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Xu W, Cheng H, Cheng J, Zhu S, Cui Y, Wang C, Wu J, Lan X, Cheng Y. A COBRA family protein, PtrCOB3, contributes to gelatinous layer formation of tension wood fibers in poplar. PLANT PHYSIOLOGY 2024; 196:323-337. [PMID: 38850037 DOI: 10.1093/plphys/kiae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Angiosperm trees usually develop tension wood (TW) in response to gravitational stimulation. TW comprises abundant gelatinous (G-) fibers with thick G-layers primarily composed of crystalline cellulose. Understanding the pivotal factors governing G-layer formation in TW fiber remains elusive. This study elucidates the role of a Populus trichocarpa COBRA family protein, PtrCOB3, in the G-layer formation of TW fibers. PtrCOB3 expression was upregulated, and its promoter activity was enhanced during TW formation. Comparative analysis with wild-type trees revealed that ptrcob3 mutants, mediated by Cas9/gRNA gene editing, were incapable of producing G-layers within TW fibers and showed severely impaired stem lift. Fluorescence immunolabeling data revealed a dearth of crystalline cellulose in the tertiary cell wall (TCW) of ptrcob3 TW fibers. The role of PtrCOB3 in G-layer formation is contingent upon its native promoter, as evidenced by the comparative phenotypic assessments of pCOB11::PtrCOB3, pCOB3::PtrCOB3, and pCOB3::PtrCOB11 transgenic lines in the ptrcob3 background. Overexpression of PtrCOB3 under the control of its native promoter expedited G-layer formation within TW fibers. We further identified 3 transcription factors that bind to the PtrCOB3 promoter and positively regulate its transcriptional levels. Alongside the primary TCW synthesis genes, these findings enable the construction of a 2-layer transcriptional regulatory network for the G-layer formation of TW fibers. Overall, this study uncovers mechanistic insight into TW formation, whereby a specific COB protein executes the deposition of cellulose, and consequently, G-layer formation within TW fibers.
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Affiliation(s)
- Wenjing Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiyao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Siran Zhu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yongyao Cui
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jianzhen Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xingguo Lan
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Pushkova EN, Povkhova LV, Dvorianinova EM, Novakovskiy RO, Rozhmina TA, Gryzunov AA, Sigova EA, Zhernova DA, Borkhert EV, Turba AA, Yablokov AG, Bolsheva NL, Dmitriev AA, Melnikova NV. Expression of FAD and SAD Genes in Developing Seeds of Flax Varieties under Different Growth Conditions. PLANTS (BASEL, SWITZERLAND) 2024; 13:956. [PMID: 38611485 PMCID: PMC11013676 DOI: 10.3390/plants13070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Flax seed is one of the richest plant sources of linolenic acid (LIN) and also contains unsaturated linoleic acid (LIO) and oleic acid (OLE). Stearoyl-ACP desaturases (SADs) and fatty acid desaturases (FADs) play key roles in the synthesis of flax fatty acids (FAs). However, there is no holistic view of which genes from the SAD and FAD families and at which developmental stages have the highest expression levels in flax seeds, as well as the influence of genotype and growth conditions on the expression profiles of these genes. We sequenced flax seed transcriptomes at 3, 7, 14, 21, and 28 days after flowering (DAF) for ten flax varieties with different oil FA compositions grown under three temperature/watering conditions. The expression levels of 25 genes of the SAD, FAD2, and FAD3 families were evaluated. FAD3b, FAD3a, FAD2b-2, SAD3-1, SAD2-1, SAD2-2, SAD3-2, FAD2a-1, and FAD2a-2 had the highest expression levels, which changed significantly during seed development. These genes probably play a key role in FA synthesis in flax seeds. High temperature and insufficient watering shifted the maximum expression levels of FAD and SAD genes to earlier developmental stages, while the opposite trend was observed for low temperature and excessive watering. Differences in the FAD and SAD expression profiles under different growth conditions may affect the FA composition of linseed oil. Stop codons in the FAD3a gene, resulting in a reduced LIN content, decreased the level of FAD3a transcript. The obtained results provide new insights into the synthesis of linseed oil.
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Affiliation(s)
- Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia;
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Arthur G. Yablokov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (L.V.P.); (E.M.D.); (R.O.N.); (T.A.R.); (E.A.S.); (D.A.Z.); (E.V.B.); (A.A.T.); (A.G.Y.); (N.L.B.)
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Dvorianinova EM, Zinovieva OL, Pushkova EN, Zhernova DA, Rozhmina TA, Povkhova LV, Novakovskiy RO, Sigova EA, Turba AA, Borkhert EV, Krasnov GS, Ruan C, Dmitriev AA, Melnikova NV. Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data. Int J Mol Sci 2023; 24:14885. [PMID: 37834335 PMCID: PMC10573214 DOI: 10.3390/ijms241914885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.
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Affiliation(s)
| | - Olga L. Zinovieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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4
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Chabi M, Goulas E, Galinousky D, Blervacq AS, Lucau-Danila A, Neutelings G, Grec S, Day A, Chabbert B, Haag K, Müssig J, Arribat S, Planchon S, Renaut J, Hawkins S. Identification of new potential molecular actors related to fiber quality in flax through Omics. FRONTIERS IN PLANT SCIENCE 2023; 14:1204016. [PMID: 37528984 PMCID: PMC10390313 DOI: 10.3389/fpls.2023.1204016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 08/03/2023]
Abstract
One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.
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Affiliation(s)
- Malika Chabi
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Dmitry Galinousky
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Anne-Sophie Blervacq
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Anca Lucau-Danila
- Université de Lille, UMRT 1158 BioEcoAgro, Institut Charles Viollette, Lille, France
| | - Godfrey Neutelings
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Arnaud Day
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Fibres Recherche Développement, Technopole de l’Aube en Champagne – Hôtel de Bureaux 2, 2 rue Gustave Eiffel, CS 90601, Troyes, France
| | - Brigitte Chabbert
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France
| | - Katharina Haag
- Fraunhofer-Institute for Manufacturing Technology and Advanced Materials IFAM, Bremen, Germany
| | - Jörg Müssig
- The Biological Materials Group, HSB – City University of Applied Sciences, Bremen, Germany
| | - Sandrine Arribat
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Planchon
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Simon Hawkins
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Review: Tertiary cell wall of plant fibers as a source of inspiration in material design. Carbohydr Polym 2022; 295:119849. [DOI: 10.1016/j.carbpol.2022.119849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022]
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Sousa-Baena MS, Onyenedum JG. Bouncing back stronger: Diversity, structure, and molecular regulation of gelatinous fiber development. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102198. [PMID: 35286861 DOI: 10.1016/j.pbi.2022.102198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Gelatinous fibers (G-fibers) are specialized contractile cells found in a diversity of vascular plant tissues, where they provide mechanical support and/or facilitate plant mobility. G-fibers are distinct from typical fibers by the presence of an innermost thickened G-layer, comprised mainly of axially oriented cellulose microfibrils. Despite the disparate developmental origins-tension wood fibers from the vascular cambium or primary phloem fibers from the procambium-G-fiber development, composition, and molecular signatures are remarkably similar; however, important distinctions do exist. Here, we synthesize current knowledge of the phylogenetic diversity, compositional makeup, and the molecular profiles that characterize G-fiber development and highlight open questions for future investigation.
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Affiliation(s)
- Mariane S Sousa-Baena
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA.
| | - Joyce G Onyenedum
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
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7
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WANG S, XU J, WANG Z, LI Z, YI L, YAO L, WANG X. Gene screening for fatty acid synthesis of flax based on transcriptome sequencing. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.93721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shuyan WANG
- Inner Mongolia Agricultural University, China
| | - Jun XU
- Inner Mongolia Agricultural University, China
| | - Zhuo WANG
- Inner Mongolia Grass Digital Ecological Industry Co., LTD, China
| | - Zhiwei LI
- Inner Mongolia Agricultural University, China
| | - Liuxi YI
- Inner Mongolia Agricultural University, China
| | - Lijun YAO
- Inner Mongolia Agricultural University, China
| | - Xia WANG
- Inner Mongolia Agricultural University, China
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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10
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Petrova A, Kozlova L, Gorshkov O, Nazipova A, Ageeva M, Gorshkova T. Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers. FRONTIERS IN PLANT SCIENCE 2021; 12:660375. [PMID: 33936149 PMCID: PMC8080151 DOI: 10.3389/fpls.2021.660375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/03/2021] [Indexed: 05/29/2023]
Abstract
In the fibers of many plant species after the formation of secondary cell walls, cellulose-enriched cell wall layers (often named G-layers or tertiary cell walls) are deposited which are important in many physiological situations. Flax (Linum usitatissimum L.) phloem fibers constitutively develop tertiary cell walls during normal plant growth. During the gravitropic response after plant inclination, the deposition of a cellulose-enriched cell wall layer is induced in xylem fibers on one side of the stem, providing a system similar to that of tension wood in angiosperm trees. Atomic force microscopy (AFM), immunochemistry, and transcriptomic analyses demonstrated that the G-layer induced in flax xylem fibers was similar to the constitutively formed tertiary cell wall of bast (phloem) fibers but different from the secondary cell wall. The tertiary cell walls, independent of tissue of origin and inducibility, were twice as stiff as the secondary cell walls. In the gravitropic response, the tertiary cell wall deposition rate in xylem was higher than that of the secondary cell wall. Rhamnogalacturonan I (RG-I) with galactan side chains was a prominent component in cellulose-rich layers of both phloem and xylem flax fibers. Transcriptomic events underlying G-layer deposition in phloem and xylem fibers had much in common. At the induction of tertiary cell wall deposition, several genes for rhamnosyltransferases of the GT106 family were activated in xylem samples. The same genes were expressed in the isolated phloem fibers depositing the tertiary cell wall. The comparison of transcriptomes in fibers with both inducible and constitutive tertiary cell wall deposition and xylem tissues that formed the secondary cell walls is an effective system that revealed important molecular players involved in the formation of cellulose-enriched cell walls.
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Affiliation(s)
- Anna Petrova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Liudmila Kozlova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Oleg Gorshkov
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Alsu Nazipova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Marina Ageeva
- Microscopy Cabinet, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, Russia
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11
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Dmitriev AA, Novakovskiy RO, Pushkova EN, Rozhmina TA, Zhuchenko AA, Bolsheva NL, Beniaminov AD, Mitkevich VA, Povkhova LV, Dvorianinova EM, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Melnikova NV. Transcriptomes of Different Tissues of Flax ( Linum usitatissimum L.) Cultivars With Diverse Characteristics. Front Genet 2020; 11:565146. [PMID: 33363567 PMCID: PMC7755106 DOI: 10.3389/fgene.2020.565146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Alexander A Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok, Russia.,All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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12
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Galinousky D, Mokshina N, Padvitski T, Ageeva M, Bogdan V, Kilchevsky A, Gorshkova T. The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality. Front Genet 2020; 11:589881. [PMID: 33281880 PMCID: PMC7690631 DOI: 10.3389/fgene.2020.589881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective manipulation of technical fiber quality. A key step was to identify genes with tissue and stage-specific pattern of expression in the developing fibers. In the current study, we investigated the relationship between gene expression evaluated in bast fibers of developing flax plants and the quality parameters of technical fibers measured after plant harvesting. Based on previously published transcriptomic data, two sets of genes that are upregulated in fibers during intrusive growth and tertiary cell wall deposition were selected. The expression level of the selected genes and fiber quality parameters were measured in fiber flax, linseed (oil flax) cultivars, and wild species that differ in type of yield and fiber quality parameters. Based on gene expression data, linear regression models for technical stem length, fiber tensile strength, and fiber flexibility were constructed, resulting in the identification of genes that have high potential for manipulating fiber quality. Chromosomal localization and single nucleotide polymorphism distribution in the selected genes were characterized for the efficacy of their use in conventional breeding and genome editing programs. Transcriptome-based selection is a highly targeted functional approach that could be used during the development of new cultivars of various crops.
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Affiliation(s)
- Dmitry Galinousky
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Tsimafei Padvitski
- Cellular Network and Systems Biology Group, University of Cologne, CECAD, Cologne, Germany
| | - Marina Ageeva
- Laboratory of Microscopy, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Victor Bogdan
- Laboratory of Fiber Flax Breeding, Institute of Flax, Ustie, Belarus
| | - Alexander Kilchevsky
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
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13
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Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. Front Genet 2020; 11:581664. [PMID: 33193706 PMCID: PMC7652851 DOI: 10.3389/fgene.2020.581664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nelly Badalato
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, UMR FARE A 614, Reims, France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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14
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Erdogmus S, Ates D, Nemli S, Yagmur B, Asciogul TK, Ozkuru E, Karaca N, Yilmaz H, Esiyok D, Tanyolac MB. Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.). Genomics 2020; 112:4536-4546. [PMID: 32763354 DOI: 10.1016/j.ygeno.2020.03.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 12/16/2022]
Abstract
SNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg-1 with an average of 1,280.9 mg kg-1 and the Mn concentration ranged from 4.87 to 27.54 mg kg-1 with a mean of 11.76 mg kg-1. A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of ΔK was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. Of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. In 2016, six SNPs (on Pv1-4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1-4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. In Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively.
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Affiliation(s)
- Semih Erdogmus
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Duygu Ates
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Seda Nemli
- Ege University, Faculty of Fisheries, Bornova-Izmir 35100, Turkey
| | - Bulent Yagmur
- Ege University, Department of Soil Science and Plant Nutrition, Bornova-Izmir 35100, Turkey
| | | | - Esin Ozkuru
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Nur Karaca
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Hasan Yilmaz
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Dursun Esiyok
- Ege University, Department of Horticulture, Bornova-Izmir, 35040, Turkey
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15
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Xie J, Li J, Jie Y, Xie D, Yang D, Shi H, Zhong Y. Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie). BMC Genomics 2020; 21:40. [PMID: 31931705 PMCID: PMC6958601 DOI: 10.1186/s12864-020-6457-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. RESULTS In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER. CONCLUSIONS Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.
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Affiliation(s)
- Jiyong Xie
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiaqi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yucheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Deyu Xie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Di Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yingli Zhong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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16
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Mokshina N, Makshakova O, Nazipova A, Gorshkov O, Gorshkova T. Flax rhamnogalacturonan lyases: phylogeny, differential expression and modeling of protein structure. PHYSIOLOGIA PLANTARUM 2019; 167:173-187. [PMID: 30474196 DOI: 10.1111/ppl.12880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
Rhamnogalacturonan lyases (RGLs; EC 4.2.2.23) degrade the rhamnogalacturonan I (RG-I) backbone of pectins present in the plant cell wall. These enzymes belong to polysaccharide lyase family 4, members of which are mainly from plants and plant pathogens. RGLs are investigated, as a rule, as pathogen 'weapons' for plant cell wall degradation and subsequent infection. Despite the presence of genes annotated as RGLs in plant genomes and the presence of substrates for enzyme activity in plant cells, evidence supporting the involvement of this enzyme in certain processes is limited. The differential expression of some RGL genes in flax (Linum usitatissimum L.) tissues, revealed in our previous work, prompted us to carry out a total revision (phylogenetic analysis, analysis of expression and protein structure modeling) of all the sequences of flax predicted as coding for RGLs. Comparison of the expressions of LusRGL in various tissues of flax stem revealed that LusRGLs belong to distinct phylogenetic clades, which correspond to two co-expression groups. One of these groups comprised LusRGL6-A and LusRGL6-B genes and was specifically upregulated in flax fibers during deposition of the tertiary cell wall, which has complex RG-I as a key noncellulosic component. The results of homology modeling and docking demonstrated that the topology of the LusRGL6-A catalytic site allowed binding to the RG-I ligand. These findings lead us to suggest the presence of RGL activity in planta and the involvement of special isoforms of RGLs in the modification of RG-I of the tertiary cell wall in plant fibers.
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Affiliation(s)
- Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Alsu Nazipova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
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17
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Xu X, Backes A, Legay S, Berni R, Faleri C, Gatti E, Hausman J, Cai G, Guerriero G. Cell wall composition and transcriptomics in stem tissues of stinging nettle ( Urtica dioica L.): Spotlight on a neglected fibre crop. PLANT DIRECT 2019; 3:e00151. [PMID: 31417976 PMCID: PMC6689792 DOI: 10.1002/pld3.151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 06/01/2023]
Abstract
Stinging nettle (Urtica dioica L.) produces silky cellulosic fibres, as well as bioactive molecules. To improve the knowledge on nettle and enhance its opportunities of exploitation, a draft transcriptome of the "clone 13" (a fibre clone) is here presented. The transcriptome of whole internodes sampled at the top and middle of the stem is then compared with the core and cortical tissues sampled at the bottom. Young internodes show an enrichment in genes involved in the biosynthesis of phytohormones (auxins and jasmonic acid) and secondary metabolites (flavonoids). The core of internodes collected at the bottom of the stem is enriched in genes partaking in different aspects of secondary cell wall formation (cellulose, hemicellulose, lignin biosynthesis), while the cortical tissues reveal the presence of a C starvation signal probably due to the UDP-glucose demand necessary for the thickening phase of bast fibres. Cell wall analysis indicates a difference in rhamnogalacturonan structure/composition of mature bast fibres, as evidenced by the higher levels of galactose measured, as well as the occurrence of more water-soluble pectins in elongating internodes. The targeted quantification of phenolics shows that the middle internode and the cortical tissues at the bottom have higher contents than top internodes. Ultrastructural analyses reveal the presence of a gelatinous layer in bast fibres with a lamellar structure. The data presented will be an important resource and reference for future molecular studies on a neglected fibre crop.
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Affiliation(s)
- Xuan Xu
- Environmental Research and Innovation (ERIN) DepartmentLuxembourg Institute of Science and Technology (LIST)Esch/AlzetteLuxembourg
| | - Aurélie Backes
- Environmental Research and Innovation (ERIN) DepartmentLuxembourg Institute of Science and Technology (LIST)Esch/AlzetteLuxembourg
- Present address:
Unité de Recherche Résistance Induite et BioProtection des PlantesUFR Sciences Exactes et NaturellesSFR Condorcet FR CNRS 3417Université de Reims‐Champagne‐ArdenneReims Cedex 2France
| | - Sylvain Legay
- Environmental Research and Innovation (ERIN) DepartmentLuxembourg Institute of Science and Technology (LIST)Esch/AlzetteLuxembourg
| | - Roberto Berni
- Department of Life SciencesUniversity of SienaSienaItaly
- Trees and Timber Institute‐National Research Council of Italy (CNR‐IVALSA)FollonicaItaly
| | - Claudia Faleri
- Department of Life SciencesUniversity of SienaSienaItaly
| | - Edoardo Gatti
- Institute of Biometeorology (IBIMET)National Research CouncilBolognaItaly
| | - Jean‐Francois Hausman
- Environmental Research and Innovation (ERIN) DepartmentLuxembourg Institute of Science and Technology (LIST)Esch/AlzetteLuxembourg
| | - Giampiero Cai
- Department of Life SciencesUniversity of SienaSienaItaly
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) DepartmentLuxembourg Institute of Science and Technology (LIST)Esch/AlzetteLuxembourg
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18
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Morello L, Pydiura N, Galinousky D, Blume Y, Breviario D. Flax tubulin and CesA superfamilies represent attractive and challenging targets for a variety of genome- and base-editing applications. Funct Integr Genomics 2019; 20:163-176. [PMID: 30826923 DOI: 10.1007/s10142-019-00667-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Flax is both a valuable resource and an interesting model crop. Despite a long history of flax genetic transformation only one transgenic linseed cultivar has been so far registered in Canada. Implementation and use of the genome-editing technologies that allow site-directed modification of endogenous genes without the introduction of foreign genes might improve this situation. Besides its potential for boosting crop yields, genome editing is now one of the best tools for carrying out reverse genetics and it is emerging as an especially versatile tool for studying basic biology. A complex interplay between the flax tubulin family (6 α-, 14 β-, and 2 γ-tubulin genes), the building block of microtubules, and the CesA (15-16 genes), the subunit of the multimeric cellulose-synthesizing complex devoted to the oriented deposition of the cellulose microfibrils is fundamental for the biosynthesis of the cell wall. The role of the different members of each family in providing specificities to the assembled complexes in terms of structure, dynamics, activity, and interaction remains substantially obscure. Genome-editing strategies, recently shown to be successful in flax, can therefore be useful to unravel the issue of functional redundancy and provide evidence for specific interactions between different members of the tubulin and CesA gene families, in relation to different phase and mode of cell wall biosynthesis.
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Affiliation(s)
- Laura Morello
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy
| | - Nikolay Pydiura
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072, Minsk, Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine.
| | - Diego Breviario
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy.
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19
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Gorshkov O, Chernova T, Mokshina N, Gogoleva N, Suslov D, Tkachenko A, Gorshkova T. Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles. PLANTS (BASEL, SWITZERLAND) 2019; 8:E47. [PMID: 30791461 PMCID: PMC6409982 DOI: 10.3390/plants8020047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitatissimum L.) stem revealed all 124 known flax miRNA from 23 gene families and the potential targets of differentially expressed miRNAs. A comparison of the expression between phloem fibers at different developmental stages, and parenchyma and xylem tissues demonstrated that members of miR159, miR166, miR167, miR319, miR396 families were down-regulated in intrusively growing fibers. Some putative target genes of these miRNA families, such as those putatively encoding growth-regulating factors, an argonaute family protein, and a homeobox-leucine zipper family protein were up-regulated in elongating fibers. miR160, miR169, miR390, and miR394 showed increased expression. Changes in the expression levels of miRNAs and their target genes did not match expectations for the majority of predicted target genes. Taken together, poorly understood intrusive fiber elongation, the key process of phloem fiber development, was characterized from a miRNA-target point of view, giving new insights into its regulation.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlyovskaya Str., 18, 420021 Kazan, Russia.
| | - Dmitry Suslov
- Department of Plant Physiology and Biochemistry, Faculty of Biology, Saint Petersburg State University, Universiteskaya emb., 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander Tkachenko
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Universiteskaya emb., 7/9, 199034 Saint Petersburg, Russia.
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russia.
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20
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Wróbel-Kwiatkowska M, Kropiwnicki M, Żebrowski J, Beopoulos A, Dymińska L, Hanuza J, Rymowicz W. Effect of mcl-PHA synthesis in flax on plant mechanical properties and cell wall composition. Transgenic Res 2018; 28:77-90. [PMID: 30484148 PMCID: PMC6353814 DOI: 10.1007/s11248-018-0105-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 11/21/2018] [Indexed: 01/10/2023]
Abstract
The high demand for new biomaterials makes synthesis of polyhydroxyalkanoates (PHA) in plants an interesting and desirable achievement. Production of polymers in plants is an example of application of biotechnology for improving the properties of plants, e.g. industrial properties, but it can also provide knowledge about plant physiology and metabolism. The subject of the present study was an industrially important plant: flax, Linum usitatissimum L., of a fibre cultivar (cv Nike). In the study the gene encoding PHA synthase from Pseudomonas aeruginosa, fused to a peroxisomal targeting signal, was expressed in flax plants with the aim of modifying the mechanical properties of plants. Medium-chain-length (mcl) hydroxy acids in flax plants from tissue cultures were detected by GC-FID and FTIR method. The introduced changes did not affect fatty acid content and composition in generated flax plants. Since mcl-PHA are known as elastomers, the mechanical properties of created plants were examined. Modified plants showed increases in the values of all measured parameters (except strain at break evaluated for one modified line). The largest increase was noted for tensile stiffness, which was 2- to 3-fold higher than in wild-type plants. The values estimated for another parameter, Young's modulus, was almost at the same level in generated flax plants, and they were about 2.7-fold higher when compared to unmodified plants. The created plants also exhibited up to about 2.4-fold higher tensile strength. The observed changes were accompanied by alterations in the expression of selected genes, related to cell wall metabolism in line with the highest expression of phaC1 gene. Biochemical data were confirmed by spectroscopic methods, which also revealed that crystallinity index values of cellulose in modified flax plants were increased in comparison to wild-type flax plants and correlated with biomechanical properties of plants.
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Affiliation(s)
- Magdalena Wróbel-Kwiatkowska
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Chełmońskiego St. 37, 51-630, Wrocław, Poland.
| | - Mateusz Kropiwnicki
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Chełmońskiego St. 37, 51-630, Wrocław, Poland
| | - Jacek Żebrowski
- Department of Plant Physiology, Faculty of Biotechnology, University of Rzeszów, Rzeszów, Poland
| | - Athanasios Beopoulos
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Lucyna Dymińska
- Department of Bioorganic Chemistry, Institute of Chemistry and Food Technology, Faculty of Engineering and Economics, Wrocław University of Economics, Komandorska Str. 118/120, Wrocław, Poland
| | - Jerzy Hanuza
- Institute of Low Temperatures and Structure Research, Polish Academy of Sciences, Okólna Str.2, Wrocław, Poland
| | - Waldemar Rymowicz
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Chełmońskiego St. 37, 51-630, Wrocław, Poland
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Gorshkova T, Chernova T, Mokshina N, Gorshkov V, Kozlova L, Gorshkov O. Transcriptome Analysis of Intrusively Growing Flax Fibers Isolated by Laser Microdissection. Sci Rep 2018; 8:14570. [PMID: 30275452 PMCID: PMC6167358 DOI: 10.1038/s41598-018-32869-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
The intrusive growth, a type of plant cell elongation occurring in the depths of plant tissues, is characterized by the invasion of a growing cell between its neighbours due to a higher rate of elongation. In order to reveal the largely unknown molecular mechanisms of intrusive growth, we isolated primary flax phloem fibers specifically at the stage of intrusive growth by laser microdissection. The comparison of the RNA-Seq data from several flax stem parts enabled the characterization of those processes occurring specifically during the fiber intrusive elongation. The revealed molecular players are summarized as those involved in the supply of assimilates and support of turgor pressure, cell wall enlargement and modification, regulation by transcription factors and hormones, and responses to abiotic stress factors. The data obtained in this study provide a solid basis for developing approaches to manipulate fiber intrusive elongation, which is of importance both for plant biology and the yield of fiber crops.
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Affiliation(s)
- Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation.
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Liudmila Kozlova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
| | - Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of RAS" 420111, Lobachevsky Str., 2/31, Kazan, Russian Federation
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22
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Expression Analysis of Cell Wall-Related Genes in Cannabis sativa: The “Ins and Outs” of Hemp Stem Tissue Development. FIBERS 2018. [DOI: 10.3390/fib6020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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23
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Key Stages of Fiber Development as Determinants of Bast Fiber Yield and Quality. FIBERS 2018. [DOI: 10.3390/fib6020020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Gorshkova T, Chernova T, Mokshina N, Ageeva M, Mikshina P. Plant 'muscles': fibers with a tertiary cell wall. THE NEW PHYTOLOGIST 2018; 218:66-72. [PMID: 29364532 DOI: 10.1111/nph.14997] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/15/2017] [Indexed: 05/25/2023]
Abstract
Plants, although sessile organisms, are nonetheless able to move their body parts; for example, during root contraction of geophytes or in the gravitropic reaction by woody stems. One of the major mechanisms enabling these movements is the development of specialized structures that possess contractile properties. Quite unlike animal muscles, for which the action is driven by protein-protein interactions in the protoplasma, the action of plant 'muscles' is polysaccharide-based and located in the uniquely designed, highly cellulosic cell wall that is deposited specifically in fibers. This review describes the development of such cell walls as a widespread phenomenon in the plant kingdom, gives reasons why it should be considered as a tertiary cell wall, and discusses the mechanism of action of the 'muscles'. The origin of the contractile properties lies in the tension of the axially oriented cellulose microfibrils due to entrapment of rhamnogalacturonan-I aggregates that limits the lateral interaction of microfibrils. Long side chains of the nascent rhamnogalacturonan-I are trimmed off during cell wall maturation leading to tension development. Similarities in the tertiary cell wall design in fibers of different plant origin indicate that the basic principles of tension creation may be universal in various ecophysiological situations.
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Affiliation(s)
- Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation
| | - Marina Ageeva
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation
| | - Polina Mikshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, Kazan, 420111, Russian Federation
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25
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Wei Q, Jiao C, Ding Y, Gao S, Guo L, Chen M, Hu P, Xia S, Ren G, Fei Z. Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo. TREE PHYSIOLOGY 2018; 38:641-654. [PMID: 29077967 DOI: 10.1093/treephys/tpx129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/24/2017] [Indexed: 05/16/2023]
Abstract
Few studies about bamboo naturally occurring mutants have been reported so far. Using an integrated anatomy, mathematics and genomics approach, we systematically characterized the cellular and molecular basis underlying the abnormal internode development of Pseudosasa japonica var. tsutsumiana, a stable variant with dwarf and swollen internodes that are caused by the compressed spiral growth and the swollen cells in the bottom part of the internode. P. japonica var. tsutsumiana is a slow-growth variant with disorderly cell division and cell growth during the fast growth stage. Comparative transcriptome analysis identified a number of genes related to cell growth that were significantly down-regulated in the variant, including those related to auxin, vesicle transport, cytoskeleton organization and cell wall modification, consistent with the thinner cell walls and lower contents of cellulose that were found in the variant, which together with the mechanic force composed by the extrusion pressure from the neighboring fast growth cells and the weight pressure above the growing cells might finally result in the radial and irregular growth of the variant cells. This study provides key candidate genes involved in the fast growth of bamboo from a 'mutant' perspective, and supports a plausible mechanism underlying the dwarf and swollen internodes of P. japonica var. tsutsumiana.
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Affiliation(s)
- Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Shan Gao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Pei Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Sujuan Xia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
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Clair B, Déjardin A, Pilate G, Alméras T. Is the G-Layer a Tertiary Cell Wall? FRONTIERS IN PLANT SCIENCE 2018; 9:623. [PMID: 29868079 PMCID: PMC5952352 DOI: 10.3389/fpls.2018.00623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/19/2018] [Indexed: 05/13/2023]
Affiliation(s)
- Bruno Clair
- CNRS, UMR EcoFoG, AgroParisTech, Cirad, INRA, Université des Antilles, Université de Guyane, Kourou, France
- *Correspondence: Bruno Clair
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27
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Guerriero G, Behr M, Legay S, Mangeot-Peter L, Zorzan S, Ghoniem M, Hausman JF. Transcriptomic profiling of hemp bast fibres at different developmental stages. Sci Rep 2017; 7:4961. [PMID: 28694530 PMCID: PMC5504027 DOI: 10.1038/s41598-017-05200-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/24/2017] [Indexed: 02/08/2023] Open
Abstract
Bast fibres are long extraxylary cells which mechanically support the phloem and they are divided into xylan- and gelatinous-type, depending on the composition of their secondary cell walls. The former, typical of jute/kenaf bast fibres, are characterized by the presence of xylan and a high degree of lignification, while the latter, found in tension wood, as well as flax, ramie and hemp bast fibres, have a high abundance of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, subsequently they cease elongation and start to thicken. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development in textile hemp (Cannabis sativa L.), a fibre crop of great importance. Bast fibres have been sampled from different stem regions. The developmental stages corresponding to active elongation and cell wall thickening have been studied using RNA-Seq. The results show that the fibres sampled at each stem region are characterized by a specific transcriptomic signature and that the major changes in cell wall-related processes take place at the internode containing the snap point. The data generated also identify several interesting candidates for future functional analysis.
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Affiliation(s)
- Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg.
| | - Marc Behr
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Université catholique de Louvain, Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Louvain-la-Neuve, B-1348, Belgium
| | - Sylvain Legay
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Lauralie Mangeot-Peter
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Institut National de la Recherche Agronomique, Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, F-54280, France
| | - Simone Zorzan
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Mohammad Ghoniem
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
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28
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Mokshina N, Gorshkov O, Ibragimova N, Chernova T, Gorshkova T. Cellulosic fibres of flax recruit both primary and secondary cell wall cellulose synthases during deposition of thick tertiary cell walls and in the course of graviresponse. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:820-831. [PMID: 32480610 DOI: 10.1071/fp17105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 05/19/2017] [Indexed: 05/13/2023]
Abstract
Cellulose synthesising complex consists of cellulose synthase (CESA) subunits encoded by a multigene family; different sets of CESA genes are known to be expressed during primary and secondary cell wall formation. We examined the expression of LusCESAs in flax (Linum usitatissimum L.) cellulosic fibres at various stages of development and in the course of graviresponse by means of RNA-Seq and quantitative PCR. Transcripts for both primary and secondary cell wall-related CESAs were abundant in fibres depositing highly cellulosic tertiary cell walls. Gravistimulation of flax plants temporally increased the abundance of CESA transcripts, specifically in phloem fibres located at the pulling stem side. Construction of coexpression networks for LusCESAs revealed that both primary and secondary cell wall-related CESAs were involved in the joint coexpression group in fibres depositing tertiary cell walls, as distinct from other tissues, where these genes were within separate groups. The obtained data suggest that fibres depositing tertiary cell walls have a specific mechanism of cellulose biosynthesis and a specific way of its regulation.
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Affiliation(s)
- Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, Russia 420111
| | - Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, Russia 420111
| | - Nadezda Ibragimova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, Russia 420111
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, Russia 420111
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, Russia 420111
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