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Fan H, He Q, Dong Y, Xu W, Lou Y, Hua X, Xu T. Selection of suitable candidate genes for mRNA expression normalization in bulbil development of Pinellia ternata. Sci Rep 2022; 12:8849. [PMID: 35614175 PMCID: PMC9133075 DOI: 10.1038/s41598-022-12782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Pinellia ternata (Thunb.) Breit. (Abbreviated as P. ternata). It is a commonly prescribed Chinese traditional medicinal herb for the treatment of phlegm, cough, and morning sick. Bulbil reproduction is one of the main reproductive methods of P. ternata. The accurate quantification of gene expression patterns associated with bulbil development might be helpful to explore the molecular mechanism involved in P. ternata reproduction. Quantitative real-time PCR was the most preferred method for expression profile and function analysis of mRNA. However, the reference genes in different tissues of P. ternata in different periods of bulbil development have not been studied in detail. In present study, the expression stability of eight candidate reference genes were determined with programs: geNorm, NormFinder, BestKeeper, and refFinder. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the top- rated reference gene in all samples of P. ternata, while different combinations of reference gene proved to be the most stable depending on development stage and tissue type. Furthermore, the reliability of GAPDH expression was verified by six P. ternata related genes in hormone and nutrient biosynthesis pathways, and the expression profiles of these genes were agreed with the results of RNA-seq digital gene expression analysis. These results can contribute to studies of gene expression patterns and functional analysis of P. ternata involved in bulbil development.
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Affiliation(s)
- Haoyu Fan
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qiuling He
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
| | - Yiheng Dong
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wenxin Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yanlin Lou
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuejun Hua
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tao Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China.
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The Influence of Abiotic Factors on the Induction of Seaweed Callus. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Seaweeds are a major source of functional foods, nutraceuticals, and pharmaceuticals. Seaweed can be sustainably harvested through callus culture, which yields homogenous cells and bioproducts under controlled conditions. Callus induction is a crucial early step in callus culture and is influenced by several abiotic factors. This review aims to discuss the influence of abiotic factors on callus induction in seaweeds, a prerequisite for the application and development of seaweed callus culture. We used three online databases (Springer, Science Direct, and Wiley) to search for the literature on seaweed callus induction published between 1987 and 2020. Thirty-three articles for review were identified and analyzed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The analysis covers 56 seaweed species (3% Chlorophyta, 44% Phaeophyta, and 53% Rhodophyta) under various abiotic treatments, including light irradiance (23%), temperature (15%), media type (21%), plant growth regulators (26%), gelling conditions (9%), and other factors (6%). The information on these abiotic factors is intended to be a practical reference and to foster the further study of the callus culture of seaweed. More studies are needed to determine how to maintain and increase callus mass in suspension culture for the industrial production of seaweed and its metabolites.
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The Hulks and the Deadpools of the Cytokinin Universe: A Dual Strategy for Cytokinin Production, Translocation, and Signal Transduction. Biomolecules 2021; 11:biom11020209. [PMID: 33546210 PMCID: PMC7913349 DOI: 10.3390/biom11020209] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
Cytokinins are plant hormones, derivatives of adenine with a side chain at the N6-position. They are involved in many physiological processes. While the metabolism of trans-zeatin and isopentenyladenine, which are considered to be highly active cytokinins, has been extensively studied, there are others with less obvious functions, such as cis-zeatin, dihydrozeatin, and aromatic cytokinins, which have been comparatively neglected. To help explain this duality, we present a novel hypothesis metaphorically comparing various cytokinin forms, enzymes of CK metabolism, and their signalling and transporter functions to the comics superheroes Hulk and Deadpool. Hulk is a powerful but short-lived creation, whilst Deadpool presents a more subtle and enduring force. With this dual framework in mind, this review compares different cytokinin metabolites, and their biosynthesis, translocation, and sensing to illustrate the different mechanisms behind the two CK strategies. This is put together and applied to a plant developmental scale and, beyond plants, to interactions with organisms of other kingdoms, to highlight where future study can benefit the understanding of plant fitness and productivity.
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Triflumizole as a Novel Lead Compound for Strigolactone Biosynthesis Inhibitor. Molecules 2020; 25:molecules25235525. [PMID: 33255720 PMCID: PMC7728069 DOI: 10.3390/molecules25235525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Strigolactones (SLs) are carotenoid-derived plant hormones involved in the development of various plants. SLs also stimulate seed germination of the root parasitic plants, Striga spp. and Orobanche spp., which reduce crop yield. Therefore, regulating SL biosynthesis may lessen the damage of root parasitic plants. Biosynthetic inhibitors effectively control biological processes by targeted regulation of biologically active compounds. In addition, biosynthetic inhibitors regulate endogenous levels in developmental stage- and tissue-specific manners. To date, although some chemicals have been found as SL biosynthesis inhibitor, these are derived from only three lead chemicals. In this study, to find a novel lead chemical for SL biosynthesis inhibitor, 27 nitrogen-containing heterocyclic derivatives were screened for inhibition of SL biosynthesis. Triflumizole most effectively reduced the levels of rice SL, 4-deoxyorobanchol (4DO), in root exudates. In addition, triflumizole inhibited endogenous 4DO biosynthesis in rice roots by inhibiting the enzymatic activity of Os900, a rice enzyme that converts the SL intermediate carlactone to 4DO. A Striga germination assay revealed that triflumizole-treated rice displayed a reduced level of germination stimulation for Striga. These results identify triflumizole as a novel lead compound for inhibition of SL biosynthesis.
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Li X, Ye L, Zhang X, Tan H, Li Q. Root-tip cutting and uniconazole treatment improve the colonization rate of Tuber indicum on Pinus armandii seedlings in the greenhouse. Microb Biotechnol 2020; 13:535-547. [PMID: 31920011 PMCID: PMC7017816 DOI: 10.1111/1751-7915.13511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/23/2019] [Accepted: 10/26/2019] [Indexed: 11/30/2022] Open
Abstract
The Chinese black truffle Tuber indicum is commercially valuable. The main factors influencing the success or failure of a truffle crop include the mycorrhizal colonization rate and host plant quality. The effects of a plant growth regulator (uniconazole) and plant growth management technique (root‐tip cutting) on T. indicum colonization rate and Pinus armandii seedling growth were assessed under greenhouse conditions. The results indicated that 10 mg l−1 uniconazole or the combination of 5 mg l−1 uniconazole and root‐tip cutting constitutes an effective method for ectomycorrhizal synthesis based on an overall evaluation of colonization rate, plant biomass, plant height, root weight, stem circumference and antioxidant enzyme activities (SOD and POD) of P. armandii. The abundance of Proteobacteria in the rhizosphere of colonized seedlings might serve as an indicator of stable mycorrhizal colonization. This research inspires the potential application of uniconazole and root‐tip cutting treatments for mycorrhizal synthesis and truffle cultivation.
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Affiliation(s)
- Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Xiaoping Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Hao Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
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Kroll CK, Brenner WG. Cytokinin Signaling Downstream of the His-Asp Phosphorelay Network: Cytokinin-Regulated Genes and Their Functions. FRONTIERS IN PLANT SCIENCE 2020; 11:604489. [PMID: 33329676 PMCID: PMC7718014 DOI: 10.3389/fpls.2020.604489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/26/2020] [Indexed: 05/17/2023]
Abstract
The plant hormone cytokinin, existing in several molecular forms, is perceived by membrane-localized histidine kinases. The signal is transduced to transcription factors of the type-B response regulator family localized in the nucleus by a multi-step histidine-aspartate phosphorelay network employing histidine phosphotransmitters as shuttle proteins across the nuclear envelope. The type-B response regulators activate a number of primary response genes, some of which trigger in turn further signaling events and the expression of secondary response genes. Most genes activated in both rounds of transcription were identified with high confidence using different transcriptomic toolkits and meta analyses of multiple individual published datasets. In this review, we attempt to summarize the existing knowledge about the primary and secondary cytokinin response genes in order to try connecting gene expression with the multitude of effects that cytokinin exerts within the plant body and throughout the lifespan of a plant.
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Kawada K, Takahashi I, Arai M, Sasaki Y, Asami T, Yajima S, Ito S. Synthesis and Biological Evaluation of Novel Triazole Derivatives as Strigolactone Biosynthesis Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6143-6149. [PMID: 31083983 DOI: 10.1021/acs.jafc.9b01276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Strigolactones (SLs) are one of the plant hormones that control several important agronomic traits, such as shoot branching, leaf senescence, and stress tolerance. Manipulation of the SL biosynthesis can increase the crop yield. We previously reported that a triazole derivative, TIS108, inhibits SL biosynthesis. In this study, we synthesized a number of novel TIS108 derivatives. Structure-activity relationship studies revealed that 4-(2-phenoxyethoxy)-1-phenyl-2-(1 H-1,2,4-triazol-1-yl)butan-1-one (KK5) inhibits the level of 4-deoxyorobanchol in roots more strongly than TIS108. We further found that KK5-treated Arabidopsis showed increased branching phenotype with the upregulated gene expression of AtMAX3 and AtMAX4. These results indicate that KK5 is a specific SL biosynthesis inhibitor in rice and Arabidopsis.
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Affiliation(s)
- Kojiro Kawada
- Department of Bioscience , Tokyo University of Agriculture , 1-1-1 Sakuragaoka , Setagaya, Tokyo 156-8502 , Japan
| | - Ikuo Takahashi
- Department of Applied Biological Chemistry , The University of Tokyo , 1-1-1 Yayoi , Bunkyo, Tokyo 113-8657 , Japan
| | - Minori Arai
- Department of Bioscience , Tokyo University of Agriculture , 1-1-1 Sakuragaoka , Setagaya, Tokyo 156-8502 , Japan
| | - Yasuyuki Sasaki
- Department of Bioscience , Tokyo University of Agriculture , 1-1-1 Sakuragaoka , Setagaya, Tokyo 156-8502 , Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry , The University of Tokyo , 1-1-1 Yayoi , Bunkyo, Tokyo 113-8657 , Japan
- Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
- Department of Biochemistry , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Shunsuke Yajima
- Department of Bioscience , Tokyo University of Agriculture , 1-1-1 Sakuragaoka , Setagaya, Tokyo 156-8502 , Japan
| | - Shinsaku Ito
- Department of Bioscience , Tokyo University of Agriculture , 1-1-1 Sakuragaoka , Setagaya, Tokyo 156-8502 , Japan
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Jiang K, Asami T. Chemical regulators of plant hormones and their applications in basic research and agriculture*. Biosci Biotechnol Biochem 2018; 82:1265-1300. [DOI: 10.1080/09168451.2018.1462693] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ABSTRACT
Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology. Here, we summarize the available chemical regulators and their contributions to plant hormone studies. We also pose questions that remain to be addressed in plant hormone studies and that might be solved with the help of chemical regulators.
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Affiliation(s)
- Kai Jiang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Yin X, Komatsu S. Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress. J Proteomics 2017; 169:225-232. [PMID: 28137666 DOI: 10.1016/j.jprot.2017.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. BIOLOGICAL SIGNIFICANCE Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Best NB, Johal G, Dilkes BP. Phytohormone inhibitor treatments phenocopy brassinosteroid-gibberellin dwarf mutant interactions in maize. PLANT DIRECT 2017; 1:PLD39. [PMID: 31240275 PMCID: PMC6508556 DOI: 10.1002/pld3.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/14/2017] [Indexed: 05/12/2023]
Abstract
Phytohormone biosynthesis produces metabolites with profound effects on plant growth and development. Modulation of hormone levels during developmental events, in response to the environment, by genetic polymorphism, or by chemical application, can reveal the plant processes most responsive to a phytohormone. Applications of chemical inhibitors and subsequent measurements of specific phytohormones can determine whether, and which, phytohormone is affected by a molecule. In many cases, the sensitivity of biochemical testing has determined multiple pathways affected by a single inhibitor. Genetic studies are not subject to this problem, and a wealth of data about the morphological impacts of hormone biosynthetic inhibition have accumulated through the study of enzyme mutants. In this work, we sought to assess the specificity of three triazole inhibitors of cytochrome P450s by determining their abilities to recapitulate the phenotypes of single and double mutants affected in the production of brassinosteroid (BR) and gibberellin (GA) biosynthesis. The GA biosynthetic inhibitors uniconazole (UCZ) and paclobutrazol (PAC) were applied to the BR biosynthetic mutant nana plant2 (na2), and all double-mutant phenotypes were recovered in the UCZ treatment. PAC was unable to suppress the retention of pistils in the tassels of na2 mutant plants. The BR biosynthetic inhibitor propiconazole (PCZ) suppressed tiller outgrowth in the GA biosynthetic mutant dwarf5 (d5). All treatments were additive with genetic mutants for effects on plant height. Due to additional measurements performed here but not in previous studies of the double mutants, we detected new interactions between GA and BR biosynthesis affecting the days to tassel emergence and tassel branching. These experiments, a refinement of our previous model, and a discussion of the extension of this type of work are presented.
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Affiliation(s)
- Norman B. Best
- Department of Horticulture & Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
- Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Guri Johal
- Department of Botany & Plant PathologyPurdue UniversityWest LafayetteINUSA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteINUSA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
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11
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Wei Y, Dong C, Zhang H, Zheng X, Shu B, Shi S, Li W. Transcriptional changes in litchi (Litchi chinensis Sonn.) inflorescences treated with uniconazole. PLoS One 2017; 12:e0176053. [PMID: 28419137 PMCID: PMC5395186 DOI: 10.1371/journal.pone.0176053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/04/2017] [Indexed: 11/19/2022] Open
Abstract
In Arabidopsis, treating shoots with uniconazole can result in enhanced primary root elongation and bolting delay. Uniconazole spraying has become an important cultivation technique in controlling the flowering and improving the fruit-setting of litchi. However, the mechanism by which uniconazole regulates the complicated developmental processes in litchi remains unclear. This study aimed to determine which signal pathways and genes drive the responses of litchi inflorescences to uniconazole treatment. We monitored the transcriptional activity in inflorescences after uniconazole treatment by Illumina sequencing technology. The global expression profiles of uniconazole-treated litchi inflorescences were compared with those of the control, and 4051 differentially expressed genes were isolated. KEGG pathway enrichment analysis indicated that the plant hormone signal transduction pathway served key functions in the flower developmental stage under uniconazole treatment. Basing on the transcriptional analysis of genes involved in flower development, we hypothesized that uniconazole treatment increases the ratio of female flowers by activating the transcription of pistil-related genes. This phenomenon increases opportunities for pollination and fertilization, thereby enhancing the fruit-bearing rate. In addition, uniconazole treatment regulates the expression of unigenes involved in numerous transcription factor families, especially the bHLH and WRKY families. These findings suggest that the uniconazole-induced morphological changes in litchi inflorescences are related to the control of hormone signaling, the regulation of flowering genes, and the expression levels of various transcription factors. This study provides comprehensive inflorescence transcriptome data to elucidate the molecular mechanisms underlying the response of litchi flowers to uniconazole treatment and enumerates possible candidate genes that can be used to guide future research in controlling litchi flowering.
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Affiliation(s)
- Yongzan Wei
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Chen Dong
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Hongna Zhang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Xuewen Zheng
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Bo Shu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Shengyou Shi
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Weicai Li
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
- * E-mail:
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Wu C, Cui K, Wang W, Li Q, Fahad S, Hu Q, Huang J, Nie L, Mohapatra PK, Peng S. Heat-Induced Cytokinin Transportation and Degradation Are Associated with Reduced Panicle Cytokinin Expression and Fewer Spikelets per Panicle in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:371. [PMID: 28367158 PMCID: PMC5355447 DOI: 10.3389/fpls.2017.00371] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 03/02/2017] [Indexed: 05/06/2023]
Abstract
Cytokinins (CTKs) regulate panicle size and mediate heat tolerance in crops. To investigate the effect of high temperature on panicle CTK expression and the role of such expression in panicle differentiation in rice, four rice varieties (Nagina22, N22; Huanghuazhan, HHZ; Liangyoupeijiu, LYPJ; and Shanyou63, SY63) were grown under normal conditions and subjected to three high temperature treatments and one control treatment in temperature-controlled greenhouses for 15 days during the early reproductive stage. The high temperature treatments significantly reduced panicle CTK abundance in heat-susceptible LYPJ, HHZ, and N22 varieties, which showed fewer spikelets per panicle in comparison with control plants. Exogenous 6-benzylaminopurine application mitigated the effect of heat injury on the number of spikelets per panicle. The high temperature treatments significantly decreased the xylem sap flow rate and CTK transportation rate, but enhanced cytokinin oxidase/dehydrogenase (CKX) activity in heat-susceptible varieties. In comparison with the heat-susceptible varieties, heat-tolerant variety SY63 showed less reduction in panicle CTK abundance, an enhanced xylem sap flow rate, an improved CTK transport rate, and stable CKX activity under the high temperature treatments. Enzymes involved in CTK synthesis (isopentenyltransferase, LONELY GUY, and cytochrome P450 monooxygenase) were inhibited by the high temperature treatments. Heat-induced changes in CTK transportation from root to shoot through xylem sap flow and panicle CTK degradation via CKX were closely associated with the effects of heat on panicle CTK abundance and panicle size. Heat-tolerant variety SY63 showed stable panicle size under the high temperature treatments because of enhanced transport of root-derived CTKs and stable panicle CKX activity. Our results provide insight into rice heat tolerance that will facilitate the development of rice varieties with tolerance to high temperature.
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Affiliation(s)
- Chao Wu
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Kehui Cui
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
- Hubei Collaborative Innovation for Grain Industry, JingzhouChina
| | - Wencheng Wang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Shah Fahad
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Qiuqian Hu
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Jianliang Huang
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | - Lixiao Nie
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
| | | | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural UniversityWuhan, China
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13
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Yin X, Hiraga S, Hajika M, Nishimura M, Komatsu S. Transcriptomic analysis reveals the flooding tolerant mechanism in flooding tolerant line and abscisic acid treated soybean. PLANT MOLECULAR BIOLOGY 2017; 93:479-496. [PMID: 28012053 DOI: 10.1007/s11103-016-0576-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/07/2016] [Indexed: 06/06/2023]
Abstract
Soybean is highly sensitive to flooding stress and exhibits markedly reduced plant growth and grain yield under flooding conditions. To explore the mechanisms underlying initial flooding tolerance in soybean, RNA sequencing-based transcriptomic analysis was performed using a flooding-tolerant line and ABA-treated soybean. A total of 31 genes included 12 genes that exhibited similar temporal patterns were commonly changed in these plant groups in response to flooding and they were mainly involved in RNA regulation and protein metabolism. The mRNA expression of matrix metalloproteinase, glucose-6-phosphate isomerase, ATPase family AAA domain-containing protein 1, and cytochrome P450 77A1 was up-regulated in wild-type soybean under flooding conditions; however, no changes were detected in the flooding-tolerant line or ABA-treated soybean. The mRNA expression of cytochrome P450 77A1 was specifically up-regulated in root tips by flooding stress, but returned to the level found in control plants following treatment with the P450 inhibitor uniconazole. The survival ratio and root fresh weight of plants were markedly improved by 3-h uniconazole treatment under flooding stress. Taken together, these results suggest that cytochrome P450 77A1 is suppressed by uniconazole treatment and that this inhibition may enhance soybean tolerance to flooding stress.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, 305-8518, Japan
| | - Susumu Hiraga
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, 305-8518, Japan
| | - Makita Hajika
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, 305-8518, Japan
| | - Minoru Nishimura
- Graduate School of Life and Food Sciences, Niigata University, Niigata, 950-2181, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, 305-8518, Japan.
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14
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Liu X, Hu P, Huang M, Tang Y, Li Y, Li L, Hou X. The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat Commun 2016; 7:12768. [PMID: 27624486 PMCID: PMC5027291 DOI: 10.1038/ncomms12768] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/30/2016] [Indexed: 12/18/2022] Open
Abstract
The antagonistic crosstalk between gibberellic acid (GA) and abscisic acid (ABA) plays a pivotal role in the modulation of seed germination. However, the molecular mechanism of such phytohormone interaction remains largely elusive. Here we show that three Arabidopsis NUCLEAR FACTOR-Y C (NF-YC) homologues NF-YC3, NF-YC4 and NF-YC9 redundantly modulate GA- and ABA-mediated seed germination. These NF-YCs interact with the DELLA protein RGL2, a key repressor of GA signalling. The NF-YC–RGL2 module targets ABI5, a gene encoding a core component of ABA signalling, via specific CCAAT elements and collectively regulates a set of GA- and ABA-responsive genes, thus controlling germination. These results suggest that the NF-YC–RGL2–ABI5 module integrates GA and ABA signalling pathways during seed germination. Crosstalk between gibberellic acid (GA) and abscisic acid (ABA) regulates seed germination. Here the authors show that NF-YC transcription factors can interact with the RGL2 DELLA protein to regulate expression of ABI5 and therefore modulate ABA- and GA-responsive gene expression.
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Affiliation(s)
- Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Pengwei Hu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mingkun Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Tang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ling Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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15
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Kakei Y, Shimada Y. AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles. PLANT & CELL PHYSIOLOGY 2015; 56:e7. [PMID: 25505006 DOI: 10.1093/pcp/pcu174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In transcriptome experiments, the experimental conditions (e.g. mutants and/or treatments) cause transcriptional changes. Identifying experimental conditions that induce similar or opposite transcriptional changes can be useful to identify experimental conditions that affect the same biological process. AtCAST (http://atpbsmd.yokohama-cu.ac.jp) is a web-based tool to analyze the relationship between experimental conditions among transcriptome data. Users can analyze 'user's transcriptome data' of a new mutant or a new chemical compound whose function remains unknown to generate novel biological hypotheses. This tool also allows for mining of related 'experimental conditions' from the public microarray data, which are pre-included in AtCAST. This tool extracts a set of genes (i.e. module) that show significant transcriptional changes and generates a network graph to present related transcriptome data. The updated AtCAST now contains data on >7,000 microarrays, including experiments on various stresses, mutants and chemical treatments. Gene ontology term enrichment (GOE) analysis is introduced to assist the characterization of transcriptome data. The new AtCAST supports input from multiple platforms, including the 'Arabisopsis gene 1.1 ST array', a new microarray chip from Affymetrix and RNA sequencing (RNA-seq) data obtained using next-generation sequencing (NGS). As a pilot study, we conducted microarray analysis of Arabidopsis under auxin treatment using the new Affymetrix chip, and then analyzed the data in AtCAST. We also analyzed RNA-seq data of the pifq mutant using AtCAST. These new features will facilitate analysis of associations between transcriptome data obtained using different platforms.
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Affiliation(s)
- Yusuke Kakei
- Plant Biotechnology Division, Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku Yokohama, Kanagawa, 244-0813 Japan
| | - Yukihisa Shimada
- Plant Biotechnology Division, Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku Yokohama, Kanagawa, 244-0813 Japan
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16
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Jung WY, Lee SS, Kim CW, Kim HS, Min SR, Moon JS, Kwon SY, Jeon JH, Cho HS. RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 2014; 9:e111982. [PMID: 25375764 PMCID: PMC4222968 DOI: 10.1371/journal.pone.0111982] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
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Affiliation(s)
- Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Sang Sook Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Chul Wook Kim
- Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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17
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Wang L, Han X, Zhang Y, Li D, Wei X, Ding X, Zhang X. Deep resequencing reveals allelic variation in Sesamum indicum. BMC PLANT BIOLOGY 2014; 14:225. [PMID: 25138716 PMCID: PMC4148021 DOI: 10.1186/s12870-014-0225-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 08/12/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Characterization of genome-wide patterns of allelic variation and linkage disequilibrium can be used to detect reliable phenotype-genotype associations and signatures of molecular selection. However, the use of Sesamum indicum germplasm for breeding is limited by the lack of polymorphism data. RESULTS Here we describe the massively parallel resequencing of 29 sesame strains from 12 countries at a depth of ≥ 13-fold coverage for each of the samples tested. We detected an average of 127,347 SNPs, 17,961 small InDels, and 9,266 structural variants per sample. The population SNP rate, population diversity (π) and Watterson's estimator of segregating sites (θw) were estimated at 8.6 × 10⁻³, 2.5 × 10⁻³ and 3.0 × 10⁻³ bp⁻¹, respectively. Of these SNPs, 23.2% were located within coding regions. Polymorphism patterns were nonrandom among gene families, with genes mediating interactions with the biotic or abiotic environment exhibiting high levels of polymorphism. The linkage disequilibrium (LD) decay distance was estimated at 150 kb, with no distinct structure observed in the population. Phylogenetic relationships between each of the 29 sesame strains were consistent with the hypothesis of sesame originating on the Indian subcontinent. In addition, we proposed novel roles for adenylate isopentenyltransferase (ITP) genes in determining the number of flowers per leaf axil of sesame by mediating zeatin biosynthesis. CONCLUSIONS This study represents the first report of genome-wide patterns of genetic variation in sesame. The high LD distance and abundant polymorphisms described here increase our understanding of the forces shaping population-wide sequence variation in sesame and will be a valuable resource for future gene-phenotype and genome-wide association studies (GWAS).
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Affiliation(s)
- Linhai Wang
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Xuelian Han
- />Beijing Genomics Institute (BGI) − Shenzhen, Shenzhen, China
- />1gene, Hangzhou, China
| | - Yanxin Zhang
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Donghua Li
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Xin Wei
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Xia Ding
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Xiurong Zhang
- />Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
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18
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Sobol S, Chayut N, Nave N, Kafle D, Hegele M, Kaminetsky R, Wünsche JN, Samach A. Genetic variation in yield under hot ambient temperatures spotlights a role for cytokinin in protection of developing floral primordia. PLANT, CELL & ENVIRONMENT 2014; 37:643-57. [PMID: 23961724 DOI: 10.1111/pce.12184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/06/2013] [Indexed: 05/11/2023]
Abstract
Unusually hot ambient temperatures (HAT) can cause pre-anthesis abortion of flowers in many diverse species, limiting crop production. This limitation is becoming more substantial with climate change. Flower primordia of passion fruit (Passiflora edulis Sims) vines exposed to HAT summers, normally abort. Flower abortion can also be triggered by gibberellin application. We screened for, and identified a genotype capable of reaching anthesis during summer as well as controlled HAT conditions, and also more resistant to gibberellin. Leaves of this genotype contained higher levels of endogenous cytokinin. We investigated a possible connection between higher cytokinin levels and response to gibberellin. Indeed, the effects of gibberellin application were partially suppressed in plants pretreated with cytokinin. Can higher cytokinin levels protect flowers from aborting under HAT conditions? In passion fruit, flowers at a specific stage showed more resistance in response to HAT after cytokinin application. We further tested this hypothesis in Arabidopsis. Transgenic lines with high or low cytokinin levels and cytokinin applications to wild-type plants supported a protective role for cytokinin on developing flowers exposed to HAT. Such findings may have important implications in future breeding programmes as well as field application of growth regulators.
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Affiliation(s)
- Shiri Sobol
- The Institute for Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel
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