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Ai Y, Qian X, Wang X, Chen Y, Zhang T, Chao Y, Zhao Y. Uncovering early transcriptional regulation during adventitious root formation in Medicago sativa. BMC PLANT BIOLOGY 2023; 23:176. [PMID: 37016323 PMCID: PMC10074720 DOI: 10.1186/s12870-023-04168-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) as an important legume plant can quickly produce adventitious roots (ARs) to form new plants by cutting. But the regulatory mechanism of AR formation in alfalfa remains unclear. RESULTS To better understand the rooting process of alfalfa cuttings, plant materials from four stages, including initial separation stage (C stage), induction stage (Y stage), AR primordium formation stage (P stage) and AR maturation stage (S stage) were collected and used for RNA-Seq. Meanwhile, three candidate genes (SAUR, VAN3 and EGLC) were selected to explore their roles in AR formation. The numbers of differentially expressed genes (DEGs) of Y-vs-C (9,724) and P-vs-Y groups (6,836) were larger than that of S-vs-P group (150), indicating highly active in the early AR formation during the complicated development process. Pathways related to cell wall and sugar metabolism, root development, cell cycle, stem cell, and protease were identified, indicating that these genes were involved in AR production. A large number of hormone-related genes associated with the formation of alfalfa ARs have also been identified, in which auxin, ABA and brassinosteroids are thought to play key regulatory roles. Comparing with TF database, it was found that AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, C2H2, bZIP, GRAS played a major regulatory role in the production of ARs of alfalfa. Furthermore, three identified genes showed significant promotion effect on AR formation. CONCLUSIONS Stimulation of stem basal cells in alfalfa by cutting induced AR production through the regulation of various hormones, transcription factors and kinases. This study provides new insights of AR formation in alfalfa and enriches gene resources in crop planting and cultivation.
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Affiliation(s)
- Ye Ai
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Xu Qian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqian Wang
- Beijing Tide Pharmaceutical Co., Ltd, Beijing, 100176, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, 010021, China.
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Justamante MS, Acosta-Motos JR, Cano A, Villanova J, Birlanga V, Albacete A, Cano EÁ, Acosta M, Pérez-Pérez JM. Integration of Phenotype and Hormone Data during Adventitious Rooting in Carnation ( Dianthus caryophyllus L.) Stem Cuttings. PLANTS (BASEL, SWITZERLAND) 2019; 8:E226. [PMID: 31311180 PMCID: PMC6681402 DOI: 10.3390/plants8070226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/04/2019] [Accepted: 07/12/2019] [Indexed: 01/24/2023]
Abstract
The rooting of stem cuttings is a highly efficient procedure for the vegetative propagation of ornamental plants. In cultivated carnations, an increased auxin level in the stem cutting base produced by active auxin transport from the leaves triggers adventitious root (AR) formation from the cambium. To provide additional insight into the physiological and genetic basis of this complex trait, we studied AR formation in a collection of 159 F1 lines derived from a cross between two hybrid cultivars (2003 R 8 and 2101-02 MFR) showing contrasting rooting performances. In three different experiments, time-series for several stem and root architectural traits were quantified in detail in a subset of these double-cross hybrid lines displaying extreme rooting phenotypes and their parental genotypes. Our results indicate that the water content and area of the AR system directly contributed to the shoot water content and shoot growth. Moreover, morphometric data and rooting quality parameters were found to be associated with some stress-related metabolites such as 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor, and the conjugated auxin indol-3-acetic acid-aspartic acid (IAA-Asp).
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Affiliation(s)
| | - José Ramón Acosta-Motos
- Universidad Católica San Antonio de Murcia, Campus de los Jerónimos, 30107 Guadalupe, Spain
- CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Antonio Cano
- Departamento de Biología Vegetal, Universidad de Murcia, 30100 Murcia, Spain
| | - Joan Villanova
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Virginia Birlanga
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Alfonso Albacete
- CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | | | - Manuel Acosta
- Departamento de Biología Vegetal, Universidad de Murcia, 30100 Murcia, Spain
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Druege U, Hilo A, Pérez-Pérez JM, Klopotek Y, Acosta M, Shahinnia F, Zerche S, Franken P, Hajirezaei MR. Molecular and physiological control of adventitious rooting in cuttings: phytohormone action meets resource allocation. ANNALS OF BOTANY 2019; 123:929-949. [PMID: 30759178 PMCID: PMC6589513 DOI: 10.1093/aob/mcy234] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 12/03/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Adventitious root (AR) formation in excised plant parts is a bottleneck for survival of isolated plant fragments. AR formation plays an important ecological role and is a critical process in cuttings for the clonal propagation of horticultural and forestry crops. Therefore, understanding the regulation of excision-induced AR formation is essential for sustainable and efficient utilization of plant genetic resources. SCOPE Recent studies of plant transcriptomes, proteomes and metabolomes, and the use of mutants and transgenic lines have significantly expanded our knowledge concerning excision-induced AR formation. Here, we integrate new findings regarding AR formation in the cuttings of diverse plant species. These findings support a new system-oriented concept that the phytohormone-controlled reprogramming and differentiation of particular responsive cells in the cutting base interacts with a co-ordinated reallocation of plant resources within the whole cutting to initiate and drive excision-induced AR formation. Master control by auxin involves diverse transcription factors and mechanically sensitive microtubules, and is further linked to ethylene, jasmonates, cytokinins and strigolactones. Hormone functions seem to involve epigenetic factors and cross-talk with metabolic signals, reflecting the nutrient status of the cutting. By affecting distinct physiological units in the cutting, environmental factors such as light, nitrogen and iron modify the implementation of the genetically controlled root developmental programme. CONCLUSION Despite advanced research in the last decade, important questions remain open for future investigations on excision-induced AR formation. These concern the distinct roles and interactions of certain molecular, hormonal and metabolic factors, as well as the functional equilibrium of the whole cutting in a complex environment. Starting from model plants, cell type- and phase-specific monitoring of controlling processes and modification of gene expression are promising methodologies that, however, need to be integrated into a coherent model of the whole system, before research findings can be translated to other crops.
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Affiliation(s)
- Uwe Druege
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
| | - Alexander Hilo
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Stadt Seeland, Germany
| | | | - Yvonne Klopotek
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
| | - Manuel Acosta
- Universidad de Murcia, Facultad de Biología, Campus de Espinardo, Murcia, Spain
| | - Fahimeh Shahinnia
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Stadt Seeland, Germany
| | - Siegfried Zerche
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
| | - Mohammad R Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Stadt Seeland, Germany
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Genome-Wide Identification and Characterization of Aquaporins and Their Role in the Flower Opening Processes in Carnation ( Dianthus caryophyllus). Molecules 2018; 23:molecules23081895. [PMID: 30060619 PMCID: PMC6222698 DOI: 10.3390/molecules23081895] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023] Open
Abstract
Aquaporins (AQPs) are associated with the transport of water and other small solutes across biological membranes. Genome-wide identification and characterization will pave the way for further insights into the AQPs’ roles in the commercial carnation (Dianthus caryophyllus). This study focuses on the analysis of AQPs in carnation (DcaAQPs) involved in flower opening processes. Thirty DcaAQPs were identified and grouped to five subfamilies: nine PIPs, 11 TIPs, six NIPs, three SIPs, and one XIP. Subsequently, gene structure, protein motifs, and co-expression network of DcaAQPs were analyzed and substrate specificity of DcaAQPs was predicted. qRT-PCR, RNA-seq, and semi-qRTRCR were used for DcaAQP genes expression analysis. The analysis results indicated that DcaAQPs were relatively conserved in gene structure and protein motifs, that DcaAQPs had significant differences in substrate specificity among different subfamilies, and that DcaAQP genes’ expressions were significantly different in roots, stems, leaves and flowers. Five DcaAQP genes (DcaPIP1;3, DcaPIP2;2, DcaPIP2;5, DcaTIP1;4, and DcaTIP2;2) might play important roles in flower opening process. However, the roles they play are different in flower organs, namely, sepals, petals, stamens, and pistils. Overall, this study provides a theoretical basis for further functional analysis of DcaAQPs.
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Sánchez-García AB, Ibáñez S, Cano A, Acosta M, Pérez-Pérez JM. A comprehensive phylogeny of auxin homeostasis genes involved in adventitious root formation in carnation stem cuttings. PLoS One 2018; 13:e0196663. [PMID: 29709027 PMCID: PMC5927418 DOI: 10.1371/journal.pone.0196663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/17/2018] [Indexed: 11/23/2022] Open
Abstract
Understanding the functional basis of auxin homeostasis requires knowledge about auxin biosynthesis, auxin transport and auxin catabolism genes, which is not always directly available despite the recent whole-genome sequencing of many plant species. Through sequence homology searches and phylogenetic analyses on a selection of 11 plant species with high-quality genome annotation, we identified the putative gene homologs involved in auxin biosynthesis, auxin catabolism and auxin transport pathways in carnation (Dianthus caryophyllus L.). To deepen our knowledge of the regulatory events underlying auxin-mediated adventitious root formation in carnation stem cuttings, we used RNA-sequencing data to confirm the expression profiles of some auxin homeostasis genes during the rooting of two carnation cultivars with different rooting behaviors. We also confirmed the presence of several auxin-related metabolites in the stem cutting tissues. Our findings offer a comprehensive overview of auxin homeostasis genes in carnation and provide a solid foundation for further experiments investigating the role of auxin homeostasis in the regulation of adventitious root formation in carnation.
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Affiliation(s)
| | - Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
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Cano A, Sánchez-García AB, Albacete A, González-Bayón R, Justamante MS, Ibáñez S, Acosta M, Pérez-Pérez JM. Enhanced Conjugation of Auxin by GH3 Enzymes Leads to Poor Adventitious Rooting in Carnation Stem Cuttings. FRONTIERS IN PLANT SCIENCE 2018; 9:566. [PMID: 29755501 PMCID: PMC5932754 DOI: 10.3389/fpls.2018.00566] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/10/2018] [Indexed: 05/05/2023]
Abstract
Commercial carnation (Dianthus caryophyllus) cultivars are vegetatively propagated from axillary stem cuttings through adventitious rooting; a process which is affected by complex interactions between nutrient and hormone levels and is strongly genotype-dependent. To deepen our understanding of the regulatory events controlling this process, we performed a comparative study of adventitious root (AR) formation in two carnation cultivars with contrasting rooting performance, "2101-02 MFR" and "2003 R 8", as well as in the reference cultivar "Master". We provided molecular evidence that localized auxin response in the stem cutting base was required for efficient adventitious rooting in this species, which was dynamically established by polar auxin transport from the leaves. In turn, the bad-rooting behavior of the "2003 R 8" cultivar was correlated with enhanced synthesis of indole-3-acetic acid conjugated to aspartic acid by GH3 proteins in the stem cutting base. Treatment of stem cuttings with a competitive inhibitor of GH3 enzyme activity significantly improved rooting of "2003 R 8". Our results allowed us to propose a working model where endogenous auxin homeostasis regulated by GH3 proteins accounts for the cultivar dependency of AR formation in carnation stem cuttings.
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Affiliation(s)
- Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | | | - Alfonso Albacete
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | | | | | - Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | - José Manuel Pérez-Pérez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
- *Correspondence: José Manuel Pérez-Pérez, arolab.edu.umh.es;
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Martínková J, Klimešová J. Enforced Clonality Confers a Fitness Advantage. FRONTIERS IN PLANT SCIENCE 2016; 7:2. [PMID: 26858732 PMCID: PMC4726766 DOI: 10.3389/fpls.2016.00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/06/2016] [Indexed: 05/24/2023]
Abstract
In largely clonal plants, splitting of a maternal plant into potentially independent plants (ramets) is usually spontaneous; however, such fragmentation also occurs in otherwise non-clonal species due to application of external force. This process might play an important yet largely overlooked role for otherwise non-clonal plants by providing a mechanism to regenerate after disturbance. Here, in a 5-year garden experiment on two short-lived, otherwise non-clonal species, Barbarea vulgaris and Barbarea stricta, we compared the fitness of plants fragmented by simulated disturbance ("enforced ramets") both with plants that contemporaneously originate in seed and with individuals unscathed by the disturbance event. Because the ability to regrow from fragments is related to plant age and stored reserves, we compared the effects of disturbance applied during three different ontogenetic stages of the plants. In B. vulgaris, enforced ramet fitness was higher than the measured fitness values of both uninjured plants and plants established from seed after the disturbance. This advantage decreased with increasing plant age at the time of fragmentation. In B. stricta, enforced ramet fitness was lower than or similar to fitness of uninjured plants and plants grown from seed. Our results likely reflect the habitat preferences of the study species, as B. vulgaris occurs in anthropogenic, disturbed habitats where body fragmentation is more probable and enforced clonality thus more advantageous than in the more natural habitats preferred by B. stricta. Generalizing from our results, we see that increased fitness yielded by enforced clonality would confer an evolutionary advantage in the face of disturbance, especially in habitats where a seed bank has not been formed, e.g., during invasion or colonization. Our results thus imply that enforced clonality should be taken into account when studying population dynamics and life strategies of otherwise non-clonal species in disturbed habitats.
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Villacorta-Martín C, Sánchez-García AB, Villanova J, Cano A, van de Rhee M, de Haan J, Acosta M, Passarinho P, Pérez-Pérez JM. Gene expression profiling during adventitious root formation in carnation stem cuttings. BMC Genomics 2015; 16:789. [PMID: 26467528 PMCID: PMC4606512 DOI: 10.1186/s12864-015-2003-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/03/2015] [Indexed: 12/29/2022] Open
Abstract
Background Adventitious root (AR) formation is a critical step in vegetative propagation of most ornamental plants, such as carnation. AR formation from stem cuttings is usually divided into several stages according to physiological and metabolic markers. Auxin is often applied exogenously to promote the development of ARs on stem cuttings of difficult-to-root genotypes. Results By whole transcriptome sequencing, we identified the genes involved in AR formation in carnation cuttings and in response to exogenous auxin. Their expression profiles have been analysed through RNA-Seq during a time-course experiment in the stem cutting base of two cultivars with contrasting efficiencies of AR formation. We explored the kinetics of root primordia formation in these two cultivars and in response to exogenously-applied auxin through detailed histological and physiological analyses. Conclusions Our results provide, for the first time, a number of molecular, histological and physiological markers that characterize the different stages of AR formation in this species and that could be used to monitor adventitious rooting on a wide collection of carnation germplasm with the aim to identify the best-rooting cultivars for breeding purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2003-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Joan Villanova
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain.
| | - Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain.
| | - Miranda van de Rhee
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
| | - Jorn de Haan
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain.
| | - Paul Passarinho
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
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