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"2013-09-13T13:25:57" } } }, "security": { "owner": "robert", "supervisor": "karen", "allowedToRead": [ "edinburgh", "halliday", "millar", "public", "robust" ], "allowedToWrite": [ "halliday", "millar" ] }, "open_access_info": { "grantedBy": "karen", "grantedOn": "2013-09-13T13:27:29", "licence": "CC_BY", "comment": "System generated on 17-Oct-2014" }, "desc": { "experiment_type": "Literature data", "id": "13790751359110", "status": "described", "name": "Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, prr5, toc1;prr5", "purpose": "In Arabidopsis thaliana, many circadian clock-associated genes have been identified. Among them, the eveningexpressed TOC1 (TIMING OF CAB EXPRESSION 1)\ngene plays a role by forming a transcriptional feedback core loop together with the morning-expressed CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene and its homologous LHY (LATE ELONGATED HYPOCOTYL) gene. TOC1 encodes a member of the PSEUDORESPONSE REGULATOR (PRR) family, including PRR9, PRR7, PRR5, PRR3,and PRR1/TOC1. The PRR genes other than TOC1 (or PRR1) also appear to be crucial for certain circadian-associated events. To clarify missing genetic linkages amongst these PRR genes, here we constructed a toc1 prr5 double knockdown mutant. In freerunning circadian rhythms, the resulting toc1-2 prr5-11 mutant plants showed an extremely short period and reduced amplitude phenotype, which was more severe than that of the toc1-2 single mutant plant, suggesting a non-linear genetic interaction between TOC1 and PRR5. Surprisingly, the hallmark early flowering phenotype of toc1-2 in the shortday conditions had been converted to a markedly late flowering phenotype in the long-day conditions, when combined with the prr5-11 allele, which itself showed a subtle flowering phenotype. This unexpected genetic result (i.e. phenotypic sign conversion) suggested that the TOC1 and PRR5 genes are coordinately implicated in a non-linear and closed genetic circuitry. In the toc1-2 prr5-11 double mutant, the diurnal expression profile of CDF1 (CYCLING DOF FACTOR 1) was markedly de-repressed in the evening in the long-day conditions. These and other results of this study led us to propose the novel view that TOC1 might play bipartite roles in the control of flowering time within a closed circuitry; the one is a GI (GIGANTEA)-dependent negative role through CCA1/LHY, and the other is a CDF1-dependent positive role through cooperating closely with PRR5.", "pubmed_id": "18178585", "provenance": { "site": "Mizuno", "author": "Ito, S.", "start_date": "2008-01-04" }, "growth_condition": [ { "name": "Ito2008_LD", "medium": "MS 1% sucrose", "stratification": "3 days at 4C", "duration": "10.0", "temperature_conditions": { "label": "const. 22.0C", "env_conditions": { "type": "constant_temp", "label": "const. 22.0C", "duration": "10", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "10", "cycle_length": "24", "base_value": "22.0", "second_value": "22.0" } } }, "light_conditions": { "label": "W: LD 16:00:08:00", "light_channel": { "spectrum": "white", "intensity": "90-100", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 16:00:08:00", "duration": "10", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "10", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "16:00" } } } } } }, { "name": "Ito2008_SD", "medium": "MS 1% sucrose", "stratification": "3 days at 4C", "duration": "7.0", "temperature_conditions": { "label": "const. 22.0C", "env_conditions": { "type": "constant_temp", "label": "const. 22.0C", "duration": "7", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "7", "cycle_length": "24", "base_value": "22.0", "second_value": "22.0" } } }, "light_conditions": { "label": "W: LD 10:00:14:00", "light_channel": { "spectrum": "white", "intensity": "120-150", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 10:00:14:00", "duration": "7", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "7", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "10:00" } } } } } } ], "experimental_condition": [ { "name": "Ito2008_LD", "medium": "MS 1% sucrose", "duration": "1.0", "temperature_conditions": { "label": "const. 22.0C", "env_conditions": { "type": "constant_temp", "label": "const. 22.0C", "duration": "1", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "1", "cycle_length": "24", "base_value": "22.0", "second_value": "22.0" } } }, "light_conditions": { "label": "W: LD 16:00:08:00", "light_channel": { "spectrum": "white", "intensity": "90-100", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 16:00:08:00", "duration": "1", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "1", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "16:00" } } } } } }, { "name": "Ito2008_SD", "medium": "MS 1% sucrose", "duration": "1.0", "temperature_conditions": { "label": "const. 22.0C", "env_conditions": { "type": "constant_temp", "label": "const. 22.0C", "duration": "1", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "1", "cycle_length": "24", "base_value": "22.0", "second_value": "22.0" } } }, "light_conditions": { "label": "W: LD 10:00:14:00", "light_channel": { "spectrum": "white", "intensity": "120-150", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 10:00:14:00", "duration": "1", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "1", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "10:00" } } } } } } ], "measurement": { "technique": "RT-PCR", "param": [ { "@name": "RD error_type", "@value": "none" }, { "@name": "RD first_data_col", "@value": "2" }, { "@name": "RD first_data_row", "@value": "3" }, { "@name": "RD time_col", "@value": "1" } ] }, "sample_preparation": { "method": "For real-time PCR, seedlings were grown on MS plates containing 1% sucrose under the conditions of LoD (16 h light/8 h dark) or ShD (10 h light/14 h dark) for 10 or 7 d. They were then harvested (3 h intervals) to quantify mRNA of genes involved in flowering regulation. Total RNA was purified by an RNeasy plant kit (Qiagen, Valencia, CA, USA). To synthesize cDNA, 1 mg of each RNA was reverse transcribed with Rever Tra Ace (TOYOBO, Osaka, Japan) and oligo(dT) primer. The synthesized cDNAs were amplified with iQ SYBR Green supermix (Bio-Rad Laboratories, Hercules, CA, USA) and a primer set using a MiniOpticon real-time PCR system (Bio-Rad Laboratories). The following standard thermal cycling\nprogram was used for all PCRs: 95oC for 120 s, 40 cycles of 95oC for 10 s, and 60oC for 60 s. Data were analyzed using Opticon Monitor version 3.1 software (Bio-Rad Laboratories). The oligonucleotide primers used in this study have all been described previously (Niwa et al. 2007)." }, "samples": { "sample": [ { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "2", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "3", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "4", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "5", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "6", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "7", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "8", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "9", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "10", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "11", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "12", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "13", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "14", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "15", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "16", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "17", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "18", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "19", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "20", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD", "ignored": "false" }, { "sample_id": "21", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "22", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "23", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "24", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "25", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "26", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "27", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "28", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "29", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "30", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "31", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" }, { "sample_id": "32", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5", "line": "unknown" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD", "ignored": "false" } ] } }, "pedro": { "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", "@xsi:schemaLocation": "/Z:/communal/DataDescription/models/literature/model/full_literature.xsd", "name": "Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, prr5, toc1;prr5", "purpose": "In Arabidopsis thaliana, many circadian clock-associated genes have been identified. Among them, the eveningexpressed TOC1 (TIMING OF CAB EXPRESSION 1)\ngene plays a role by forming a transcriptional feedback core loop together with the morning-expressed CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene and its homologous LHY (LATE ELONGATED HYPOCOTYL) gene. TOC1 encodes a member of the PSEUDORESPONSE REGULATOR (PRR) family, including PRR9, PRR7, PRR5, PRR3,and PRR1/TOC1. The PRR genes other than TOC1 (or PRR1) also appear to be crucial for certain circadian-associated events. To clarify missing genetic linkages amongst these PRR genes, here we constructed a toc1 prr5 double knockdown mutant. In freerunning circadian rhythms, the resulting toc1-2 prr5-11 mutant plants showed an extremely short period and reduced amplitude phenotype, which was more severe than that of the toc1-2 single mutant plant, suggesting a non-linear genetic interaction between TOC1 and PRR5. Surprisingly, the hallmark early flowering phenotype of toc1-2 in the shortday conditions had been converted to a markedly late flowering phenotype in the long-day conditions, when combined with the prr5-11 allele, which itself showed a subtle flowering phenotype. This unexpected genetic result (i.e. phenotypic sign conversion) suggested that the TOC1 and PRR5 genes are coordinately implicated in a non-linear and closed genetic circuitry. In the toc1-2 prr5-11 double mutant, the diurnal expression profile of CDF1 (CYCLING DOF FACTOR 1) was markedly de-repressed in the evening in the long-day conditions. These and other results of this study led us to propose the novel view that TOC1 might play bipartite roles in the control of flowering time within a closed circuitry; the one is a GI (GIGANTEA)-dependent negative role through CCA1/LHY, and the other is a CDF1-dependent positive role through cooperating closely with PRR5.", "pubmed_id": "18178585", "provenance": { "pub_title": "Insight into missing genetic links between two evening-expressed pseudo-response regulator genes TOC1 and PRR5 in the circadian-clock controlled circuitry in Arabidopsis thaliana.", "first_author": "Ito, S.", "group": "Mizuno", "pub_date": "2008-01-04" }, "growth_condition": [ { "name": "Ito2008_LD", "medium": "MS 1% sucrose", "stratification": "3 days at 4C", "duration": "10", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "22" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "90-100", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "16" } } } }, { "name": "Ito2008_SD", "medium": "MS 1% sucrose", "stratification": "3 days at 4C", "duration": "7", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "22" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "120-150", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "10" } } } } ], "experimental_condition": [ { "name": "Ito2008_LD", "medium": "MS 1% sucrose", "duration": "1", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "22" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "90-100", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "16" } } } }, { "name": "Ito2008_SD", "medium": "MS 1% sucrose", "duration": "1", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "22" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "120-150", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "10" } } } } ], "measurement": { "technique": "RT-PCR" }, "sample_preparation": { "method": "For real-time PCR, seedlings were grown on MS plates containing 1% sucrose under the conditions of LoD (16 h light/8 h dark) or ShD (10 h light/14 h dark) for 10 or 7 d. They were then harvested (3 h intervals) to quantify mRNA of genes involved in flowering regulation. Total RNA was purified by an RNeasy plant kit (Qiagen, Valencia, CA, USA). To synthesize cDNA, 1 mg of each RNA was reverse transcribed with Rever Tra Ace (TOYOBO, Osaka, Japan) and oligo(dT) primer. The synthesized cDNAs were amplified with iQ SYBR Green supermix (Bio-Rad Laboratories, Hercules, CA, USA) and a primer set using a MiniOpticon real-time PCR system (Bio-Rad Laboratories). The following standard thermal cycling\nprogram was used for all PCRs: 95oC for 120 s, 40 cycles of 95oC for 10 s, and 60oC for 60 s. Data were analyzed using Opticon Monitor version 3.1 software (Bio-Rad Laboratories). The oligonucleotide primers used in this study have all been described previously (Niwa et al. 2007)." }, "samples": { "sample": [ { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "2", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "3", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "4", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "GI", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "5", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "6", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "7", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "8", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "FKF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "9", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "10", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "11", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "12", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "CDF1", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "13", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "14", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "15", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "16", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "CO", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "17", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "18", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "19", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "20", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "FT", "growth_cond_name": "Ito2008_LD", "experiment_cond_name": "Ito2008_LD" }, { "sample_id": "21", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "22", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "23", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "24", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "CDF1", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "25", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "26", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "27", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "28", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "CO", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "29", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "30", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1-2" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "31", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr5-11" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" }, { "sample_id": "32", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "toc1;prr5" }, "marker": "FT", "growth_cond_name": "Ito2008_SD", "experiment_cond_name": "Ito2008_SD" } ] } }, "biblio": { "principal": "Ito S", "institution": "Nagoya University", "author": [ "Ito S", "Kawamura H", "Niwa Y", "Nakamichi N", "Yamashino T", "Mizuno T" ], "curator": "Robert Smith" } }