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Nguyen DT, Zavadil Kokáš F, Gonin M, Lavarenne J, Colin M, Gantet P, Bergougnoux V. Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2024; 24:438. [PMID: 38778283 PMCID: PMC11110440 DOI: 10.1186/s12870-024-05160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. RESULTS Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. CONCLUSIONS This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.
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Affiliation(s)
- Dieu Thu Nguyen
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Department of Biochemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Filip Zavadil Kokáš
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Present address: Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Mathieu Gonin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jérémy Lavarenne
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Colin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia.
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Kumar A, Verma K, Kashyap R, Joshi VJ, Sircar D, Yadav SR. Auxin-responsive ROS homeostasis genes display dynamic expression pattern during rice crown root primordia morphogenesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108307. [PMID: 38159549 DOI: 10.1016/j.plaphy.2023.108307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Reactive oxygen species (ROS) are generated continuously as a by-product of aerobic metabolism in plants. While excessive ROS cause oxidative stresses in cells, they act as signaling molecules when maintained at an optimum concentration through the dynamic equilibrium of ROS metabolizing mechanisms to regulate growth, development and response to environmental stress. Auxin and its crosstalk with other signaling cascades are crucial for maintaining ROS homeostasis and orchestrating root architecture but dissecting the underlying mechanism requires detailed investigation at the molecular level. Rice fibrous root system is primarily composed of shoot-derived adventitious roots (also called crown roots). Here, we uncover auxin-ROS cross-talk during initiation and growth of rice roots. Potassium iodide treatment changes ROS levels that results in an altered rice root architecture. We reveal that auxin induction recover root growth and development defects by recouping level of hydrogen peroxide. By comparing global datasets previously generated by auxin induction and laser capture microdissection-RNA sequencing, we identify the redox-related antioxidants genes from peroxidase, glutathione reductase, glutathione S-transferase, and thioredoxin reductase families whose expression is regulated by the auxin signaling and also display dynamic expression patterns during crown root primordia morphogenesis. The auxin-mediated differential transcriptome data were validated by quantifying expression levels of a set of genes upon auxin induction. Further, in-depth spatio-temporal expression pattern analysis by RNA in situ hybridization shows the spatially restricted expression of selected genes in the developing crown root primordia. Together, our findings uncover molecular components of auxin-ROS crosstalk involved in root organogenesis.
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Affiliation(s)
- Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Komal Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Vedika Jayant Joshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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3
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Garg T, Yadav M, Mushahary KKK, Kumar A, Pal V, Singh H, Jain M, Yadav SR. Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice. PLANTA 2023; 258:52. [PMID: 37491477 DOI: 10.1007/s00425-023-04210-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
MAIN CONCLUSION This study reveals that the process of crown root development and auxin-induced de novo root organogenesis during in vitro plantlet regeneration share a common auxin-OsWOX10 regulatory module in rice. In the fibrous-type root system of rice, the crown roots (CR) are developed naturally from the shoot tissues. Generation of robust auxin response, followed by activation of downstream cell fate determinants and signaling pathways at the onset of crown root primordia (CRP) establishment is essential for new root initiation. During rice tissue culture, embryonic calli are induced to regenerate shoots in vitro which undergo de novo root organogenesis on an exogenous auxin-supplemented medium, but the mechanism underlying spatially restricted root organogenesis remains unknown. Here, we reveal the dynamics of progressive activation of genes involved in auxin homeostasis and signaling during initiation and outgrowth of rice crown root primordia. By comparative global dataset analysis, we identify the crown root primordia-expressed genes whose expression is also regulated by auxin signaling. In-depth spatio-temporal expression pattern analysis shows that the exogenous application of auxin induces a set of key transcription factors exclusively in the spatially positioned CRP. Further, functional analysis of rice WUSCHEL-RELATED HOMEOBOX 10 (OsWOX10) during in vitro plantlet regeneration from embryogenic calli shows that it promotes de novo root organogenesis from regenerated shoots. Expression of rice OsWOX10 also induces adventitious roots (AR) in Arabidopsis, independent of homologous endogenous Arabidopsis genes. Together, our findings reveal that a common auxin-transcription factor regulatory module is involved in root organogenesis under different conditions.
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Affiliation(s)
- Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Manoj Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Biochemistry, All India Institute of Medical Sciences, Raebareli, Uttar Pradesh, India
| | | | - Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Vivek Pal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Center for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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4
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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Gonin M, Jeong K, Coudert Y, Lavarenne J, Hoang GT, Bes M, To HTM, Thiaw MN, Do TV, Moukouanga D, Guyomarc'h S, Bellande K, Brossier J, Parizot B, Nguyen HT, Beeckman T, Bergougnoux V, Rouster J, Sallaud C, Laplaze L, Champion A, Gantet P. CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:546-566. [PMID: 35596715 PMCID: PMC9542200 DOI: 10.1111/tpj.15838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
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Affiliation(s)
- Mathieu Gonin
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kwanho Jeong
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyon69007France
| | - Jeremy Lavarenne
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Martine Bes
- CIRAD, UMR AGAPF‐34398MontpellierFrance
- UMR AGAPUniversité de Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, LMIRICE2Vietnam Academy of Science and Technology11300HanoiVietnam
| | - Marie‐Rose Ndella Thiaw
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Toan Van Do
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Daniel Moukouanga
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Soazig Guyomarc'h
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kevin Bellande
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Jean‐Rémy Brossier
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Boris Parizot
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Hieu Trang Nguyen
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jacques Rouster
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Christophe Sallaud
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Laurent Laplaze
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Antony Champion
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Pascal Gantet
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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6
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Li C, Wang J, Li L, Li J, Zhuang M, Li B, Li Q, Huang J, Du Y, Wang J, Fan Z, Mao X, Jing R. TaMOR is essential for root initiation and improvement of root system architecture in wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:862-875. [PMID: 34890129 PMCID: PMC9055823 DOI: 10.1111/pbi.13765] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 12/07/2021] [Indexed: 05/13/2023]
Abstract
Optimal root system architecture is beneficial for water-fertilizer use efficiency, stress tolerance and yield improvement of crops. However, because of the complexity of root traits and difficulty in phenotyping deep roots, the study on mechanisms of root development is rarely reported in wheat (Triticum aestivum L.). In this study, we identified that the LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene TaMOR (MORE ROOT in wheat) determines wheat crown root initiation. The mor mutants exhibited less or even no crown root, dwarfism, less grain number and lodging caused by few roots. The observation of cross sections showed that crown root initiation is inhibited in the mor mutants. Molecular assays revealed that TaMOR interacts with the auxin response factor ARF5 to directly induce the expression of the auxin transporter gene PIN2 (PIN-FORMED 2) in the root base to regulate crown root initiation. In addition, a 159-bp MITE (miniature inverted-repeat transposable element) insertion causing DNA methylation and lower expression of TaMOR-B was identified in TaMOR-B promoter, which is associated with lower root dry weight and shorter plant height. The results bring new light into regulation mechanisms of crown root initiation and offer a new target for the improvement of root system architecture in wheat.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Mengjia Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Junfang Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Du
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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7
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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8
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Lavenus J, Lucas M. How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic Data. Methods Mol Biol 2022; 2395:13-31. [PMID: 34822147 DOI: 10.1007/978-1-0716-1816-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Over the last few decades, many genes have been functionally characterized and shown to be involved in various metabolic, developmental, and signaling pathways. However it still remains unclear how all these genes and pathways integrate into a unique regulatory network to coordinate the development and the growth, or the response to the environment. This is why unraveling the topology of gene regulatory networks (GRN) has become central to our understanding of all these processes. The recent advancement of high-throughput methods has provided enormous amount of -omics data. These data can now be exploited for rapid network reconstruction with statistical inference methods. We recently published a new GRN inference algorithm called TDCor which reconstructs GRN from time-series transcriptomic data. The algorithm has been released in the form of an R package. Here, I describe into details how to install and use the package.
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Affiliation(s)
- Julien Lavenus
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Mikaël Lucas
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France.
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9
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Lavarenne J, Gonin M, Champion A, Javelle M, Adam H, Rouster J, Conejéro G, Lartaud M, Verdeil JL, Laplaze L, Sallaud C, Lucas M, Gantet P. Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice. PLoS One 2020; 15:e0238736. [PMID: 33211715 PMCID: PMC7676735 DOI: 10.1371/journal.pone.0238736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/22/2020] [Indexed: 12/04/2022] Open
Abstract
Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.
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Affiliation(s)
- Jérémy Lavarenne
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Mathieu Gonin
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
| | - Antony Champion
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
| | - Marie Javelle
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Hélène Adam
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
| | - Jacques Rouster
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Geneviève Conejéro
- CIRAD, UMR1334 AGAP, PHIV-MRI, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Marc Lartaud
- CIRAD, UMR1334 AGAP, PHIV-MRI, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Luc Verdeil
- CIRAD, UMR1334 AGAP, PHIV-MRI, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Laurent Laplaze
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
| | - Christophe Sallaud
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Mikael Lucas
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, IRD, UMR DIADE, Montpellier, France
- * E-mail:
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10
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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