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Baruah PM, Bordoloi KS, Gill SS, Agarwala N. CircRNAs responsive to winter dormancy and spring flushing conditions of tea leaf buds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111828. [PMID: 37586421 DOI: 10.1016/j.plantsci.2023.111828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Circular RNAs (circRNAs) are important regulators of diverse biological processes of plants. However, the evolution and potential functions of circRNAs during winter dormancy and spring bud flushing of tea plant is largely unknown. Using RNA-seq data, a total of 1184 circRNAs were identified in the winter dormant and spring bud flushing leaf samples of tea plants in two different cultivars exhibiting different duration of winter dormancy. A total of 156 circRNAs are found to be differentially expressed and the weighted gene co-expression network (WGCNA) analysis revealed that 22 and 20 differentially expressed-circRNAs (DE-circRNAs) positively correlated with the flushing and dormant leaf traits, respectively, in both the tea cultivars used. Some transcription factors (TFs) viz. MYB, WRKY, ERF, bHLH and several genes related to secondary metabolite biosynthetic pathways are found to co-express with circRNAs. DE-circRNAs also predicted to interact with miRNAs and can regulate phytohormone biosynthesis and various signalling pathways in tea plant. This study uncovers the potential roles of circRNAs to determine winter dormancy and spring bud flushing conditions in tea plants.
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Affiliation(s)
- Pooja Moni Baruah
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India
| | - Kuntala Sarma Bordoloi
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India; Mangaldai College, Upahupara, Mangaldai 784125, Assam, India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India.
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2
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Garighan J, Dvorak E, Estevan J, Loridon K, Huettel B, Sarah G, Farrera I, Leclercq J, Grynberg P, Coiti Togawa R, Mota do Carmo Costa M, Costes E, Andrés F. The Identification of Small RNAs Differentially Expressed in Apple Buds Reveals a Potential Role of the Mir159-MYB Regulatory Module during Dormancy. PLANTS (BASEL, SWITZERLAND) 2021; 10:2665. [PMID: 34961136 PMCID: PMC8703471 DOI: 10.3390/plants10122665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warmer temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of 17 micro RNAs (miRNAs) that change their pattern of expression in apple buds during dormancy. Furthermore, the functional analysis of their predicted target genes suggests a main role of the 17 miRNAs in phenylpropanoid biosynthesis, gene regulation, plant development and growth, and response to stimulus. Finally, we studied the conservation of the Arabidopsis thaliana regulatory miR159-MYB module in apple in the context of the plant hormone abscisic acid homeostasis.
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Affiliation(s)
- Julio Garighan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Etienne Dvorak
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Joan Estevan
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Karine Loridon
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Bruno Huettel
- Genome Centre, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany;
| | - Gautier Sarah
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Isabelle Farrera
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Julie Leclercq
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
- UMR AGAP Institute, CIRAD, F-34398 Montpellier, France
| | - Priscila Grynberg
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Roberto Coiti Togawa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Marcos Mota do Carmo Costa
- Bioinformatica Laboratory, Embrapa Recursos Genéticos e Biotecnologia—Cenargen, Brasilia 02372, Brazil; (P.G.); (R.C.T.); (M.M.d.C.C.)
| | - Evelyne Costes
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
| | - Fernando Andrés
- UMR AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34398 Montpellier, France; (J.G.); (E.D.); (J.E.); (K.L.); (G.S.); (I.F.); (J.L.); (E.C.)
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3
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Yu J, Bennett D, Dardick C, Zhebentyayeva T, Abbott AG, Liu Z, Staton ME. Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. Front Mol Biosci 2021; 8:612881. [PMID: 33968979 PMCID: PMC8098804 DOI: 10.3389/fmolb.2021.612881] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States
| | - Margaret E Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.,Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
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Prudencio ÁS, Hoeberichts FA, Dicenta F, Martínez-Gómez P, Sánchez-Pérez R. Identification of early and late flowering time candidate genes in endodormant and ecodormant almond flower buds. TREE PHYSIOLOGY 2021; 41:589-605. [PMID: 33200186 PMCID: PMC8033246 DOI: 10.1093/treephys/tpaa151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/22/2020] [Accepted: 10/23/2020] [Indexed: 05/13/2023]
Abstract
Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
| | | | - Federico Dicenta
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, PO Box 164, 30100 Espinardo, Murcia, Spain
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Rothkegel K, Sandoval P, Soto E, Ulloa L, Riveros A, Lillo-Carmona V, Cáceres-Molina J, Almeida AM, Meneses C. Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy. FRONTIERS IN PLANT SCIENCE 2020; 11:1115. [PMID: 32765576 PMCID: PMC7380246 DOI: 10.3389/fpls.2020.01115] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
Temperate deciduous fruit tree species like sweet cherry (Prunus avium) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety 'Royal Dawn' and high chill variety 'Kordia', we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in 'Royal Dawn' and 443 CH in 'Kordia' and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in 'Kordia' with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While 'Royal Dawn' showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.
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Affiliation(s)
- Karin Rothkegel
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Paula Sandoval
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Esteban Soto
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Lissette Ulloa
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Anibal Riveros
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Victoria Lillo-Carmona
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Javier Cáceres-Molina
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Andrea Miyasaka Almeida
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- ;*Correspondence: Andrea Miyasaka Almeida, ; Claudio Meneses,
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP, Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
- ;*Correspondence: Andrea Miyasaka Almeida, ; Claudio Meneses,
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Yu J, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu Z, Abbott AG, Staton ME. Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach. FRONTIERS IN PLANT SCIENCE 2020; 11:180. [PMID: 32180783 PMCID: PMC7059448 DOI: 10.3389/fpls.2020.00180] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/06/2020] [Indexed: 05/07/2023]
Abstract
Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
| | - Anna O. Conrad
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States
| | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Universite de Bordeaux, Villenave d'Ornon, France
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, the Pennsylvania State University, University Park, PA, United States
| | - Daniel E. Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Dennis Bennett
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Guillaume Roch
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Jean-Marc Audergon
- GAFL Fruit and Vegetable Genetics and Breeding, INRA Centre PACA, Montfavet, France
| | - Christopher Dardick
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Zongrang Liu
- Appalachian Fruit Research Station, United States Department of Agriculture—Agriculture Research Service, Kearneysville, WV, United States
| | - Albert G. Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States
| | - Margaret E. Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States
- Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Margaret E. Staton,
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