 could directly bind to the promoter of DEP1 by EMSA with three 59-bp sequences around the peak summit and subsummits as probes and found that IPA1 could bind to all the three probes but could not bind to a probe containing the mutated binding core motif (Figure 2C). These results demonstrate that IPA1 can directly bind to the promoter of DEP1 at different sites and the GTAC core motifs are responsible for IPA1 binding, suggesting that DEP1 is a direct target of IPA1. To further understand the biological functions of DEP1 as a direct target of IPA1, we generated recombinant inbred lines by crossing Ri22, an ipa1-carrying cultivar (Jiao et al., 2010), with LJ5, a rice variety carrying the dep1 mutation (Huang et al.2009). As shown in Figures 3A and3B, the plant height of the RIL-ipa1/dep1 lines was reduced to a similar level to the RIL-IPA1/dep1 lines. Consistent with the previous result that dep1 does not affect rice tillering, the tiller number of RIL-ipa1/dep1 lines exhibited no significant difference from RIL-ipa1/DEP1 lines. We also noticed that the panicle morphology of the RIL-ipa1/dep1 lines was dense and erect (Figures 3C and 3D). Compared with the RIL-ipa1/DEP1 lines, the panicle length of RIL-ipa1/dep1 lines was significantly reduced, but no obvious change in panicle branches was found. Like IPA1, DEP1 was also strongly expressed in culms, SAs, and YPs, but weakly in roots (Figure 3E), suggesting that IPA1 may regulate the expression of DEP1. We further examined the expression of DEP1 in NIL-ipa1 lines and found that DEP1 transcripts were significantly increased in the SA of NIL-ipa1 lines, but only slightly in YP (Figure 3F). Therefore, it is likely that IPA1 functions as a positive regulator of DEP1 in regulating plant height and panicle length in rice. <br /> <br /> ===Protein===<br /> 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).<br /> <br /> 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). Therefore, it has been suggested that Os SPL14 alleles have great potential for breeding (Jiao et al., 2010; Miura et al., 2010).<br /> <br /> ==Labs working on this gene==<br /> State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Zefu Lu, Hong Yu, Yonghong Wang, Jiayang Li)<br /> State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China(Xingming Hu, Qian Qian)<br /> State Key Laboratory of Plant Cell and Chromosome Engineering and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Xiangdong Fu)<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li .Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture. The Plant Cell, 2013, 25(10): 3743-3759&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Yongqing Jiao, Yonghong Wang, Dawei Xue, Jing Wang, Meixian Yan, Guifu Liu, Guojun Dong, Dali Zeng, Zefu Lu, Xudong Zhu, Qian Qian, Jiayang Li. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice .Nature Genetics, 2010, 42(6): 541-544&lt;/ref&gt;<br /> <br /> ==Structured Information==<br /> <br /> LOCUS GU136674 7229 bp DNA linear PLN 29-JUN-2010<br /> DEFINITION Oryza sativa Japonica Group IPA1 (IPA1) gene, complete cds.<br /> ACCESSION GU136674<br /> VERSION GU136674.1 GI:299482811<br /> KEYWORDS .<br /> SOURCE Oryza sativa (rice)<br /> ORGANISM Oryza sativa<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> REFERENCE 1 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Xue,D., Wang,J., Yan,M., Liu,G., Dong,G.,<br /> Zeng,D., Lu,Z., Zhu,X., Qian,Q. and Li,J.<br /> TITLE Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture<br /> in rice<br /> JOURNAL Nat. Genet. 42 (6), 541-544 (2010)<br /> PUBMED 20495565<br /> REFERENCE 2 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Qian,Q. and Li,J.<br /> TITLE Direct Submission<br /> JOURNAL Submitted (22-OCT-2009) State Key Laboratory of Plant Genomics and<br /> National Center for Plant Gene Research, Institute of Genetics and<br /> Developmental Biology, Chinese Academy of Sciences, No.1 West<br /> Beichen Road, Chaoyang District, Beijing 100101, China<br /> FEATURES Location/Qualifiers<br /> source 1..7229<br /> /organism=&quot;Oryza sativa&quot;<br /> /mol_type=&quot;genomic DNA&quot;<br /> /db_xref=&quot;taxon:4530&quot;<br /> /chromosome=&quot;8&quot;<br /> /map=&quot;RM149-RM1345&quot;<br /> gene 995..5150<br /> /gene=&quot;IPA1&quot;<br /> mRNA join(995..1566,3997..4130,4233..5150)<br /> /gene=&quot;IPA1&quot;<br /> /product=&quot;IPA1&quot;<br /> CDS join(1118..1566,3997..4130,4233..4903)<br /> /gene=&quot;IPA1&quot;<br /> /note=&quot;transcription factor&quot;<br /> /codon_start=1<br /> /product=&quot;IPA1&quot;<br /> /protein_id=&quot;ADJ19220.1&quot;<br /> /db_xref=&quot;GI:299482812&quot;<br /> /translation=&quot;MEMASGGGAAAAAGGGVGGSGGGGGGGDEHRQLHGLKFGKKIYF<br /> EDAAAAAGGGGTGSGSGSASAAPPSSSSKAAGGGRGGGGKNKGKGVAAAAPPPPPPPP<br /> RCQVEGCGADLSGIKNYYCRHKVCFMHSKAPRVVVAGLEQRFCQQCSRFHLLPEFDQG<br /> KRSCRRRLAGHNERRRRPQTPLASRYGRLAASVGEHRRFRSFTLDFSYPRVPSSVRNA<br /> WPAIQPGDRISGGIQWHRNVAPHGHSSAVAGYGANTYSGQGSSSSGPPVFAGPNLPPG<br /> GCLAGVGAATDSSCALSLLSTQPWDTTTHSAAASHNQAAAMSTTTSFDGNPVAPSAMA<br /> GSYMAPSPWTGSRGHEGGGRSVAHQLPHEVSLDEVHPGPSHHAHFSGELELALQGNGP<br /> APAPRIDPGSGSTFDQTSNTMDWSL&quot;<br /> ORIGIN <br /> 1 gcaatgtaga gccacgtagg caagtcgctt gcgtggagga gagaggggag tggggaccgt<br /> 61 tcccaaccca gcttcgtgtg accaagtttg gccacacggg ccaaacgaac ctcagcaact<br /> 121 tttgtcagaa agaaaagaac ctccgcgaga aacaagaaag cgagagaggg agagaaagga<br /> 181 ggctcgtcgg agtaggggcg ctcggggtat ggggctcggc ggaggctcgc tggagtaggg<br /> 241 gccgccactg cgtggggctc gccggagtag gggcgctcgg ggagcctccc gagatccgcc<br /> 301 gctcagcggc gccgccgtct tccgggcaga gctctcgaag ctcgccctcc tcgcgcgccg<br /> 361 gtggcgttgg cggggcccgc gtgtggctac gcagctccgg tgctgcgcct ccaccgtcga<br /> 421 cgacagcgcc gcttggcgct gccgccgtct tccgccgcgc cgctggacgc cgccagatct<br /> 481 gctgctcgtc gccgcgtggg ccgctccacc cggttggagg aggagaggcg gcgccgcgct<br /> 541 tgggctgccc caccgccgag ctctgccgcg ccgttcgccg gtgctgccga gctccgccgc<br /> 601 gcctgccgga gcacgctgcc atggccgccc tggagaagac acgagagaat taggtggagg<br /> 661 gtgggggaag ggtgagattt tttatattat ctatgggtcc cattataaat tttctaaacc<br /> 721 acacttatac tgtgggtgca gtgtcattta gagttcccaa accacctatg ttgcagctgt<br /> 781 ggtataacaa tttgctagga cgcattgcta ctgcccttgt accctgctat aagaagataa<br /> 841 ccaatgacat ctccactcga ttttctcggc gcgcgtgtga gggtgtgagg ataattttta<br /> 901 ttttaagtgg tttttaaggg cggagagaga gagagagaga gggcaccgca ctacttctac<br /> 961 ttgtgtgtgt gtcgctcgct gggcttcgcc acctttccgt ctctttcctc tctcttctct<br /> 1021 ctccccctct cctggaggag agagaggaga agaggagggg gggccgcgcc aagagccacg<br /> 1081 cgcgctacag tctccttccc acccgcgacc gcgagcaatg gagatggcca gtggaggagg<br /> 1141 cgccgccgcc gccgccggcg gcggagtagg cggcagcggc ggcggtggtg gtggagggga<br /> 1201 cgagcaccgc cagctgcacg gtctcaagtt cggcaagaag atctacttcg aggacgccgc<br /> 1261 cgcggcagca ggcggcggcg gcactggcag tggcagtggc agcgcgagcg ccgcgccgcc<br /> 1321 gtcctcgtct tccaaggcgg cgggtggtgg acgcggcgga gggggcaaga acaaggggaa<br /> 1381 gggcgtggcc gcggcggcgc caccgccgcc gccgccgccg ccgcggtgcc aggtggaggg<br /> 1441 gtgcggcgcg gatctgagcg ggatcaagaa ctactactgc cgccacaagg tgtgcttcat<br /> 1501 gcattccaag gctccccgcg tcgtcgtcgc cggcctcgag cagcgcttct gccagcagtg<br /> 1561 cagcaggtca ctctctcact cacctcgcca ttgctgatgt caccactgct tttgctttgc<br /> 1621 tttgcttgct ctccctcctc tttcacctat ctctcttgtt tatttgcttc ttgttcttgt<br /> 1681 ttagtgctag tacatgtgtt gttattgttg tgccgttttg tcttttgggt tattgtgttg<br /> 1741 ttgttactac tcgttttact ataggttttt aaggtttatg agcacggcca ccacattaga<br /> 1801 tgcactgtca agtggtgtgt gtgggacctt tcctgctaaa acaagctgat ttcaactctc<br /> 1861 tgaaacttcc tgcatttcat ctatttttat ctttgattgt gttgggagta ctacactagt<br /> 1921 agtgttaata ttttgactgg tgcttatgag atttttaagt tggtaggttg atgaggaaaa<br /> 1981 tactccttta tatggttgag tgatgtgact tgcctgtctg cctgcctgcc tgccgctttg<br /> 2041 cataagattc ctctgtgtta gtaagagcca ctgtttattt gtactggtgc ttactctact<br /> 2101 tagttaatta gccattagct ataaaattcc gttgatgttg caagcttagc aatggccacg<br /> 2161 gtaagaatgg gagagagaag ttggctaaag ctgttgcttt gtagtttgta ctatatatgt<br /> 2221 gtctttgtgt tgcaagatat gcaactccta ctatgctgtg acttgagctc aaggttttca<br /> 2281 gttatctata gatccttact actactgagc atactaccac ttctgtatgg tagcatatgg<br /> 2341 tagcatagtc caagttccaa cgcctcgcca gttgttcata atctatacta ccacttctgt<br /> 2401 gcatttgtta cttttattta atagtttgtc tcattagctg acaagcatat gcctgttttg<br /> 2461 atatctgccc ctcttgtaat agtctatgga tagcttggac tgtttgatgc tttaattttt<br /> 2521 tactagcaac acttagggcc cctttgaaat ggaggattag caaaggaatt ttggaggatt<br /> 2581 cattttccta aggatttttt cctatagagc cctttgattc atagaaagag gataggaaaa<br /> 2641 cttccgtagg attgcattcc tatgatcaat tccataggaa aataagcaag aggttagacc<br /> 2701 tcttgtgaaa ctttcctttg ttgagtgtat cttgtggtat aatcaaaggg ctcttctctc<br /> 2761 catttcatgt gttttcaatt cctgtaggat tggaaaaaca tacaacttca attcctacgt<br /> 2821 ttttcctatt cctatgtttt tcctatcctg cgtttcaaag gggcccttaa ggatgaaggg<br /> 2881 aagtaagaga aacatactag agaatatgta gtagtatttc tacattccat atttgtagca<br /> 2941 ctagcccaca aatatctttg ccttgtactt acttcatacc agttcccccc ttttcagagc<br /> 3001 aaaccaacaa tttctgttgc cttatatatc tagtgtcttc gtactaatat atctgttcca<br /> 3061 aaatgtacct gtccaaattc atagctagaa atagctttat ttaggacgga agtaataact<br /> 3121 gttgttagag acttggttca gacttttggt tatgttgagg ctactatcat ttcctttacg<br /> 3181 ggccaaatta ctacaaatga gaattcataa aaatgtcaag attttatgat tgttgtagct<br /> 3241 ttatttagga cggaggtagt aattgttgtt agagacttgg ttcagacttt tggttacgtt<br /> 3301 gaagctacta tcatttcctt tatggtcaaa ttactaacaa tgagtattca taaaaatgtc<br /> 3361 aagattttat aattgagctg tgccagtgct aagtgtgtca ctatctgatg ccataatgca<br /> 3421 tcattataaa agccagatgg accattagct tttatgtgta ggacacctgc cgtccaatta<br /> 3481 gatggataac catctagtgt ttgtgtactg ttattttaag cccgacatct cacaactcca<br /> 3541 tgaatgatta cagtcttcct ttcacatggt gtccttttgt tgtgttagga atagcatttt<br /> 3601 ttatttatgg gtgtaattat gaaaggcact aggagagttg ctgctttatc ttgatgggat<br /> 3661 ttgtagtaat accatcttta ggatgacaag aaatcttgtt ctgagttagc atgggctgcc<br /> 3721 ttttgacctg agctacggtt tgctatgttt ggcttgcatc atgcagatct attaggataa<br /> 3781 taagcatata aaagttgctt gcattgtgca ttgcttgttt taccttgatt catgtaggag<br /> 3841 taatttgctc gccatgcctc gttttgcttt ctgagtcaac agccaaattt agatgatgta<br /> 3901 ccttctgttg cttcaaaaac tcagtcactg cacagcagca gtggatagga ttcagaatca<br /> 3961 atctatccat gattctctgt tcacataata tgacaggttc cacctgctgc ctgaatttga<br /> 4021 ccaaggaaaa cgcagctgcc gcagacgcct tgcaggtcat aatgagcgcc ggaggaggcc<br /> 4081 gcaaacccct ttggcatcac gctacggtcg actagctgca tctgttggtg gtatcatcag<br /> 4141 aggctcttgt tttctttgca tcttgtgtgt ttgttggtaa ctactggttg cattcgctga<br /> 4201 tgtgttgttt gttgcgattc ttgatccaga agagcatcgc aggttcagaa gctttacgtt<br /> 4261 ggatttctcc tacccaaggg ttccaagcag cgtaaggaat gcatggccag caattcaacc<br /> 4321 aggcgatcgg atctccggtg gtatccagtg gcacaggaac gtagctcctc atggtcactc<br /> 4381 tagtgcagtg gcgggatatg gtgccaacac atacagcggc caaggtagct cttcttcagg<br /> 4441 gccaccggtg ttcgctggcc caaatctccc tccaggtgga tgtctcgcag gggtcggtgc<br /> 4501 cgccaccgac tcgagctgtg ctctctctct tctgtcaacc cagccatggg atactactac<br /> 4561 ccacagtgcc gctgccagcc acaaccaggc tgcagccatg tccactacca ccagctttga<br /> 4621 tggcaatcct gtggcaccct ccgccatggc gggtagctac atggcaccaa gcccctggac<br /> 4681 aggttctcgg ggccatgagg gtggtggtcg gagcgtggcg caccagctac cacatgaagt<br /> 4741 ctcacttgat gaggtgcacc ctggtcctag ccatcatgcc cacttctccg gtgagcttga<br /> 4801 gcttgctctg caggggaacg gtccagcccc agcaccacgc atcgatcctg ggtccggcag<br /> 4861 caccttcgac caaaccagca acacgatgga ttggtctctg tagaggctgt tccagctgcc<br /> 4921 atcgatctgt cgtcccgcaa ggcgagtcat ggaactgaag aacctcatgc tgcctgccct<br /> 4981 tattttgtgt tcaaattttc ctttccagta tggaaaggaa attctaaggt gactggcgat<br /> 5041 taatctccct gtgatgaata ataatgcgcg cccttgaact caattaattg ctgtgccgca<br /> 5101 tccatctatg taactctcca tgaattttta agtatcagtg ttaatgctgt attgtcgagg<br /> 5161 acttctgctc gatatgttat ttctcttatg ttgttcatca tgaatctttt tctgcttatt<br /> 5221 attctggtgc cgggttgtcc ttaccacaga agattcagtt tcggttggcg agagtaaaca<br /> 5281 ccttccctgg ttgtgacaaa agctccaacc ttttcacttc tcggcctgta tttgatcttc<br /> 5341 cccttctgac gctgttatac tacttttaag cctgtatgtt tccagccttc caggtgaagg<br /> 5401 gccatactga agagaaaaca tgctttcagg gtttgatgca ttgtgtactt tacaagtgta<br /> 5461 cttaagattt tgtacaattt atatatgtac ctgctctgct gctgagtatt gtaggaaaga<br /> 5521 atcagttcga agggcgtgtg ttcatgtaaa gtgagaccac atgcacagcg tggatttgca<br /> 5581 gcatgctctc tgcaccagtg gtgttctgtt gatgcctttg atgggctggc tgaggtgaga<br /> 5641 ggaggatgat ccatgttggc agcttcttca ctctgaaaaa taaaagagaa gaaatgttca<br /> 5701 gatttgcaga caagtggaga gcagtgatat attctacaat aaaacattac caccttgctt<br /> 5761 ttctgtgatg atagatactc catggaattt tgcatcaagc atctcttgtt ttccagccac<br /> 5821 tgtttgctgg gttgttgctt caatttcgtc ccaattgatt ggtcaccttt ggttgtgact<br /> 5881 tgagagcact gagcactgaa acttttgctg tcagcaggca atgcacctca tccatgtcac<br /> 5941 gacagaggga gagagcccac ataaatggcc aaagaggaca catacagtgg cactgatgca<br /> 6001 gtcattgcaa cataattgac atcatgctaa acagtggtgt aaccatatgt tagctagcct<br /> 6061 gtgatcagca aacagtgatt atggatctta atgtcacatg caagatttga cacagttgta<br /> 6121 aaaccatcat tgcattgaag atagatccca gcaacaggtg tatgatgtat tgctagaatg<br /> 6181 aatcaaaaat atcagtgcca tcctaaacac agtactacca acttgaacag ttatcaccgt<br /> 6241 gattggaaaa cagaaatgta taattgcttt ggcgccatct gcttatcatt atcatatgtc<br /> 6301 gcagatcact tgttccattg acacgactct ttttcactgt gaggagaggc accttgattt<br /> 6361 ggacttttca agagctgtag caagggctcc tttgaagcct tctacatgga ggagcagagc<br /> 6421 ataccatatg cagaactgta aactcttcct gaagctttcc agttccaccc ttgtagcttt<br /> 6481 aagctgccgc aagagaatta tcatttctaa cattgagatg tgatactgaa atgtgaaagg<br /> 6541 tgattcgcag tataggtccc aaaatatcgt ttacagcaac ttgcaaatcc tgcatgatac<br /> 6601 agttaattca tcaaaatatt agaccattag tactacagtc tacaaatacc ccttaactga<br /> 6661 acatgtatga taaggacaag attctgaagc tccagtgcat caggaatcca acgcagtatg<br /> 6721 caaatcatta ctgaacaaga ttcctgcact tacagaatca tcacctgttg taacaaggac<br /> 6781 cattctttgt tgccccagac acagcgaatt aatggtcatc ttcatttggc ccaggacatt<br /> 6841 catttgccaa tgcttctgct gattcatact gaaaagggga caatgcgtcc aattttaaaa<br /> 6901 gcatggaaga tgctataaaa gatcacccta tttaaaatgc agagaaaacc aaagatccaa<br /> 6961 catgatatgg taatcacaga ttcccaacag taatgccgtc cagtaggcag taggggcatg<br /> 7021 cacataaaca ctagtactat gtagagctga agcttatttc cagaatgaag ctgaccttgc<br /> 7081 aaccgcaata aaggcaatag tagtgttcat cgcgcagctt agccaatata ttttgcaaat<br /> 7141 cctgcaagaa taaacacagg tcaatctcgt cctttcagca aaatttgcag tcttgcataa<br /> 7201 gatttctcag ataaaaaagg aagtctaga<br /> //</div>

April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=IPA1&diff=175407 2014-06-01T06:45:23Z

<p>April Cui: </p> <hr /> <div><br /> 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.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ==== IPA1 Suppresses Rice Tillering Mainly through Positive Regulation of Os TB1 ====<br /> <br /> Os TB1 acts as a negative regulator of rice tillering (Takeda et al., 2003; Minakuchi et al.,<br /> 2010) and that Os TB1 is a potential direct target of IPA1. The peak summits for IPA1 binding sites were located 96 and 187 bp upstream of the Os TB1 TSS in the two YP replicates, respectively.<br /> [[File: IPA1 figure 1.png|left|thumb|200px|'''Figure 1''' Figure 1. IPA1 Directly and Positively Regulates the Expression of Os TB1.<br /> (A) IPA1 binding profile in the promoter of Os TB1. The open arrowhead refers to the GTAC around the peak summit and the solid arrowhead to the GTAC around the subsummit. The red vertical line denotes the peak summit. The primer pair Os TB1 Pro (see Supplemental Table 1 online) was used for amplifying the Os TB1 promoter.<br /> (B) Validation of IPA1 direct binding sites in the Os TB1 promoter by ChIP-qPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) EMSA showing that GST-IPA1 could directly bind to the promoter of Os TB1. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition.<br /> (D) Comparison of Os TB1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (E) Suppression of tiller number by tb1/fc1 in RIL-ipa1/tb1 lines. Bar = 20 cm. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> However, the Os TB1 promoter was significantly enriched in both SAs and YPs by the ChIP-qPCR analysis, indicating that Os TB1 is probably under the control of IPA1 in both tissues (Figure 1B). Further analysis of binding peaks revealed that the GTAC motif, rather than the TGGGCC/T motif, existed in the Os TB1 promoter. To test whether IPA1 can directly bind to the GTAC motif in the Os TB1 promoter, we performed an EMSA assay and found that GST-IPA1 could bind to a 59-bp probe from the Os TB1 promoter (Figure 1C). The mutation of GTAC to ATAC abolished its binding<br /> affinity, demonstrating that the binding was dependent on the GTAC motif. As a negative regulator in rice tiller development, Os TB1 is expressed in axillary buds, and its deficiency results in a semidwarf phenotype with a significant increase in tiller number (Takeda et al., 2003; Minakuchi et al., 2010). This suggests that the reduced tiller phenotype of ipa1 plants may result from the direct activation of Os TB1 by IPA1. The RNA level of Os TB1 was significantly upregulated in SAs in NIL-ipa1, but much less significantly in YPs (Figure 1 D). Furthermore, the double mutant analysis showed that the mutation of Os TB1 could suppress the tillering phenotype of ipa1 (Figure 1E). Since Os TB1 is homologous to PCF1 and PCF2, we tested whether Os TB1 could also interact with IPA1. A weak interaction was detected in the yeast two-hybrid assay , and EMSA further showed that Os TB1 could directly bind the TGGGCC/T motif,<br /> indicating that Os TB1 also functions as an adaptor for the interaction between IPA1 and the TGGGCC/T motif. Considering that Os TB1 is not only a target of IPA1, but also can interact with IPA1, we propose that Os TB1 is probably involved in the feedback regulation of IPA1 transcriptional activity.<br /> <br /> ====Increased Plant Height and Panicle Branches ====<br /> <br /> DEP1 is another important regulatory gene that affects rice architecture, especially panicle morphology. A truncated mutation of DEP1 enhances panicle meristematic activity, resulting in reduced length of inflorescence internodes, increased number of grains per panicle, and a consequent increase in grain yield (Huang et al., 2009). IPA1 ChIP-seq analysis revealed that DEP1<br /> was also a direct target of IPA1 . The peak summits of IPA1 binding were located 566, 514, 440, and 500 bp upstream of the DEP1 TSS in SA rep 1, SA rep 2, YP rep 1, and YP rep 2, respectively (Figure 2A). Within the peaks in the DEP1 promoter, besides the highest peak summit, there are other two subsummits showing local max sequencing reads (Figure 2A). Through analyzing the DEP1 promoter sequence, several GTAC motifs were found, and three sites around the peak summits and subsummits were considered to be responsible for the binding of IPA1. To confirm this, ChIP-qPCR was performed. As shown in Figure 2B, the two specific regions were significantly enriched. We then tested whether IPA1 could directly bind to the promoter of DEP1 by EMSA with three 59-bp sequences around the peak summit and subsummits as probes and found that IPA1 could bind to all the three probes but could not bind to a probe containing the mutated binding core motif (Figure 2C). These results demonstrate that IPA1 can directly bind to the promoter of DEP1 at different sites and the GTAC core motifs are responsible for IPA1 binding, suggesting that DEP1 is a direct target of IPA1. To further understand the biological functions of DEP1 as a direct target of IPA1, we generated recombinant inbred lines by crossing Ri22, an ipa1-carrying cultivar (Jiao et al., 2010), with LJ5, a rice variety carrying the dep1 mutation (Huang et al.2009). As shown in Figures 3A and3B, the plant height of the RIL-ipa1/dep1 lines was reduced to a similar level to the RIL-IPA1/dep1 lines. Consistent with the previous result that dep1 does not affect rice tillering, the tiller number of RIL-ipa1/dep1 lines exhibited no significant difference from RIL-ipa1/DEP1 lines. We also noticed that the panicle morphology of the RIL-ipa1/dep1 lines was dense and erect (Figures 3C and 3D). Compared with the RIL-ipa1/DEP1 lines, the panicle length of RIL-ipa1/dep1 lines was significantly reduced, but no obvious change in panicle branches was found. Like IPA1, DEP1 was also strongly expressed in culms, SAs, and YPs, but weakly in roots (Figure 3E), suggesting that IPA1 may regulate the expression of DEP1. We further examined the expression of DEP1 in NIL-ipa1 lines and found that DEP1 transcripts were significantly increased in the SA of NIL-ipa1 lines, but only slightly in YP (Figure 3F). Therefore, it is likely that IPA1 functions as a positive regulator of DEP1 in regulating plant height and panicle length in rice. <br /> [[File:IPA1 figure 2.png|left|thumb|200px|'''Figure 2'''Figure 2. IPA1 Directly Binds to the DEP1 Promoter.<br /> (A) IPA1 binding profile in the promoter of DEP1. The open arrowhead refers to the GTAC around the peak summit, solid arrowheads to other GTAC sequences around subsummits, and red vertical lines to peak summits. Primer pairs DEP1-Pro1 and DEP1-Pro2 were used for amplifying DEP1 Pro-1 and DEP1 pro-2,respectively.<br /> (B) Validation of IPA1 direct binding sites in the DEP1 promoter by ChIPqPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significance difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) Direct binding of IPA1 to the DEP1 promoter in EMSA. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File:IPA1 figure 3.png|left|thumb|200px|'''Figure 3''' Figure 3. DEP1 Is Positively Regulated by IPA1.<br /> (A) Suppression of plant height by dep1 in RIL-ipa1/dep1 lines. Bar = 20 cm.<br /> (B) Statistical analysis of (A). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences between different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (C) Suppression of panicle length by dep1 in RIL-ipa1/dep1 lines. Bar = 5 cm.<br /> (D) Statistical analysis of (C). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences among different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (E) Expression patterns of IPA1 and DEP1 in different tissues revealed by qPCR analyses. R, roots; C, culms; B, leaf blades; S, leaf sheathes; A, SAs; Y, YPs; M, mature panicles. Rice Ubiquitin was used as reference. Values are means 6 SE (n = 3).<br /> (F) Comparison of DEP1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> ===Protein===<br /> 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).<br /> <br /> 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). Therefore, it has been suggested that Os SPL14 alleles have great potential for breeding (Jiao et al., 2010; Miura et al., 2010).<br /> <br /> ==Labs working on this gene==<br /> State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Zefu Lu, Hong Yu, Yonghong Wang, Jiayang Li)<br /> State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China(Xingming Hu, Qian Qian)<br /> State Key Laboratory of Plant Cell and Chromosome Engineering and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Xiangdong Fu)<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li .Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture. The Plant Cell, 2013, 25(10): 3743-3759&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Yongqing Jiao, Yonghong Wang, Dawei Xue, Jing Wang, Meixian Yan, Guifu Liu, Guojun Dong, Dali Zeng, Zefu Lu, Xudong Zhu, Qian Qian, Jiayang Li. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice .Nature Genetics, 2010, 42(6): 541-544&lt;/ref&gt;<br /> <br /> ==Structured Information==<br /> <br /> LOCUS GU136674 7229 bp DNA linear PLN 29-JUN-2010<br /> DEFINITION Oryza sativa Japonica Group IPA1 (IPA1) gene, complete cds.<br /> ACCESSION GU136674<br /> VERSION GU136674.1 GI:299482811<br /> KEYWORDS .<br /> SOURCE Oryza sativa (rice)<br /> ORGANISM Oryza sativa<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> REFERENCE 1 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Xue,D., Wang,J., Yan,M., Liu,G., Dong,G.,<br /> Zeng,D., Lu,Z., Zhu,X., Qian,Q. and Li,J.<br /> TITLE Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture<br /> in rice<br /> JOURNAL Nat. Genet. 42 (6), 541-544 (2010)<br /> PUBMED 20495565<br /> REFERENCE 2 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Qian,Q. and Li,J.<br /> TITLE Direct Submission<br /> JOURNAL Submitted (22-OCT-2009) State Key Laboratory of Plant Genomics and<br /> National Center for Plant Gene Research, Institute of Genetics and<br /> Developmental Biology, Chinese Academy of Sciences, No.1 West<br /> Beichen Road, Chaoyang District, Beijing 100101, China<br /> FEATURES Location/Qualifiers<br /> source 1..7229<br /> /organism=&quot;Oryza sativa&quot;<br /> /mol_type=&quot;genomic DNA&quot;<br /> /db_xref=&quot;taxon:4530&quot;<br /> /chromosome=&quot;8&quot;<br /> /map=&quot;RM149-RM1345&quot;<br /> gene 995..5150<br /> /gene=&quot;IPA1&quot;<br /> mRNA join(995..1566,3997..4130,4233..5150)<br /> /gene=&quot;IPA1&quot;<br /> /product=&quot;IPA1&quot;<br /> CDS join(1118..1566,3997..4130,4233..4903)<br /> /gene=&quot;IPA1&quot;<br /> /note=&quot;transcription factor&quot;<br /> /codon_start=1<br /> /product=&quot;IPA1&quot;<br /> /protein_id=&quot;ADJ19220.1&quot;<br /> /db_xref=&quot;GI:299482812&quot;<br /> /translation=&quot;MEMASGGGAAAAAGGGVGGSGGGGGGGDEHRQLHGLKFGKKIYF<br /> EDAAAAAGGGGTGSGSGSASAAPPSSSSKAAGGGRGGGGKNKGKGVAAAAPPPPPPPP<br /> RCQVEGCGADLSGIKNYYCRHKVCFMHSKAPRVVVAGLEQRFCQQCSRFHLLPEFDQG<br /> KRSCRRRLAGHNERRRRPQTPLASRYGRLAASVGEHRRFRSFTLDFSYPRVPSSVRNA<br /> WPAIQPGDRISGGIQWHRNVAPHGHSSAVAGYGANTYSGQGSSSSGPPVFAGPNLPPG<br /> GCLAGVGAATDSSCALSLLSTQPWDTTTHSAAASHNQAAAMSTTTSFDGNPVAPSAMA<br /> GSYMAPSPWTGSRGHEGGGRSVAHQLPHEVSLDEVHPGPSHHAHFSGELELALQGNGP<br /> APAPRIDPGSGSTFDQTSNTMDWSL&quot;<br /> ORIGIN <br /> 1 gcaatgtaga gccacgtagg caagtcgctt gcgtggagga gagaggggag tggggaccgt<br /> 61 tcccaaccca gcttcgtgtg accaagtttg gccacacggg ccaaacgaac ctcagcaact<br /> 121 tttgtcagaa agaaaagaac ctccgcgaga aacaagaaag cgagagaggg agagaaagga<br /> 181 ggctcgtcgg agtaggggcg ctcggggtat ggggctcggc ggaggctcgc tggagtaggg<br /> 241 gccgccactg cgtggggctc gccggagtag gggcgctcgg ggagcctccc gagatccgcc<br /> 301 gctcagcggc gccgccgtct tccgggcaga gctctcgaag ctcgccctcc tcgcgcgccg<br /> 361 gtggcgttgg cggggcccgc gtgtggctac gcagctccgg tgctgcgcct ccaccgtcga<br /> 421 cgacagcgcc gcttggcgct gccgccgtct tccgccgcgc cgctggacgc cgccagatct<br /> 481 gctgctcgtc gccgcgtggg ccgctccacc cggttggagg aggagaggcg gcgccgcgct<br /> 541 tgggctgccc caccgccgag ctctgccgcg ccgttcgccg gtgctgccga gctccgccgc<br /> 601 gcctgccgga gcacgctgcc atggccgccc tggagaagac acgagagaat taggtggagg<br /> 661 gtgggggaag ggtgagattt tttatattat ctatgggtcc cattataaat tttctaaacc<br /> 721 acacttatac tgtgggtgca gtgtcattta gagttcccaa accacctatg ttgcagctgt<br /> 781 ggtataacaa tttgctagga cgcattgcta ctgcccttgt accctgctat aagaagataa<br /> 841 ccaatgacat ctccactcga ttttctcggc gcgcgtgtga gggtgtgagg ataattttta<br /> 901 ttttaagtgg tttttaaggg cggagagaga gagagagaga gggcaccgca ctacttctac<br /> 961 ttgtgtgtgt gtcgctcgct gggcttcgcc acctttccgt ctctttcctc tctcttctct<br /> 1021 ctccccctct cctggaggag agagaggaga agaggagggg gggccgcgcc aagagccacg<br /> 1081 cgcgctacag tctccttccc acccgcgacc gcgagcaatg gagatggcca gtggaggagg<br /> 1141 cgccgccgcc gccgccggcg gcggagtagg cggcagcggc ggcggtggtg gtggagggga<br /> 1201 cgagcaccgc cagctgcacg gtctcaagtt cggcaagaag atctacttcg aggacgccgc<br /> 1261 cgcggcagca ggcggcggcg gcactggcag tggcagtggc agcgcgagcg ccgcgccgcc<br /> 1321 gtcctcgtct tccaaggcgg cgggtggtgg acgcggcgga gggggcaaga acaaggggaa<br /> 1381 gggcgtggcc gcggcggcgc caccgccgcc gccgccgccg ccgcggtgcc aggtggaggg<br /> 1441 gtgcggcgcg gatctgagcg ggatcaagaa ctactactgc cgccacaagg tgtgcttcat<br /> 1501 gcattccaag gctccccgcg tcgtcgtcgc cggcctcgag cagcgcttct gccagcagtg<br /> 1561 cagcaggtca ctctctcact cacctcgcca ttgctgatgt caccactgct tttgctttgc<br /> 1621 tttgcttgct ctccctcctc tttcacctat ctctcttgtt tatttgcttc ttgttcttgt<br /> 1681 ttagtgctag tacatgtgtt gttattgttg tgccgttttg tcttttgggt tattgtgttg<br /> 1741 ttgttactac tcgttttact ataggttttt aaggtttatg agcacggcca ccacattaga<br /> 1801 tgcactgtca agtggtgtgt gtgggacctt tcctgctaaa acaagctgat ttcaactctc<br /> 1861 tgaaacttcc tgcatttcat ctatttttat ctttgattgt gttgggagta ctacactagt<br /> 1921 agtgttaata ttttgactgg tgcttatgag atttttaagt tggtaggttg atgaggaaaa<br /> 1981 tactccttta tatggttgag tgatgtgact tgcctgtctg cctgcctgcc tgccgctttg<br /> 2041 cataagattc ctctgtgtta gtaagagcca ctgtttattt gtactggtgc ttactctact<br /> 2101 tagttaatta gccattagct ataaaattcc gttgatgttg caagcttagc aatggccacg<br /> 2161 gtaagaatgg gagagagaag ttggctaaag ctgttgcttt gtagtttgta ctatatatgt<br /> 2221 gtctttgtgt tgcaagatat gcaactccta ctatgctgtg acttgagctc aaggttttca<br /> 2281 gttatctata gatccttact actactgagc atactaccac ttctgtatgg tagcatatgg<br /> 2341 tagcatagtc caagttccaa cgcctcgcca gttgttcata atctatacta ccacttctgt<br /> 2401 gcatttgtta cttttattta atagtttgtc tcattagctg acaagcatat gcctgttttg<br /> 2461 atatctgccc ctcttgtaat agtctatgga tagcttggac tgtttgatgc tttaattttt<br /> 2521 tactagcaac acttagggcc cctttgaaat ggaggattag caaaggaatt ttggaggatt<br /> 2581 cattttccta aggatttttt cctatagagc cctttgattc atagaaagag gataggaaaa<br /> 2641 cttccgtagg attgcattcc tatgatcaat tccataggaa aataagcaag aggttagacc<br /> 2701 tcttgtgaaa ctttcctttg ttgagtgtat cttgtggtat aatcaaaggg ctcttctctc<br /> 2761 catttcatgt gttttcaatt cctgtaggat tggaaaaaca tacaacttca attcctacgt<br /> 2821 ttttcctatt cctatgtttt tcctatcctg cgtttcaaag gggcccttaa ggatgaaggg<br /> 2881 aagtaagaga aacatactag agaatatgta gtagtatttc tacattccat atttgtagca<br /> 2941 ctagcccaca aatatctttg ccttgtactt acttcatacc agttcccccc ttttcagagc<br /> 3001 aaaccaacaa tttctgttgc cttatatatc tagtgtcttc gtactaatat atctgttcca<br /> 3061 aaatgtacct gtccaaattc atagctagaa atagctttat ttaggacgga agtaataact<br /> 3121 gttgttagag acttggttca gacttttggt tatgttgagg ctactatcat ttcctttacg<br /> 3181 ggccaaatta ctacaaatga gaattcataa aaatgtcaag attttatgat tgttgtagct<br /> 3241 ttatttagga cggaggtagt aattgttgtt agagacttgg ttcagacttt tggttacgtt<br /> 3301 gaagctacta tcatttcctt tatggtcaaa ttactaacaa tgagtattca taaaaatgtc<br /> 3361 aagattttat aattgagctg tgccagtgct aagtgtgtca ctatctgatg ccataatgca<br /> 3421 tcattataaa agccagatgg accattagct tttatgtgta ggacacctgc cgtccaatta<br /> 3481 gatggataac catctagtgt ttgtgtactg ttattttaag cccgacatct cacaactcca<br /> 3541 tgaatgatta cagtcttcct ttcacatggt gtccttttgt tgtgttagga atagcatttt<br /> 3601 ttatttatgg gtgtaattat gaaaggcact aggagagttg ctgctttatc ttgatgggat<br /> 3661 ttgtagtaat accatcttta ggatgacaag aaatcttgtt ctgagttagc atgggctgcc<br /> 3721 ttttgacctg agctacggtt tgctatgttt ggcttgcatc atgcagatct attaggataa<br /> 3781 taagcatata aaagttgctt gcattgtgca ttgcttgttt taccttgatt catgtaggag<br /> 3841 taatttgctc gccatgcctc gttttgcttt ctgagtcaac agccaaattt agatgatgta<br /> 3901 ccttctgttg cttcaaaaac tcagtcactg cacagcagca gtggatagga ttcagaatca<br /> 3961 atctatccat gattctctgt tcacataata tgacaggttc cacctgctgc ctgaatttga<br /> 4021 ccaaggaaaa cgcagctgcc gcagacgcct tgcaggtcat aatgagcgcc ggaggaggcc<br /> 4081 gcaaacccct ttggcatcac gctacggtcg actagctgca tctgttggtg gtatcatcag<br /> 4141 aggctcttgt tttctttgca tcttgtgtgt ttgttggtaa ctactggttg cattcgctga<br /> 4201 tgtgttgttt gttgcgattc ttgatccaga agagcatcgc aggttcagaa gctttacgtt<br /> 4261 ggatttctcc tacccaaggg ttccaagcag cgtaaggaat gcatggccag caattcaacc<br /> 4321 aggcgatcgg atctccggtg gtatccagtg gcacaggaac gtagctcctc atggtcactc<br /> 4381 tagtgcagtg gcgggatatg gtgccaacac atacagcggc caaggtagct cttcttcagg<br /> 4441 gccaccggtg ttcgctggcc caaatctccc tccaggtgga tgtctcgcag gggtcggtgc<br /> 4501 cgccaccgac tcgagctgtg ctctctctct tctgtcaacc cagccatggg atactactac<br /> 4561 ccacagtgcc gctgccagcc acaaccaggc tgcagccatg tccactacca ccagctttga<br /> 4621 tggcaatcct gtggcaccct ccgccatggc gggtagctac atggcaccaa gcccctggac<br /> 4681 aggttctcgg ggccatgagg gtggtggtcg gagcgtggcg caccagctac cacatgaagt<br /> 4741 ctcacttgat gaggtgcacc ctggtcctag ccatcatgcc cacttctccg gtgagcttga<br /> 4801 gcttgctctg caggggaacg gtccagcccc agcaccacgc atcgatcctg ggtccggcag<br /> 4861 caccttcgac caaaccagca acacgatgga ttggtctctg tagaggctgt tccagctgcc<br /> 4921 atcgatctgt cgtcccgcaa ggcgagtcat ggaactgaag aacctcatgc tgcctgccct<br /> 4981 tattttgtgt tcaaattttc ctttccagta tggaaaggaa attctaaggt gactggcgat<br /> 5041 taatctccct gtgatgaata ataatgcgcg cccttgaact caattaattg ctgtgccgca<br /> 5101 tccatctatg taactctcca tgaattttta agtatcagtg ttaatgctgt attgtcgagg<br /> 5161 acttctgctc gatatgttat ttctcttatg ttgttcatca tgaatctttt tctgcttatt<br /> 5221 attctggtgc cgggttgtcc ttaccacaga agattcagtt tcggttggcg agagtaaaca<br /> 5281 ccttccctgg ttgtgacaaa agctccaacc ttttcacttc tcggcctgta tttgatcttc<br /> 5341 cccttctgac gctgttatac tacttttaag cctgtatgtt tccagccttc caggtgaagg<br /> 5401 gccatactga agagaaaaca tgctttcagg gtttgatgca ttgtgtactt tacaagtgta<br /> 5461 cttaagattt tgtacaattt atatatgtac ctgctctgct gctgagtatt gtaggaaaga<br /> 5521 atcagttcga agggcgtgtg ttcatgtaaa gtgagaccac atgcacagcg tggatttgca<br /> 5581 gcatgctctc tgcaccagtg gtgttctgtt gatgcctttg atgggctggc tgaggtgaga<br /> 5641 ggaggatgat ccatgttggc agcttcttca ctctgaaaaa taaaagagaa gaaatgttca<br /> 5701 gatttgcaga caagtggaga gcagtgatat attctacaat aaaacattac caccttgctt<br /> 5761 ttctgtgatg atagatactc catggaattt tgcatcaagc atctcttgtt ttccagccac<br /> 5821 tgtttgctgg gttgttgctt caatttcgtc ccaattgatt ggtcaccttt ggttgtgact<br /> 5881 tgagagcact gagcactgaa acttttgctg tcagcaggca atgcacctca tccatgtcac<br /> 5941 gacagaggga gagagcccac ataaatggcc aaagaggaca catacagtgg cactgatgca<br /> 6001 gtcattgcaa cataattgac atcatgctaa acagtggtgt aaccatatgt tagctagcct<br /> 6061 gtgatcagca aacagtgatt atggatctta atgtcacatg caagatttga cacagttgta<br /> 6121 aaaccatcat tgcattgaag atagatccca gcaacaggtg tatgatgtat tgctagaatg<br /> 6181 aatcaaaaat atcagtgcca tcctaaacac agtactacca acttgaacag ttatcaccgt<br /> 6241 gattggaaaa cagaaatgta taattgcttt ggcgccatct gcttatcatt atcatatgtc<br /> 6301 gcagatcact tgttccattg acacgactct ttttcactgt gaggagaggc accttgattt<br /> 6361 ggacttttca agagctgtag caagggctcc tttgaagcct tctacatgga ggagcagagc<br /> 6421 ataccatatg cagaactgta aactcttcct gaagctttcc agttccaccc ttgtagcttt<br /> 6481 aagctgccgc aagagaatta tcatttctaa cattgagatg tgatactgaa atgtgaaagg<br /> 6541 tgattcgcag tataggtccc aaaatatcgt ttacagcaac ttgcaaatcc tgcatgatac<br /> 6601 agttaattca tcaaaatatt agaccattag tactacagtc tacaaatacc ccttaactga<br /> 6661 acatgtatga taaggacaag attctgaagc tccagtgcat caggaatcca acgcagtatg<br /> 6721 caaatcatta ctgaacaaga ttcctgcact tacagaatca tcacctgttg taacaaggac<br /> 6781 cattctttgt tgccccagac acagcgaatt aatggtcatc ttcatttggc ccaggacatt<br /> 6841 catttgccaa tgcttctgct gattcatact gaaaagggga caatgcgtcc aattttaaaa<br /> 6901 gcatggaaga tgctataaaa gatcacccta tttaaaatgc agagaaaacc aaagatccaa<br /> 6961 catgatatgg taatcacaga ttcccaacag taatgccgtc cagtaggcag taggggcatg<br /> 7021 cacataaaca ctagtactat gtagagctga agcttatttc cagaatgaag ctgaccttgc<br /> 7081 aaccgcaata aaggcaatag tagtgttcat cgcgcagctt agccaatata ttttgcaaat<br /> 7141 cctgcaagaa taaacacagg tcaatctcgt cctttcagca aaatttgcag tcttgcataa<br /> 7201 gatttctcag ataaaaaagg aagtctaga<br /> //</div>

April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:IPA1_figure_3.png&diff=175401 2014-06-01T06:41:54Z

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April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:IPA1_figure_2.png&diff=175399 2014-06-01T06:41:38Z

<p>April Cui: </p> <hr /> <div></div>

April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:IPA1_figure_1.png&diff=175398 2014-06-01T06:41:18Z

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April Cui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=IPA1&diff=175366 2014-06-01T06:18:20Z

<p>April Cui: Created page with &quot; 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 archit...&quot;</p> <hr /> <div><br /> 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.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ==== IPA1 Suppresses Rice Tillering Mainly through Positive Regulation of Os TB1 ====<br /> <br /> Os TB1 acts as a negative regulator of rice tillering (Takeda et al., 2003; Minakuchi et al.,<br /> 2010) and that Os TB1 is a potential direct target of IPA1. The peak summits for IPA1 binding sites were located 96 and 187 bp upstream of the Os TB1 TSS in the two YP replicates, respectively [[File: figure 1.png|left|thumb|200px|'''Figure 1''' Figure 1. IPA1 Directly and Positively Regulates the Expression of Os TB1.<br /> (A) IPA1 binding profile in the promoter of Os TB1. The open arrowhead refers to the GTAC around the peak summit and the solid arrowhead to the GTAC around the subsummit. The red vertical line denotes the peak summit. The primer pair Os TB1 Pro (see Supplemental Table 1 online) was used for amplifying the Os TB1 promoter.<br /> (B) Validation of IPA1 direct binding sites in the Os TB1 promoter by ChIP-qPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) EMSA showing that GST-IPA1 could directly bind to the promoter of Os TB1. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition.<br /> (D) Comparison of Os TB1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01.<br /> (E) Suppression of tiller number by tb1/fc1 in RIL-ipa1/tb1 lines. Bar = 20 cm. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> However, the Os TB1 promoter was significantly enriched in both SAs and YPs by the ChIP-qPCR analysis, indicating that Os TB1 is probably under the control of IPA1 in both tissues (Figure 1B). Further analysis of binding peaks revealed that the GTAC motif, rather than the TGGGCC/T motif, existed in the Os TB1 promoter. To test whether IPA1 can directly bind to the GTAC motif in the Os TB1 promoter, we performed an EMSA assay and found that GST-IPA1 could bind to a 59-bp probe from the Os TB1 promoter (Figure 1C). The mutation of GTAC to ATAC abolished its binding<br /> affinity, demonstrating that the binding was dependent on the GTAC motif. As a negative regulator in rice tiller development, Os TB1 is expressed in axillary buds, and its deficiency results in a semidwarf phenotype with a significant increase in tiller number (Takeda et al., 2003; Minakuchi et al., 2010). This suggests that the reduced tiller phenotype of ipa1 plants may result from the direct activation of Os TB1 by IPA1. The RNA level of Os TB1 was significantly upregulated in SAs in NIL-ipa1, but much less significantly in YPs (Figure 1 D). Furthermore, the double mutant analysis showed that the mutation of Os TB1 could suppress the tillering phenotype of ipa1 (Figure 1E). Since Os TB1 is homologous to PCF1 and PCF2, we tested whether Os TB1 could also interact with IPA1. A weak interaction was detected in the yeast two-hybrid assay , and EMSA further showed that Os TB1 could directly bind the TGGGCC/T motif,<br /> indicating that Os TB1 also functions as an adaptor for the interaction between IPA1 and the TGGGCC/T motif. Considering that Os TB1 is not only a target of IPA1, but also can interact with IPA1, we propose that Os TB1 is probably involved in the feedback regulation of IPA1 transcriptional activity.<br /> <br /> ====Increased Plant Height and Panicle Branches ====<br /> <br /> DEP1 is another important regulatory gene that affects rice architecture, especially panicle morphology. A truncated mutation of DEP1 enhances panicle meristematic activity, resulting in reduced length of inflorescence internodes, increased number of grains per panicle, and a consequent increase in grain yield (Huang et al., 2009). IPA1 ChIP-seq analysis revealed that DEP1<br /> was also a direct target of IPA1 . The peak summits of IPA1 binding were located 566, 514, 440, and 500 bp upstream of the DEP1 TSS in SA rep 1, SA rep 2, YP rep 1, and YP rep 2, respectively (Figure 2A). Within the peaks in the DEP1 promoter, besides the highest peak summit, there are other two subsummits showing local max sequencing reads (Figure 2A). Through analyzing the DEP1 promoter sequence, several GTAC motifs were found, and three sites around the peak summits and subsummits were considered to be responsible for the binding of IPA1. To confirm this, ChIP-qPCR was performed. As shown in Figure 2B, the two specific regions were significantly enriched. We then tested whether IPA1 could directly bind to the promoter of DEP1 by EMSA with three 59-bp sequences around the peak summit and subsummits as probes and found that IPA1 could bind to all the three probes but could not bind to a probe containing the mutated binding core motif (Figure 2C). These results demonstrate that IPA1 can directly bind to the promoter of DEP1 at different sites and the GTAC core motifs are responsible for IPA1 binding, suggesting that DEP1 is a direct target of IPA1. To further understand the biological functions of DEP1 as a direct target of IPA1, we generated recombinant inbred lines by crossing Ri22, an ipa1-carrying cultivar (Jiao et al., 2010), with LJ5, a rice variety carrying the dep1 mutation (Huang et al.2009). As shown in Figures 3A and3B, the plant height of the RIL-ipa1/dep1 lines was reduced to a similar level to the RIL-IPA1/dep1 lines. Consistent with the previous result that dep1 does not affect rice tillering, the tiller number of RIL-ipa1/dep1 lines exhibited no significant difference from RIL-ipa1/DEP1 lines. We also noticed that the panicle morphology of the RIL-ipa1/dep1 lines was dense and erect (Figures 3C and 3D). Compared with the RIL-ipa1/DEP1 lines, the panicle length of RIL-ipa1/dep1 lines was significantly reduced, but no obvious change in panicle branches was found. Like IPA1, DEP1 was also strongly expressed in culms, SAs, and YPs, but weakly in roots (Figure 3E), suggesting that IPA1 may regulate the expression of DEP1. We further examined the expression of DEP1 in NIL-ipa1 lines and found that DEP1 transcripts were significantly increased in the SA of NIL-ipa1 lines, but only slightly in YP (Figure 3F). Therefore, it is likely that IPA1 functions as a positive regulator of DEP1 in regulating plant height and panicle length in rice. <br /> [[File:figure 2.png|left|thumb|200px|'''Figure 2'''Figure 2. IPA1 Directly Binds to the DEP1 Promoter.<br /> (A) IPA1 binding profile in the promoter of DEP1. The open arrowhead refers to the GTAC around the peak summit, solid arrowheads to other GTAC sequences around subsummits, and red vertical lines to peak summits. Primer pairs DEP1-Pro1 and DEP1-Pro2 were used for amplifying DEP1 Pro-1 and DEP1 pro-2,respectively.<br /> (B) Validation of IPA1 direct binding sites in the DEP1 promoter by ChIPqPCR analysis. The fold enrichment was normalized against the promoter of Ubiquitin. aGFP, antibodies against GFP. Values are means 6 SE (n = 3). The double asterisks represent significance difference determined by the Student’s t test at P &lt; 0.01.<br /> (C) Direct binding of IPA1 to the DEP1 promoter in EMSA. The 10- and 40-fold excess nonlabeled or mutated probes were used for competition. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> [[File: figure 3.png|left|thumb|200px|'''Figure 3''' Figure 3. DEP1 Is Positively Regulated by IPA1.<br /> (A) Suppression of plant height by dep1 in RIL-ipa1/dep1 lines. Bar = 20 cm.<br /> (B) Statistical analysis of (A). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences between different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (C) Suppression of panicle length by dep1 in RIL-ipa1/dep1 lines. Bar = 5 cm.<br /> (D) Statistical analysis of (C). Values are means 6 SE (n = 15). Different lowercase letters indicate significant differences among different genotypes (P &lt; 0.01, one-way analysis of variance).<br /> (E) Expression patterns of IPA1 and DEP1 in different tissues revealed by qPCR analyses. R, roots; C, culms; B, leaf blades; S, leaf sheathes; A, SAs; Y, YPs; M, mature panicles. Rice Ubiquitin was used as reference. Values are means 6 SE (n = 3).<br /> (F) Comparison of DEP1 expression levels between NIL-IPA1 and NIL-ipa1 in SAs and YPs, respectively. Rice Actin was used as reference. Values are means 6 SE (n = 3). The double asterisks represent significant difference determined by the Student’s t test at P &lt; 0.01. (from reference&lt;ref name=&quot;ref1&quot; /&gt;)]].<br /> <br /> ===Protein===<br /> 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).<br /> <br /> 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). Therefore, it has been suggested that Os SPL14 alleles have great potential for breeding (Jiao et al., 2010; Miura et al., 2010).<br /> <br /> ==Labs working on this gene==<br /> State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Zefu Lu, Hong Yu, Yonghong Wang, Jiayang Li)<br /> State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China(Xingming Hu, Qian Qian)<br /> State Key Laboratory of Plant Cell and Chromosome Engineering and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China(Xiangdong Fu)<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li .Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture. The Plant Cell, 2013, 25(10): 3743-3759&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Yongqing Jiao, Yonghong Wang, Dawei Xue, Jing Wang, Meixian Yan, Guifu Liu, Guojun Dong, Dali Zeng, Zefu Lu, Xudong Zhu, Qian Qian, Jiayang Li. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice .Nature Genetics, 2010, 42(6): 541-544&lt;/ref&gt;<br /> <br /> ==Structured Information==<br /> <br /> LOCUS GU136674 7229 bp DNA linear PLN 29-JUN-2010<br /> DEFINITION Oryza sativa Japonica Group IPA1 (IPA1) gene, complete cds.<br /> ACCESSION GU136674<br /> VERSION GU136674.1 GI:299482811<br /> KEYWORDS .<br /> SOURCE Oryza sativa (rice)<br /> ORGANISM Oryza sativa<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> REFERENCE 1 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Xue,D., Wang,J., Yan,M., Liu,G., Dong,G.,<br /> Zeng,D., Lu,Z., Zhu,X., Qian,Q. and Li,J.<br /> TITLE Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture<br /> in rice<br /> JOURNAL Nat. Genet. 42 (6), 541-544 (2010)<br /> PUBMED 20495565<br /> REFERENCE 2 (bases 1 to 7229)<br /> AUTHORS Jiao,Y., Wang,Y., Qian,Q. and Li,J.<br /> TITLE Direct Submission<br /> JOURNAL Submitted (22-OCT-2009) State Key Laboratory of Plant Genomics and<br /> National Center for Plant Gene Research, Institute of Genetics and<br /> Developmental Biology, Chinese Academy of Sciences, No.1 West<br /> Beichen Road, Chaoyang District, Beijing 100101, China<br /> FEATURES Location/Qualifiers<br /> source 1..7229<br /> /organism=&quot;Oryza sativa&quot;<br /> /mol_type=&quot;genomic DNA&quot;<br /> /db_xref=&quot;taxon:4530&quot;<br /> /chromosome=&quot;8&quot;<br /> /map=&quot;RM149-RM1345&quot;<br /> gene 995..5150<br /> /gene=&quot;IPA1&quot;<br /> mRNA join(995..1566,3997..4130,4233..5150)<br /> /gene=&quot;IPA1&quot;<br /> /product=&quot;IPA1&quot;<br /> CDS join(1118..1566,3997..4130,4233..4903)<br /> /gene=&quot;IPA1&quot;<br /> /note=&quot;transcription factor&quot;<br /> /codon_start=1<br /> /product=&quot;IPA1&quot;<br /> /protein_id=&quot;ADJ19220.1&quot;<br /> /db_xref=&quot;GI:299482812&quot;<br /> /translation=&quot;MEMASGGGAAAAAGGGVGGSGGGGGGGDEHRQLHGLKFGKKIYF<br /> EDAAAAAGGGGTGSGSGSASAAPPSSSSKAAGGGRGGGGKNKGKGVAAAAPPPPPPPP<br /> RCQVEGCGADLSGIKNYYCRHKVCFMHSKAPRVVVAGLEQRFCQQCSRFHLLPEFDQG<br /> KRSCRRRLAGHNERRRRPQTPLASRYGRLAASVGEHRRFRSFTLDFSYPRVPSSVRNA<br /> WPAIQPGDRISGGIQWHRNVAPHGHSSAVAGYGANTYSGQGSSSSGPPVFAGPNLPPG<br /> GCLAGVGAATDSSCALSLLSTQPWDTTTHSAAASHNQAAAMSTTTSFDGNPVAPSAMA<br /> GSYMAPSPWTGSRGHEGGGRSVAHQLPHEVSLDEVHPGPSHHAHFSGELELALQGNGP<br /> APAPRIDPGSGSTFDQTSNTMDWSL&quot;<br /> ORIGIN <br /> 1 gcaatgtaga gccacgtagg caagtcgctt gcgtggagga gagaggggag tggggaccgt<br /> 61 tcccaaccca gcttcgtgtg accaagtttg gccacacggg ccaaacgaac ctcagcaact<br /> 121 tttgtcagaa agaaaagaac ctccgcgaga aacaagaaag cgagagaggg agagaaagga<br /> 181 ggctcgtcgg agtaggggcg ctcggggtat ggggctcggc ggaggctcgc tggagtaggg<br /> 241 gccgccactg cgtggggctc gccggagtag gggcgctcgg ggagcctccc gagatccgcc<br /> 301 gctcagcggc gccgccgtct tccgggcaga gctctcgaag ctcgccctcc tcgcgcgccg<br /> 361 gtggcgttgg cggggcccgc gtgtggctac gcagctccgg tgctgcgcct ccaccgtcga<br /> 421 cgacagcgcc gcttggcgct gccgccgtct tccgccgcgc cgctggacgc cgccagatct<br /> 481 gctgctcgtc gccgcgtggg ccgctccacc cggttggagg aggagaggcg gcgccgcgct<br /> 541 tgggctgccc caccgccgag ctctgccgcg ccgttcgccg gtgctgccga gctccgccgc<br /> 601 gcctgccgga gcacgctgcc atggccgccc tggagaagac acgagagaat taggtggagg<br /> 661 gtgggggaag ggtgagattt tttatattat ctatgggtcc cattataaat tttctaaacc<br /> 721 acacttatac tgtgggtgca gtgtcattta gagttcccaa accacctatg ttgcagctgt<br /> 781 ggtataacaa tttgctagga cgcattgcta ctgcccttgt accctgctat aagaagataa<br /> 841 ccaatgacat ctccactcga ttttctcggc gcgcgtgtga gggtgtgagg ataattttta<br /> 901 ttttaagtgg tttttaaggg cggagagaga gagagagaga gggcaccgca ctacttctac<br /> 961 ttgtgtgtgt gtcgctcgct gggcttcgcc acctttccgt ctctttcctc tctcttctct<br /> 1021 ctccccctct cctggaggag agagaggaga agaggagggg gggccgcgcc aagagccacg<br /> 1081 cgcgctacag tctccttccc acccgcgacc gcgagcaatg gagatggcca gtggaggagg<br /> 1141 cgccgccgcc gccgccggcg gcggagtagg cggcagcggc ggcggtggtg gtggagggga<br /> 1201 cgagcaccgc cagctgcacg gtctcaagtt cggcaagaag atctacttcg aggacgccgc<br /> 1261 cgcggcagca ggcggcggcg gcactggcag tggcagtggc agcgcgagcg ccgcgccgcc<br /> 1321 gtcctcgtct tccaaggcgg cgggtggtgg acgcggcgga gggggcaaga acaaggggaa<br /> 1381 gggcgtggcc gcggcggcgc caccgccgcc gccgccgccg ccgcggtgcc aggtggaggg<br /> 1441 gtgcggcgcg gatctgagcg ggatcaagaa ctactactgc cgccacaagg tgtgcttcat<br /> 1501 gcattccaag gctccccgcg tcgtcgtcgc cggcctcgag cagcgcttct gccagcagtg<br /> 1561 cagcaggtca ctctctcact cacctcgcca ttgctgatgt caccactgct tttgctttgc<br /> 1621 tttgcttgct ctccctcctc tttcacctat ctctcttgtt tatttgcttc ttgttcttgt<br /> 1681 ttagtgctag tacatgtgtt gttattgttg tgccgttttg tcttttgggt tattgtgttg<br /> 1741 ttgttactac tcgttttact ataggttttt aaggtttatg agcacggcca ccacattaga<br /> 1801 tgcactgtca agtggtgtgt gtgggacctt tcctgctaaa acaagctgat ttcaactctc<br /> 1861 tgaaacttcc tgcatttcat ctatttttat ctttgattgt gttgggagta ctacactagt<br /> 1921 agtgttaata ttttgactgg tgcttatgag atttttaagt tggtaggttg atgaggaaaa<br /> 1981 tactccttta tatggttgag tgatgtgact tgcctgtctg cctgcctgcc tgccgctttg<br /> 2041 cataagattc ctctgtgtta gtaagagcca ctgtttattt gtactggtgc ttactctact<br /> 2101 tagttaatta gccattagct ataaaattcc gttgatgttg caagcttagc aatggccacg<br /> 2161 gtaagaatgg gagagagaag ttggctaaag ctgttgcttt gtagtttgta ctatatatgt<br /> 2221 gtctttgtgt tgcaagatat gcaactccta ctatgctgtg acttgagctc aaggttttca<br /> 2281 gttatctata gatccttact actactgagc atactaccac ttctgtatgg tagcatatgg<br /> 2341 tagcatagtc caagttccaa cgcctcgcca gttgttcata atctatacta ccacttctgt<br /> 2401 gcatttgtta cttttattta atagtttgtc tcattagctg acaagcatat gcctgttttg<br /> 2461 atatctgccc ctcttgtaat agtctatgga tagcttggac tgtttgatgc tttaattttt<br /> 2521 tactagcaac acttagggcc cctttgaaat ggaggattag caaaggaatt ttggaggatt<br /> 2581 cattttccta aggatttttt cctatagagc cctttgattc atagaaagag gataggaaaa<br /> 2641 cttccgtagg attgcattcc tatgatcaat tccataggaa aataagcaag aggttagacc<br /> 2701 tcttgtgaaa ctttcctttg ttgagtgtat cttgtggtat aatcaaaggg ctcttctctc<br /> 2761 catttcatgt gttttcaatt cctgtaggat tggaaaaaca tacaacttca attcctacgt<br /> 2821 ttttcctatt cctatgtttt tcctatcctg cgtttcaaag gggcccttaa ggatgaaggg<br /> 2881 aagtaagaga aacatactag agaatatgta gtagtatttc tacattccat atttgtagca<br /> 2941 ctagcccaca aatatctttg ccttgtactt acttcatacc agttcccccc ttttcagagc<br /> 3001 aaaccaacaa tttctgttgc cttatatatc tagtgtcttc gtactaatat atctgttcca<br /> 3061 aaatgtacct gtccaaattc atagctagaa atagctttat ttaggacgga agtaataact<br /> 3121 gttgttagag acttggttca gacttttggt tatgttgagg ctactatcat ttcctttacg<br /> 3181 ggccaaatta ctacaaatga gaattcataa aaatgtcaag attttatgat tgttgtagct<br /> 3241 ttatttagga cggaggtagt aattgttgtt agagacttgg ttcagacttt tggttacgtt<br /> 3301 gaagctacta tcatttcctt tatggtcaaa ttactaacaa tgagtattca taaaaatgtc<br /> 3361 aagattttat aattgagctg tgccagtgct aagtgtgtca ctatctgatg ccataatgca<br /> 3421 tcattataaa agccagatgg accattagct tttatgtgta ggacacctgc cgtccaatta<br /> 3481 gatggataac catctagtgt ttgtgtactg ttattttaag cccgacatct cacaactcca<br /> 3541 tgaatgatta cagtcttcct ttcacatggt gtccttttgt tgtgttagga atagcatttt<br /> 3601 ttatttatgg gtgtaattat gaaaggcact aggagagttg ctgctttatc ttgatgggat<br /> 3661 ttgtagtaat accatcttta ggatgacaag aaatcttgtt ctgagttagc atgggctgcc<br /> 3721 ttttgacctg agctacggtt tgctatgttt ggcttgcatc atgcagatct attaggataa<br /> 3781 taagcatata aaagttgctt gcattgtgca ttgcttgttt taccttgatt catgtaggag<br /> 3841 taatttgctc gccatgcctc gttttgcttt ctgagtcaac agccaaattt agatgatgta<br /> 3901 ccttctgttg cttcaaaaac tcagtcactg cacagcagca gtggatagga ttcagaatca<br /> 3961 atctatccat gattctctgt tcacataata tgacaggttc cacctgctgc ctgaatttga<br /> 4021 ccaaggaaaa cgcagctgcc gcagacgcct tgcaggtcat aatgagcgcc ggaggaggcc<br /> 4081 gcaaacccct ttggcatcac gctacggtcg actagctgca tctgttggtg gtatcatcag<br /> 4141 aggctcttgt tttctttgca tcttgtgtgt ttgttggtaa ctactggttg cattcgctga<br /> 4201 tgtgttgttt gttgcgattc ttgatccaga agagcatcgc aggttcagaa gctttacgtt<br /> 4261 ggatttctcc tacccaaggg ttccaagcag cgtaaggaat gcatggccag caattcaacc<br /> 4321 aggcgatcgg atctccggtg gtatccagtg gcacaggaac gtagctcctc atggtcactc<br /> 4381 tagtgcagtg gcgggatatg gtgccaacac atacagcggc caaggtagct cttcttcagg<br /> 4441 gccaccggtg ttcgctggcc caaatctccc tccaggtgga tgtctcgcag gggtcggtgc<br /> 4501 cgccaccgac tcgagctgtg ctctctctct tctgtcaacc cagccatggg atactactac<br /> 4561 ccacagtgcc gctgccagcc acaaccaggc tgcagccatg tccactacca ccagctttga<br /> 4621 tggcaatcct gtggcaccct ccgccatggc gggtagctac atggcaccaa gcccctggac<br /> 4681 aggttctcgg ggccatgagg gtggtggtcg gagcgtggcg caccagctac cacatgaagt<br /> 4741 ctcacttgat gaggtgcacc ctggtcctag ccatcatgcc cacttctccg gtgagcttga<br /> 4801 gcttgctctg caggggaacg gtccagcccc agcaccacgc atcgatcctg ggtccggcag<br /> 4861 caccttcgac caaaccagca acacgatgga ttggtctctg tagaggctgt tccagctgcc<br /> 4921 atcgatctgt cgtcccgcaa ggcgagtcat ggaactgaag aacctcatgc tgcctgccct<br /> 4981 tattttgtgt tcaaattttc ctttccagta tggaaaggaa attctaaggt gactggcgat<br /> 5041 taatctccct gtgatgaata ataatgcgcg cccttgaact caattaattg ctgtgccgca<br /> 5101 tccatctatg taactctcca tgaattttta agtatcagtg ttaatgctgt attgtcgagg<br /> 5161 acttctgctc gatatgttat ttctcttatg ttgttcatca tgaatctttt tctgcttatt<br /> 5221 attctggtgc cgggttgtcc ttaccacaga agattcagtt tcggttggcg agagtaaaca<br /> 5281 ccttccctgg ttgtgacaaa agctccaacc ttttcacttc tcggcctgta tttgatcttc<br /> 5341 cccttctgac gctgttatac tacttttaag cctgtatgtt tccagccttc caggtgaagg<br /> 5401 gccatactga agagaaaaca tgctttcagg gtttgatgca ttgtgtactt tacaagtgta<br /> 5461 cttaagattt tgtacaattt atatatgtac ctgctctgct gctgagtatt gtaggaaaga<br /> 5521 atcagttcga agggcgtgtg ttcatgtaaa gtgagaccac atgcacagcg tggatttgca<br /> 5581 gcatgctctc tgcaccagtg gtgttctgtt gatgcctttg atgggctggc tgaggtgaga<br /> 5641 ggaggatgat ccatgttggc agcttcttca ctctgaaaaa taaaagagaa gaaatgttca<br /> 5701 gatttgcaga caagtggaga gcagtgatat attctacaat aaaacattac caccttgctt<br /> 5761 ttctgtgatg atagatactc catggaattt tgcatcaagc atctcttgtt ttccagccac<br /> 5821 tgtttgctgg gttgttgctt caatttcgtc ccaattgatt ggtcaccttt ggttgtgact<br /> 5881 tgagagcact gagcactgaa acttttgctg tcagcaggca atgcacctca tccatgtcac<br /> 5941 gacagaggga gagagcccac ataaatggcc aaagaggaca catacagtgg cactgatgca<br /> 6001 gtcattgcaa cataattgac atcatgctaa acagtggtgt aaccatatgt tagctagcct<br /> 6061 gtgatcagca aacagtgatt atggatctta atgtcacatg caagatttga cacagttgta<br /> 6121 aaaccatcat tgcattgaag atagatccca gcaacaggtg tatgatgtat tgctagaatg<br /> 6181 aatcaaaaat atcagtgcca tcctaaacac agtactacca acttgaacag ttatcaccgt<br /> 6241 gattggaaaa cagaaatgta taattgcttt ggcgccatct gcttatcatt atcatatgtc<br /> 6301 gcagatcact tgttccattg acacgactct ttttcactgt gaggagaggc accttgattt<br /> 6361 ggacttttca agagctgtag caagggctcc tttgaagcct tctacatgga ggagcagagc<br /> 6421 ataccatatg cagaactgta aactcttcct gaagctttcc agttccaccc ttgtagcttt<br /> 6481 aagctgccgc aagagaatta tcatttctaa cattgagatg tgatactgaa atgtgaaagg<br /> 6541 tgattcgcag tataggtccc aaaatatcgt ttacagcaac ttgcaaatcc tgcatgatac<br /> 6601 agttaattca tcaaaatatt agaccattag tactacagtc tacaaatacc ccttaactga<br /> 6661 acatgtatga taaggacaag attctgaagc tccagtgcat caggaatcca acgcagtatg<br /> 6721 caaatcatta ctgaacaaga ttcctgcact tacagaatca tcacctgttg taacaaggac<br /> 6781 cattctttgt tgccccagac acagcgaatt aatggtcatc ttcatttggc ccaggacatt<br /> 6841 catttgccaa tgcttctgct gattcatact gaaaagggga caatgcgtcc aattttaaaa<br /> 6901 gcatggaaga tgctataaaa gatcacccta tttaaaatgc agagaaaacc aaagatccaa<br /> 6961 catgatatgg taatcacaga ttcccaacag taatgccgtc cagtaggcag taggggcatg<br /> 7021 cacataaaca ctagtactat gtagagctga agcttatttc cagaatgaag ctgaccttgc<br /> 7081 aaccgcaata aaggcaatag tagtgttcat cgcgcagctt agccaatata ttttgcaaat<br /> 7141 cctgcaagaa taaacacagg tcaatctcgt cctttcagca aaatttgcag tcttgcataa<br /> 7201 gatttctcag ataaaaaagg aagtctaga<br /> //</div>

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