Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

Abstract Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

10.21203/rs.3.rs-44131/v1 ◽

2020 ◽

Author(s):

Ying Wang ◽

Hui-Liang Li ◽

Yong-Kai Zhou ◽

Dong Guo ◽

Jia-Hong Zhu ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Hevea Brasiliensis ◽

Molecular Mechanisms ◽

De Novo ◽

Rubber Tree ◽

Tree Breeding ◽

Molecular Regulation ◽

Auxin Signaling ◽

Abnormal Embryo ◽

Regulation Mechanisms

Abstract Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes had been identified and the molecular regulation mechanisms of late SE still not well understood. Results In this study, the transcriptomes of embryogenic calluses (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, more than 85.92% of the clean reads were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs mainly involved in phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcript factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

BMC Genomics ◽

10.1186/s12864-021-07501-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ying Wang ◽

Hui-Liang Li ◽

Yong-Kai Zhou ◽

Dong Guo ◽

Jia-Hong Zhu ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Hevea Brasiliensis ◽

Molecular Mechanisms ◽

De Novo ◽

Rubber Tree ◽

Tree Breeding ◽

Molecular Regulation ◽

Auxin Signaling ◽

Abnormal Embryo ◽

Regulation Mechanisms

Abstract Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

10.21203/rs.3.rs-44131/v2 ◽

2020 ◽

Author(s):

Ying Wang ◽

Hui-Liang Li ◽

Yong-Kai Zhou ◽

Dong Guo ◽

Jia-Hong Zhu ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Hevea Brasiliensis ◽

Molecular Mechanisms ◽

De Novo ◽

Rubber Tree ◽

Tree Breeding ◽

Molecular Regulation ◽

Auxin Signaling ◽

Abnormal Embryo ◽

Regulation Mechanisms

Abstract Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE were still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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Molecular mechanism of ethylene stimulation of latex yield in rubber tree (Hevea brasiliensis) revealed by de novo sequencing and transcriptome analysis

BMC Genomics ◽

10.1186/s12864-016-2587-4 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 23

Author(s):

Jin-Ping Liu ◽

Yu-Fen Zhuang ◽

Xiu-Li Guo ◽

Yi-Jian Li

Keyword(s):

Molecular Mechanism ◽

Transcriptome Analysis ◽

Hevea Brasiliensis ◽

De Novo ◽

Rubber Tree ◽

De Novo Sequencing ◽

Latex Yield ◽

Stimulation Of

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De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

BMC Genomics ◽

10.1186/1471-2164-13-192 ◽

2012 ◽

Vol 13 (1) ◽

pp. 192 ◽

Cited By ~ 182

Author(s):

Dejun Li ◽

Zhi Deng ◽

Bi Qin ◽

Xianghong Liu ◽

Zhonghua Men

Keyword(s):

Ssr Markers ◽

Illumina Sequencing ◽

Hevea Brasiliensis ◽

De Novo Assembly ◽

De Novo ◽

Rubber Tree

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Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

10.1101/395590 ◽

2018 ◽

Author(s):

Camila Campos Mantello ◽

Lucas Boatwright ◽

Carla Cristina da Silva ◽

Erivaldo Jose Scaloppi ◽

Paulo de Souza Gonçalves ◽

...

Keyword(s):

Cold Tolerance ◽

Hevea Brasiliensis ◽

Amazon Basin ◽

Rubber Tree ◽

Tree Breeding ◽

Snp Markers ◽

Large Field ◽

New Variety ◽

Cold Response ◽

Cold Temperatures

AbstractNatural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

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Somatic Embryogenesis and Subsequent Plant Regeneration from Zygotic Embryo Derived Callus of Rubber (Hevea brasiliensis Muell. Arg).

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v27i1.35012 ◽

2017 ◽

Vol 27 (1) ◽

pp. 51-61 ◽

Cited By ~ 1

Author(s):

Md Mahbubur Rahman ◽

Maziah Mahmood ◽

Norhani Abdullah ◽

Noor Azmi Shaharuddin ◽

Waheeda Parvin

Keyword(s):

Somatic Embryogenesis ◽

Plant Regeneration ◽

Plant Growth ◽

Growth Regulators ◽

Hevea Brasiliensis ◽

Zygotic Embryo ◽

Rubber Tree ◽

Mass Propagation ◽

Half Strength ◽

First Time

A protocol has been developed for induction, maturation and germination of the zygotic embryo derived callus of the rubber tree (Hevea brasiliensis Muell. Arg.). The influence of plant growth regulators (PGRs) including 2,4‐D, α‐NAA, picloram, GA3 and TDZ on MS and MMS were studied. Optimum calli were induced on MS supplemented with 2.0 mg/l 2, 4‐D. The best callus growth and proliferation was recorded on MS fortified with 2.0 mg/l 2, 4‐D + 2.0 mg/l BAP + 0.5 mg/l NAA. The maximum embryonic calli were induced on MS + 2.0 mg/l 2, 4‐D + 2.0 mg/l Kn medium. Embryo induction, differentiation and maturation were obtained on MMS (MS +Vit B5). The rooted plantlets were produced on half strength MS without any supplements.The novelty of this study is the induction of embryos and plant regeneration from zygotic embryo explants of Hevea for the first time. The protocol developed in this study will facilitate mass propagation of high yielding rubber clones as well as to develop transgenic rubber plants with desired genes through genetic transformation.Plant Tissue Cult. & Biotech. 27(1): 51-61, 2017 (June)

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Somatic Embryogenesis in Rubber Tree (Hevea brasiliensis Müll. Arg.)

Biotechnology in Agriculture and Forestry - Somatic Embryogenesis and Synthetic Seed I ◽

10.1007/978-3-662-03091-2_23 ◽

1995 ◽

pp. 353-369 ◽

Cited By ~ 7

Author(s):

M. P. Carron ◽

H. Etienne ◽

N. Michaux-Ferriere ◽

P. Montoro

Keyword(s):

Somatic Embryogenesis ◽

Hevea Brasiliensis ◽

Rubber Tree

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Transcriptome profiling in susceptible and tolerant rubber tree clones in response to cassiicolin Cas1, a necrotrophic effector from Corynespora cassiicola

PLoS ONE ◽

10.1371/journal.pone.0254541 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254541

Author(s):

Sébastien Ribeiro ◽

Philippe Label ◽

Dominique Garcia ◽

Pascal Montoro ◽

Valérie Pujade-Renaud

Keyword(s):

Hypersensitive Response ◽

Molecular Mechanisms ◽

De Novo ◽

Negative Impact ◽

Rubber Tree ◽

Defense Responses ◽

Differentially Expressed ◽

Corynespora Cassiicola ◽

Pathogenesis Related Protein ◽

Necrotrophic Effector

Corynespora cassiicola, a fungal plant pathogen with a large host range, causes important damages in rubber tree (Hevea brasiliensis), in Asia and Africa. A small secreted protein named cassiicolin was previously identified as a necrotrophic effector required for the virulence of C. cassiicola in specific rubber tree clones. The objective of this study was to decipher the cassiicolin-mediated molecular mechanisms involved in this compatible interaction. We comparatively analyzed the RNA-Seq transcriptomic profiles of leaves treated or not with the purified cassiicolin Cas1, in two rubber clones: PB260 (susceptible) and RRIM600 (tolerant). The reads were mapped against a synthetic transcriptome composed of all available transcriptomic references from the two clones. Genes differentially expressed in response to cassiicolin Cas1 were identified, in each clone, at two different time-points. After de novo annotation of the synthetic transcriptome, we analyzed GO enrichment of the differentially expressed genes in order to elucidate the main functional pathways impacted by cassiicolin. Cassiicolin induced qualitatively similar transcriptional modifications in both the susceptible and the tolerant clones, with a strong negative impact on photosynthesis, and the activation of defense responses via redox signaling, production of pathogenesis-related protein, or activation of the secondary metabolism. In the tolerant clone, transcriptional reprogramming occurred earlier but remained moderate. By contrast, the susceptible clone displayed a late but huge transcriptional burst, characterized by massive induction of phosphorylation events and all the features of a hypersensitive response. These results confirm that cassiicolin Cas1 is a necrotrophic effector triggering a hypersensitive response in susceptible rubber clones, in agreement with the necrotrophic-effector-triggered susceptibility model.

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