Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas

Abstract Background In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. Results Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. Conclusions Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

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SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato

Horticulture Research ◽

10.1038/s41438-021-00677-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Xiaotian Wang ◽

Zhiqiang Liu ◽

Shuai Sun ◽

Jianxin Wu ◽

Ren Li ◽

...

Keyword(s):

Regulatory Mechanism ◽

Luciferase Reporter ◽

Crop Breeding ◽

Inflorescence Architecture ◽

Inflorescence Development ◽

Branching Structures ◽

Qpcr Analysis ◽

Genetic Mechanisms ◽

Reporter Assays ◽

Selection For

AbstractSelection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.

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Plant Hormone Metabolome and Transcriptome Analysis of Dwarf and Wild-type Banana

Journal of Plant Growth Regulation ◽

10.1007/s00344-021-10447-7 ◽

2021 ◽

Author(s):

Biao Deng ◽

Xuan Wang ◽

Xing Long ◽

Ren Fang ◽

Shuangyun Zhou ◽

...

Keyword(s):

Signal Transduction ◽

Transcriptome Analysis ◽

Regulatory Mechanism ◽

Feedback Regulation ◽

Wild Type ◽

Hormone Levels ◽

Transporter Protein ◽

Repressor Proteins ◽

Differential Gene ◽

The Relationship

AbstractGibberellin (GA), auxin (IAA) and brassinosteroid (BR) are indispensable in the process of plant growth and development. Currently, research on the regulatory mechanism of phytohormones in banana dwarfism is mainly focused on GA, and few studies are focused on IAA and BR. In this study, we measured the contents of endogenous GA, IAA and BR and compared the transcriptomes of wild-type Williams banana and its dwarf mutant across five successive growth periods. We investigated the relationship between hormones and banana dwarfism and explored differential gene expression through transcriptome analysis, thus revealing the possible metabolic regulatory mechanism. We inferred a complex regulatory network of banana dwarfing. In terms of endogenous hormone levels, GA and IAA had significant effects on banana dwarfing, while BR had little effect. The key gene in GA biosynthesis of is GA2ox, and the key genes in IAA biosynthesis are TDC and YUCCA. The differential expression of these genes might be the main factor affecting hormone levels and plant height. In terms of hormone signal transduction, DELLA and AUX/IAA repressor proteins were the core regulators of GA and IAA, respectively. They inhibited the process of signal transduction and had feedback regulation on hormone levels. Finally, the transporter protein PIN, AUX1/LAX protein family and ABCB subfamily played supplementary roles in the transport of IAA. These results provide new insights into GA and IAA regulation of banana growth and a reliable foundation for the improvement of dwarf varieties.

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De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.625520 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tao Liu ◽

Xiaoting Liu ◽

Rangrang Zhou ◽

Hong Chen ◽

Huaigang Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Regulatory Mechanism ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Processing Technique ◽

Sodium Selenate ◽

Control Group ◽

Primary Mechanism ◽

High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

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Transcriptome analysis of reproductive tissue differentiation in Jatropha curcas Linn.

Genomics Data ◽

10.1016/j.gdata.2017.05.008 ◽

2017 ◽

Vol 13 ◽

pp. 11-14 ◽

Cited By ~ 3

Author(s):

Nisha Govender ◽

Siju Senan ◽

Zeti-Azura Mohamed-Hussein ◽

Wickneswari Ratnam

Keyword(s):

Transcriptome Analysis ◽

Jatropha Curcas ◽

Tissue Differentiation ◽

Reproductive Tissue

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Preparation of corn-oil as an alternative fuel and transcriptome analysis of metabolic pathway related to fuel component accumulation

Fuel ◽

10.1016/j.fuel.2020.117931 ◽

2020 ◽

Vol 275 ◽

pp. 117931

Author(s):

Songhao Zhang ◽

Xiyuan Zhang ◽

Zhenlong Geng ◽

Xin Liu ◽

Yehao Wang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Metabolic Pathway ◽

Corn Oil ◽

Alternative Fuel ◽

Fuel Component

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RNA-Seq transcriptome analysis of Jatropha curcas L. accessions after salt stimulus and unigene-derived microsatellite mining

Industrial Crops and Products ◽

10.1016/j.indcrop.2020.112168 ◽

2020 ◽

Vol 147 ◽

pp. 112168 ◽

Cited By ~ 2

Author(s):

Marislane Carvalho Paz de Souza ◽

Manassés Daniel da Silva ◽

Eliseu Binneck ◽

George André de Lima Cabral ◽

Ana Maria Benko Iseppon ◽

...

Keyword(s):

Transcriptome Analysis ◽

Jatropha Curcas ◽

Rna Seq ◽

Jatropha Curcas L

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De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas

GigaScience ◽

10.1093/gigascience/giaa009 ◽

2020 ◽

Vol 9 (2) ◽

Cited By ~ 2

Author(s):

Mao-Sheng Chen ◽

Longjian Niu ◽

Mei-Li Zhao ◽

Chuanjia Xu ◽

Bang-Zhen Pan ◽

...

Keyword(s):

Gene Transcription ◽

Genome Assembly ◽

Jatropha Curcas ◽

Woody Plants ◽

Woody Plant ◽

De Novo ◽

Sex Differentiation ◽

Chromatin Organization ◽

De Novo Genome Assembly ◽

Chromatin Architecture

Abstract Background Chromatin architecture is an essential factor regulating gene transcription in different cell types and developmental phases. However, studies on chromatin architecture in perennial woody plants and on the function of chromatin organization in sex determination have not been reported. Results Here, we produced a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and a scaffold N50 of 30.7 Mb using Pacific Biosciences long reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes were significantly enriched in the changed A/B compartments and topologically associated domain regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve differentially expressed genes related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. These results demonstrate that chromatin organization participates in the regulation of gene transcription during the process of sex differentiation in Jatropha. Conclusions We have revealed the features of chromatin architecture in perennial woody plants and investigated the possible function of chromatin organization in Jatropha sex differentiation. These findings will facilitate understanding of the regulatory mechanisms of sex determination in higher plants.

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