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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 DOI: 10.1038/s42003-024-06525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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2
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Zhou Z, Li J, Gao Y, Wang X, Wang R, Huang H, Zhang Y, Zhao L, Wang P. Research on drought stress in Medicago sativa L. from 1998 to 2023: a bibliometric analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1406256. [PMID: 38872890 PMCID: PMC11169798 DOI: 10.3389/fpls.2024.1406256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage crops in the world. Drought is recognized as a major challenge limiting alfalfa production and threatening food security. Although some literature reviews have been conducted in this area, bibliometric reviews based on large amounts of published data are still lacking. In this paper, a bibliometric analysis of alfalfa drought stress from 1998-2023 was conducted using the Web of Science Core Collection database in order to assess global trends in alfalfa drought stress research and to provide new directions for future research. The results showed that the annual publication output maintained an increase in most years, with China and the United States contributing significantly to the field. Most of the journals published are specialized journals in botany, environmental science, soil science and crop science, as well as related agribusiness journals. "plant growth" and "yield" were the most frequently used keywords, reflecting the important purpose of research in this field. And two main research directions were identified: research on drought response mechanism of alfalfa and exploration of drought-resistant technology. In addition, physiological, biochemical, and molecular responses of drought tolerance and high yield in alfalfa, transgenics, and microbial fertilizer research have been hot research topics in recent years and may continue in the future. The ultimate goal of this paper is to provide a foundational reference for future research on alfalfa's drought resistance and yield optimization mechanisms, thereby enhancing the crop's application in agricultural production.
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Affiliation(s)
- Zijun Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Junqin Li
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Yang Gao
- School of Karst Science, Guizhou Normal University, Guiyang, Guizhou, China
| | - Xiangtao Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Rui Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Haiyan Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Yu Zhang
- School of Karst Science, Guizhou Normal University, Guiyang, Guizhou, China
| | - Lili Zhao
- College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
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3
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Verma S, Attuluri VPS, Robert HS. Transcriptional control of Arabidopsis seed development. PLANTA 2022; 255:90. [PMID: 35318532 PMCID: PMC8940821 DOI: 10.1007/s00425-022-03870-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/04/2022] [Indexed: 05/04/2023]
Abstract
The entire process of embryo development is under the tight control of various transcription factors. Together with other proteins, they act in a combinatorial manner and control distinct events during embryo development. Seed development is a complex process that proceeds through sequences of events regulated by the interplay of various genes, prominent among them being the transcription factors (TFs). The members of WOX, HD-ZIP III, ARF, and CUC families have a preferential role in embryonic patterning. While WOX TFs are required for initiating body axis, HD-ZIP III TFs and CUCs establish bilateral symmetry and SAM. And ARF5 performs a major role during embryonic root, ground tissue, and vasculature development. TFs such as LEC1, ABI3, FUS3, and LEC2 (LAFL) are considered the master regulators of seed maturation. Furthermore, several new TFs involved in seed storage reserves and dormancy have been identified in the last few years. Their association with those master regulators has been established in the model plant Arabidopsis. Also, using chromatin immunoprecipitation (ChIP) assay coupled with transcriptomics, genome-wide target genes of these master regulators have recently been proposed. Many seed-specific genes, including those encoding oleosins and albumins, have appeared as the direct target of LAFL. Also, several other TFs act downstream of LAFL TFs and perform their function during maturation. In this review, the function of different TFs in different phases of early embryogenesis and maturation is discussed in detail, including information about their genetic and molecular interactors and target genes. Such knowledge can further be leveraged to understand and manipulate the regulatory mechanisms involved in seed development. In addition, the genomics approaches and their utilization to identify TFs aiming to study embryo development are discussed.
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Affiliation(s)
- Subodh Verma
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Venkata Pardha Saradhi Attuluri
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hélène S. Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Peng L, Qian L, Wang M, Liu W, Song X, Cheng H, Yuan F, Zhao M. Comparative transcriptome analysis during seeds development between two soybean cultivars. PeerJ 2021; 9:e10772. [PMID: 33717671 PMCID: PMC7931715 DOI: 10.7717/peerj.10772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.
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Affiliation(s)
- Li Peng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Linlin Qian
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Meinan Wang
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Wei Liu
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Xiangting Song
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Hao Cheng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Fengjie Yuan
- Institute of Crop Science, Zhejiang Academy of Agricultural Sciences, Hang Zhou, China
| | - Man Zhao
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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Detection of Embryonic Suspensor Cell Death by Whole-Mount TUNEL Assay in Tobacco. PLANTS 2020; 9:plants9091196. [PMID: 32932739 PMCID: PMC7570248 DOI: 10.3390/plants9091196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/08/2020] [Accepted: 09/10/2020] [Indexed: 12/26/2022]
Abstract
Embryonic suspensor in angiosperms is a short-lived structure that connects the embryo to surrounding maternal tissues, which is necessary for early embryogenesis. Timely degeneration via programed cell death is the most distinct feature of the suspensor during embryogenesis. Therefore, the molecular mechanism regulating suspensor cell death is worth in-depth study for embryonic development. However, this process can hardly be detected using conventional methods since early embryos are deeply embedded in the seed coats and inaccessible through traditional tissue section. Hence, it is necessary to develop a reliable protocol for terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) analysis using limited living early embryos. Here, we provide a detailed protocol for the whole-mount detection of suspensor cell death using a TUNEL system in tobacco. This method is especially useful for the direct and rapid detection of the spatial-temporal characters of programed cell death during embryogenesis, as well as for the diminishment of the artifacts during material treatment by traditional methods.
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7
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Wójcik AM. Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis. Int J Mol Sci 2020; 21:E4969. [PMID: 32674459 PMCID: PMC7420248 DOI: 10.3390/ijms21144969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.
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Affiliation(s)
- Anna Maria Wójcik
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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8
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Jacob D, Brian J. The short and intricate life of the suspensor. PHYSIOLOGIA PLANTARUM 2020; 169:110-121. [PMID: 31808953 DOI: 10.1111/ppl.13057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/04/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The suspensor is a short-lived tissue critical for proper embryonic development in many higher plants. While the tissue was initially thought to simply suspend the embryo in the endosperm, it has been found through decades of research that it serves multiple important purposes. The suspensor has been found to be vital for proper embryo patterning and numerous studies have been undertaken into the complex transcriptional cross-talk between the suspensor and the embryo proper. Indeed, many suspensor mutants also display abnormalities in the embryo. The suspensor's role as a nutrient conduit has been shown using ultrastructural and histochemical techniques. Biochemical approaches have found that the suspensor is a centre of early embryonic hormone production in several species. The suspensor has also been frequently used as a model for programmed cell death as it shows signs of termination almost immediately upon developing. This review covers the essential functions of the suspensor throughout its short existence from multiple disciplines including structural, genetic and biochemical perspectives.
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Affiliation(s)
- Downs Jacob
- Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jones Brian
- Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
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Xiong F, Ren JJ, Yu Q, Wang YY, Kong LJ, Otegui MS, Wang XL. AtBUD13 affects pre-mRNA splicing and is essential for embryo development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:714-726. [PMID: 30720904 DOI: 10.1111/tpj.14268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 05/03/2023]
Abstract
Pre-mRNA splicing is an important step for gene expression regulation. Yeast Bud13p (bud-site selection protein 13) regulates the budding pattern and pre-mRNA splicing in yeast cells; however, no Bud13p homologs have been identified in plants. Here, we isolated two mutants that carry T-DNA insertions at the At1g31870 locus and shows early embryo lethality and seed abortion. At1g31870 encodes an Arabidopsis homolog of yeast Bud13p, AtBUD13. Although AtBUD13 homologs are widely distributed in eukaryotic organisms, phylogenetic analysis revealed that their protein domain organization is more complex in multicellular species. AtBUD13 is expressed throughout plant development including embryogenesis and AtBUD13 proteins is localized in the nucleus in Arabidopsis. RNA-seq analysis revealed that AtBUD13 mutation predominantly results in the intron retention, especially for shorter introns (≤100 bases). Within this group of genes, we identified 52 genes involved in embryogenesis, out of which 22 are involved in nucleic acid metabolism. Our results demonstrate that AtBUD13 plays critical roles in early embryo development by effecting pre-mRNA splicing.
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Affiliation(s)
- Feng Xiong
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Jing-Jing Ren
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Qin Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Yu-Yi Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Lan-Jing Kong
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Marisa S Otegui
- Departments of Botany and Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, 53706, USA
| | - Xiu-Ling Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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Kyo M, Maida K, Nishioka Y, Matsui K. Coexpression of WUSCHEL related homeobox ( WOX) 2 with WOX8 or WOX9 promotes regeneration from leaf segments and free cells in Nicotiana tabacum L. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:23-30. [PMID: 31275034 PMCID: PMC6543738 DOI: 10.5511/plantbiotechnology.18.0126a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 01/26/2018] [Indexed: 05/11/2023]
Abstract
To examine the effect of the ectopic expression of three Arabidopsis genes, including WOX2, WOX8 and WOX9, on the regenerative competency of tissues and cells cultured in vitro, we developed a transgenic variety of Nicotiana tabacum, in which these genes were under the transcriptional control of a chemical-inducible expression system. We designed a two-step culture method to feasibly demonstrate the effect as follows. Leaf segments of approximately 10 mm2 were prepared from transgenic plants and their hybrids and cultured in a liquid medium based on modified Murashige and Skoog medium supplemented with an auxin, 2,4-dichrorophenoxyacetic acid and/or an expression inducer β-estradiol for 10 days in dark. The segments were subsequently cultured on a solidified medium in the absence of both the auxin and inducer in light for 3 weeks. We observed remarkable regeneration of plantlets only in segments derived from the hybrids possessing two transgenes, WOX2 combined with WOX8 or WOX9, but no regeneration in the segments derived from their parental lines. We also observed that free cells released from the hybrid explants in the liquid medium developed into embryo-like structures due to the transient application of the inducer. In a wide range of species including recalcitrants, the effect of the coexpression of these genes may be useful for developing an alternative to conventional protocols that requires cytokinin.
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Affiliation(s)
- Masaharu Kyo
- Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
- E-mail: Tel: +81-87-891-3132 Fax: +81-87-891-3012
| | - Kazuna Maida
- Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Yuki Nishioka
- Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
| | - Koitaro Matsui
- Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
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12
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 PMCID: PMC5687563 DOI: 10.1038/s41477-017-0035-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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Winnicki K, Polit JT, Żabka A, Maszewski J. Mitogen-activated protein kinases participate in determination of apical-basal symmetry in Pisum sativum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:186-195. [PMID: 28167032 DOI: 10.1016/j.plantsci.2017.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/25/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) are implicated in various processes in plants. Apart from response to biotic and abiotic stresses they are involved in regulation of embryo development. Although MAPKs were found to be indispensable during embryo development it has never been established at which stages of embryogenesis and in which regions of a plant embryo activated MAPKs can be observed. Here, we show that apical and basal regions display activation of the same types of MAPKs and the only difference concerns the level of their phosphorylation and cellular localization. Dually-phosphorylated MAPKs were found in nuclei of the apical region of an embryo both at the early and late cotyledonary stage while no immunofluorescence signals were detected in nuclei of the basal region. However, in this case phosphorylated MAPKs were immunodetected in cytoplasm in the apical domain of cortex cells, indicating their role in auxin transport from the basal to apical region of an embryo. Furthermore, obtained data indicate that nuclear localization of activated MAPKs may result from epigenetic modifications and polar auxin transport. The presented data and previous studies lead to the conclusion that activated MAPKs and their cellular localization define apical and basal regions during formation of an apical-basal axis.
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Affiliation(s)
- Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143 9, 90-236 Lodz, Poland.
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143 9, 90-236 Lodz, Poland
| | - Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143 9, 90-236 Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143 9, 90-236 Lodz, Poland
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14
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Shirakawa M, Ueda H, Shimada T, Hara-Nishimura I. FAMA: A Molecular Link between Stomata and Myrosin Cells. TRENDS IN PLANT SCIENCE 2016; 21:861-871. [PMID: 27477926 DOI: 10.1016/j.tplants.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/24/2016] [Accepted: 07/04/2016] [Indexed: 05/04/2023]
Abstract
Plants use sophisticated defense strategies against herbivores, including the myrosinase-glucosinolate system in Brassicales plants. This system sequesters myrosinase in myrosin cells, which are idioblasts in inner leaf tissues, and produces a toxic compound when cells are damaged by herbivores. Although the molecular mechanisms underlying myrosin cell development are largely unknown, recent studies have revealed that two key components, a basic helix-loop-helix (bHLH) transcription factor (FAMA) and vesicle trafficking factors (such as SYNTAXIN OF PLANTS 22), regulate the differentiation and fate determination of myrosin cells. FAMA also functions as a master regulator of guard cell (GC) differentiation. In this review, we discuss how FAMA operates two distinct genetic programs: the generation of myrosin cells in inner plant tissue and GCs in the epidermis.
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Affiliation(s)
- Makoto Shirakawa
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Haruko Ueda
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tomoo Shimada
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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15
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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16
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Zhang F, Hua L, Fei J, Wang F, Liao Y, Fang W, Chen F, Teng N. Chromosome doubling to overcome the chrysanthemum cross barrier based on insight from transcriptomic and proteomic analyses. BMC Genomics 2016; 17:585. [PMID: 27506621 PMCID: PMC4979184 DOI: 10.1186/s12864-016-2939-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/14/2016] [Indexed: 12/05/2022] Open
Abstract
Background Cross breeding is the most commonly used method in chrysanthemum (Chrysanthemum morifolium) breeding; however, cross barriers always exist in these combinations. Many studies have shown that paternal chromosome doubling can often overcome hybridization barriers during cross breeding, although the underlying mechanism has seldom been investigated. Results In this study, we performed two crosses: C. morifolium (pollen receptor) × diploid C. nankingense (pollen donor) and C. morifolium × tetraploid C. nankingense. Seeds were obtained only from the latter cross. RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) were used to investigate differentially expressed genes and proteins during key embryo development stages in the latter cross. A previously performed cross, C. morifolium × diploid C. nankingense, was compared to our results and revealed that transcription factors (i.e., the agamous-like MADS-box protein AGL80 and the leucine-rich repeat receptor protein kinase EXS), hormone-responsive genes (auxin-binding protein 1), genes and proteins related to metabolism (ATP-citrate synthase, citrate synthase and malate dehydrogenase) and other genes reported to contribute to embryo development (i.e., LEA, elongation factor and tubulin) had higher expression levels in the C. morifolium × tetraploid C. nankingense cross. In contrast, genes related to senescence and cell death were down-regulated in the C. morifolium × tetraploid C. nankingense cross. Conclusions The data resources helped elucidate the gene and protein expression profiles and identify functional genes during different development stages. When the chromosomes from the male parent are doubled, the genes contributing to normal embryo developmentare more abundant. However, genes with negative functions were suppressed, suggesting that chromosome doubling may epigenetically inhibit the expression of these genes and allow the embryo to develop normally. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2939-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengjiao Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, China
| | - Lichun Hua
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangsong Fei
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, China.
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17
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Jeong S, Eilbert E, Bolbol A, Lukowitz W. Going mainstream: How is the body axis of plants first initiated in the embryo? Dev Biol 2016; 419:78-84. [PMID: 27207388 DOI: 10.1016/j.ydbio.2016.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Vascular plants have an open body plan and continuously generate new axes of growth, such as shoot or root branches. Apical-to-basal transport of the hormone auxin is a hallmark of every axis, and the resulting pattern of auxin distribution affects plant development across scales, from overall architecture to cellular differentiation. How the first axis is initiated in the early embryo is a long-standing question. While our knowledge is still sparse, some of the key players of axialization have emerged, and recent work points to specific models for connecting cellular polarity to the asymmetric division of the zygote and domain specific gene expression to the organization of basipetal auxin flux.
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Affiliation(s)
- Sangho Jeong
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Emily Eilbert
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Ahmed Bolbol
- Botany Department, Faculty of Science, Zagazig University, 44519 Sharkira, Egypt.
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
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18
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Chitikova Z, Steiner FA. Cell type-specific epigenome profiling using affinity-purified nuclei. Genesis 2016; 54:160-9. [PMID: 26789661 DOI: 10.1002/dvg.22919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/08/2022]
Abstract
The development of a multicellular organism from a single zygote depends on the differentiation of progenitor cells to specialized cell types. The differentiation of these cell types is associated with changes in gene expression and the underlying chromatin landscape. To understand how these processes are regulated, it is desirable to understand how the chromatin features that constitute the epigenome differ between cell types at any given time during development. INTACT, a method for the cell type-specific purification of nuclei that can be used for the isolation of both RNA and chromatin, has emerged as a powerful tool to simultaneously study gene expression and chromatin profiles specifically in cell types of interest. In this review, we focus on the application of INTACT to different model organisms and discuss its potential for profiling cell types in their developmental context.
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Affiliation(s)
- Zhanna Chitikova
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
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19
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Zhai L, Xu L, Wang Y, Zhu X, Feng H, Li C, Luo X, Everlyne MM, Liu L. Transcriptional identification and characterization of differentially expressed genes associated with embryogenesis in radish (Raphanus sativus L.). Sci Rep 2016; 6:21652. [PMID: 26902837 PMCID: PMC4763228 DOI: 10.1038/srep21652] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/28/2016] [Indexed: 11/09/2022] Open
Abstract
Embryogenesis is an important component in the life cycle of most plant species. Due to the difficulty in embryo isolation, the global gene expression involved in plant embryogenesis, especially the early events following fertilization are largely unknown in radish. In this study, three cDNA libraries from ovules of radish before and after fertilization were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. A total of 5,777 differentially expressed transcripts were detected based on pairwise comparison in the three libraries (0_DAP, 7_DAP and 15_DAP). Results from Gene Ontology (GO) and pathway enrichment analysis revealed that these differentially expressed genes (DEGs) were implicated in numerous life processes including embryo development and phytohormones biosynthesis. Notably, some genes encoding auxin response factor (ARF ), Leafy cotyledon1 (LEC1) and somatic embryogenesis receptor-like kinase (SERK ) known to be involved in radish embryogenesis were differentially expressed. The expression patterns of 30 genes including LEC1-2, AGL9, LRR, PKL and ARF8-1 were validated by qRT-PCR. Furthermore, the cooperation between miRNA and mRNA may play a pivotal role in the radish embryogenesis process. This is the first report on identification of DEGs profiles related to radish embryogenesis and seed development. These results could facilitate further dissection of the molecular mechanisms underlying embryogenesis and seed development in radish.
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Affiliation(s)
- Lulu Zhai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Haiyang Feng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chao Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Muleke M. Everlyne
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China
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20
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Itoh JI, Sato Y, Sato Y, Hibara KI, Shimizu-Sato S, Kobayashi H, Takehisa H, Sanguinet KA, Namiki N, Nagamura Y. Genome-wide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice. Development 2016; 143:1217-27. [PMID: 26903508 DOI: 10.1242/dev.123661] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 02/15/2016] [Indexed: 12/11/2022]
Abstract
Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.
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Affiliation(s)
- Jun-Ichi Itoh
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yutaka Sato
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Yutaka Sato
- Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Ken-Ichiro Hibara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Sae Shimizu-Sato
- Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hiromi Kobayashi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Hinako Takehisa
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Nobukazu Namiki
- Genome Informatics Department, Mitsubishi Space Software Co., Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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21
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Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods ("omics") now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis). Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.
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Affiliation(s)
| | | | - Ueli Grossniklaus
- Department of Plant & Microbial Biology and Zurich-Basel Plant Science Center, University of ZurichZurich, Switzerland
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22
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Baroux C, Grossniklaus U. The Maternal-to-Zygotic Transition in Flowering Plants: Evidence, Mechanisms, and Plasticity. Curr Top Dev Biol 2015; 113:351-71. [PMID: 26358878 DOI: 10.1016/bs.ctdb.2015.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The maternal-to-zygotic transition (MZT) defines a developmental phase during which the embryo progressively emancipates itself from a developmental control relying largely on maternal information. The MZT is a functional readout of two processes: the clearance of maternally derived information and the de novo expression of the inherited, parental alleles enabled by zygotic genome activation (ZGA). In plants, for many years the debate about whether the MZT exists at all focused on the ZGA alone. However, several recent studies provide evidence for a progressive alleviation of the maternal control over embryogenesis that is correlated with a gradual ZGA, a process that is itself maternally controlled. Yet, several examples of zygotic genes that are expressed and/or functionally required early in embryogenesis demonstrate a certain flexibility in the dynamics and kinetics of the MZT among plant species and also intraspecific hybrids.
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Affiliation(s)
- Célia Baroux
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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23
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Danzer J, Mellott E, Bui AQ, Le BH, Martin P, Hashimoto M, Perez-Lesher J, Chen M, Pelletier JM, Somers DA, Goldberg RB, Harada JJ. Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development. PLANT PHYSIOLOGY 2015; 168:1025-35. [PMID: 25963149 PMCID: PMC4741349 DOI: 10.1104/pp.15.00432] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/30/2015] [Indexed: 05/18/2023]
Abstract
We used an RNA interference screen to assay the function of 53 transcription factor messenger RNAs (mRNAs) that accumulate specifically within soybean (Glycine max) seed regions, subregions, and tissues during development. We show that basic helix-loop-helix (bHLH) transcription factor genes represented by Glyma04g41710 and its paralogs are required for the formation of stoma in leaves and stomatal precursor complexes in mature embryo cotyledons. Phylogenetic analysis indicates that these bHLH transcription factor genes are orthologous to Arabidopsis (Arabidopsis thaliana) SPEECHLESS (SPCH) that initiate asymmetric cell divisions in the leaf protoderm layer and establish stomatal cell lineages. Soybean SPCH (GmSPCH) mRNAs accumulate primarily in embryo, seedling, and leaf epidermal layers. Expression of Glyma04g41710 under the control of the SPCH promoter rescues the Arabidopsis spch mutant, indicating that Glyma04g41710 is a functional ortholog of SPCH. Developing soybean embryos do not form mature stoma, and stomatal differentiation is arrested at the guard mother cell stage. We analyzed the accumulation of GmSPCH mRNAs during soybean seed development and mRNAs orthologous to MUTE, FAMA, and inducer of C-repeat/dehydration responsive element-binding factor expression1/scream2 that are required for stoma formation in Arabidopsis. The mRNA accumulation patterns provide a potential explanation for guard mother cell dormancy in soybean embryos. Our results suggest that variation in the timing of bHLH transcription factor gene expression can explain the diversity of stomatal forms observed during plant development.
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Affiliation(s)
- John Danzer
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Eric Mellott
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Anhthu Q Bui
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Brandon H Le
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Patrick Martin
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Meryl Hashimoto
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Jeanett Perez-Lesher
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Min Chen
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Julie M Pelletier
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - David A Somers
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - Robert B Goldberg
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
| | - John J Harada
- Monsanto Company, Agracetus Campus, Middleton, Wisconsin 53562 (J.D., E.M., P.M., J.P.-L., D.A.S);Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (A.Q.B., B.H.L., M.C., R.B.G.); andDepartment of Plant Biology, University of California, Davis, California 95616 (M.H., J.M.P., J.J.H.)
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Borg M, Berger F. Chromatin remodelling during male gametophyte development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:177-188. [PMID: 25892182 DOI: 10.1111/tpj.12856] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 05/28/2023]
Abstract
The plant life cycle alternates between a diploid sporophytic phase and haploid gametophytic phase, with the latter giving rise to the gametes. Male gametophyte development encompasses two mitotic divisions that results in a simple three-celled structure knows as the pollen grain, in which two sperm cells are encased within a larger vegetative cell. Both cell types exhibit a very different type of chromatin organization - highly condensed in sperm cell nuclei and highly diffuse in the vegetative cell. Distinct classes of histone variants have dynamic and differential expression in the two cell lineages of the male gametophyte. Here we review how the dynamics of histone variants are linked to reprogramming of chromatin activities in the male gametophyte, compaction of the sperm cell genome and zygotic transitions post-fertilization.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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25
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Nieminen K, Blomster T, Helariutta Y, Mähönen AP. Vascular Cambium Development. THE ARABIDOPSIS BOOK 2015; 13:e0177. [PMID: 26078728 PMCID: PMC4463761 DOI: 10.1199/tab.0177] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Secondary phloem and xylem tissues are produced through the activity of vascular cambium, the cylindrical secondary meristem which arises among the primary plant tissues. Most dicotyledonous species undergo secondary development, among them Arabidopsis. Despite its small size and herbaceous nature, Arabidopsis displays prominent secondary growth in several organs, including the root, hypocotyl and shoot. Together with the vast genetic resources and molecular research methods available for it, this has made Arabidopsis a versatile and accessible model organism for studying cambial development and wood formation. In this review, we discuss and compare the development and function of the vascular cambium in the Arabidopsis root, hypocotyl, and shoot. We describe the current understanding of the molecular regulation of vascular cambium and compare it to the function of primary meristems. We conclude with a look at the future prospects of cambium research, including opportunities provided by phenotyping and modelling approaches, complemented by studies of natural variation and comparative genetic studies in perennial and woody plant species.
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Affiliation(s)
- Kaisa Nieminen
- Natural Resources Institute Finland (Luke), Green Technology, Vantaa 01301, Finland
| | - Tiina Blomster
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Ykä Helariutta
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
- Cardiff University Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Ari Pekka Mähönen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
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26
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Susaki D, Takeuchi H, Tsutsui H, Kurihara D, Higashiyama T. Live Imaging and Laser Disruption Reveal the Dynamics and Cell-Cell Communication During Torenia fournieri Female Gametophyte Development. PLANT & CELL PHYSIOLOGY 2015; 56:1031-41. [PMID: 25713175 DOI: 10.1093/pcp/pcv031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/14/2015] [Indexed: 05/08/2023]
Abstract
The female gametophytes of many flowering plants contain one egg cell, one central cell, two synergid cells and three antipodal cells with respective morphological characteristics and functions. These cells are formed by cellularization of a multinuclear female gametophyte. However, the dynamics and mechanisms of female gametophyte development remain largely unknown due to the lack of a system to visualize directly and manipulate female gametophytes in living material. Here, we established an in vitro ovule culture system to examine female gametophyte development in Torenia fournieri, a unique plant species with a protruding female gametophyte. The four-nucleate female gametophyte became eight nucleate by the final (third) mitosis and successively cellularized and matured to attract a pollen tube. The duration of final mitosis was 28 ± 6.5 min, and cellularization was completed in 54 ± 20 min after the end of the third mitosis. Fusion of polar nuclei in the central cell occurred in 13.1 ± 1.1 h, and onset of expression of LURE2, a pollen tube attractant gene, was visualized by a green fluorescent protein reporter 10.7 ± 2.3 h after cellularization. Laser disruption analysis demonstrated that the egg and central cells were required for synergid cells to acquire the pollen tube attraction function. Moreover, aberrant nuclear positioning and down-regulation of LURE2 were observed in one of the two synergid cells after disrupting an immature egg cell, suggesting that cell specification was affected. Our system provides insights into the precise dynamics and mechanisms of female gametophyte development in T. fournieri.
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Affiliation(s)
- Daichi Susaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan
| | - Hidenori Takeuchi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan
| | - Hiroki Tsutsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan
| | - Daisuke Kurihara
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602 Japan
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27
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Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana. GENOMICS DATA 2015; 4:96-8. [PMID: 26484189 PMCID: PMC4536148 DOI: 10.1016/j.gdata.2015.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/26/2015] [Indexed: 11/21/2022]
Abstract
In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.
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28
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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29
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Wang D, Deal RB. Epigenome profiling of specific plant cell types using a streamlined INTACT protocol and ChIP-seq. Methods Mol Biol 2015; 1284:3-25. [PMID: 25757765 DOI: 10.1007/978-1-4939-2444-8_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Plants consist of many functionally specialized cell types, each with its own unique epigenome, transcriptome, and proteome. Characterization of these cell type-specific properties is essential to understanding cell fate specification and the responses of individual cell types to the environment. In this chapter we describe an approach to map chromatin features in specific cell types of Arabidopsis thaliana using nuclei purification from individual cell types with the INTACT method (isolation of nuclei tagged in specific cell types) followed by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). The INTACT system employs two transgenes to generate affinity-labeled nuclei in the cell type of interest, and these tagged nuclei can then be selectively purified from tissue homogenates. The primary transgene encodes the nuclear tagging fusion protein (NTF), which consists of a nuclear envelope-targeting domain, the green fluorescent protein, and a biotin ligase recognition peptide, while the second transgene encodes the E. coli biotin ligase (BirA), which selectively biotinylates NTF. Expression of NTF and BirA in a specific cell type thus yields nuclei that are coated with biotin and can be purified by virtue of their affinity for streptavidin-coated magnetic beads. Compared with the original INTACT nuclei purification protocol, the procedure presented here is greatly simplified and shortened. After nuclei purification, we provide detailed instructions for chromatin isolation, shearing, and immunoprecipitation. Finally, we present a low input ChIP-seq library preparation protocol based on the nano-ChIP-seq method of Adli and Bernstein, and we describe multiplex Illumina sequencing of these libraries to produce high quality, cell type-specific epigenome profiles at a relatively low cost. The procedures given here are optimized for Arabidopsis but should be easily adaptable to other plant species.
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Affiliation(s)
- Dongxue Wang
- Department of Biology, O. Wayne Rollins Research Center, Emory University, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
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30
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Slane D, Kong J, Berendzen KW, Kilian J, Henschen A, Kolb M, Schmid M, Harter K, Mayer U, De Smet I, Bayer M, Jürgens G. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development 2014; 141:4831-40. [PMID: 25411212 DOI: 10.1242/dev.116459] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jixiang Kong
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Kenneth W Berendzen
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Joachim Kilian
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Agnes Henschen
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Martina Kolb
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Klaus Harter
- Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ulrike Mayer
- Microscopy facility, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany
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31
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Zhang F, Wang Z, Dong W, Sun C, Wang H, Song A, He L, Fang W, Chen F, Teng N. Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding. Sci Rep 2014; 4:6536. [PMID: 25288482 PMCID: PMC4187010 DOI: 10.1038/srep06536] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/26/2014] [Indexed: 12/25/2022] Open
Abstract
Embryo abortion is the main cause of failure in chrysanthemum cross breeding, and the genes and proteins associated with embryo abortion are poorly understood. Here, we applied RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic profiles of normal and abortive embryos. More than 68,000 annotated unigenes and 700 proteins were obtained from normal and abortive embryos. Functional analysis showed that 140 differentially expressed genes (DEGs) and 41 differentially expressed proteins (DEPs) were involved in embryo abortion. Most DEGs and DEPs associated with cell death, protein degradation, reactive oxygen species scavenging, and stress-response transcriptional factors were significantly up-regulated in abortive embryos relative to normal embryos. In contrast, most genes and proteins related to cell division and expansion, the cytoskeleton, protein synthesis and energy metabolism were significantly down-regulated in abortive embryos. Furthermore, abortive embryos had the highest activity of three executioner caspase-like enzymes. These results indicate that embryo abortion may be related to programmed cell death and the senescence- or death-associated genes or proteins contribute to embryo abortion. This adds to our understanding of embryo abortion and will aid in the cross breeding of chrysanthemum and other crops in the future.
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Affiliation(s)
- Fengjiao Zhang
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Zhiquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Dong
- China Rural Technology Development Center, Beijing 100045, China
| | - Chunqing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lizhong He
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fadi Chen
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Nianjun Teng
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
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32
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Kawashima T, Berger F. Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet 2014; 15:613-24. [DOI: 10.1038/nrg3685] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The astonishingly long lives of plants and their regeneration capacity depend on the activity of plant stem cells. As in animals, stem cells reside in stem cell niches, which produce signals that regulate the balance between self-renewal and the generation of daughter cells that differentiate into new tissues. Plant stem cell niches are located within the meristems, which are organized structures that are responsible for most post-embryonic development. The continuous organ production that is characteristic of plant growth requires a robust regulatory network to keep the balance between pluripotent stem cells and differentiating progeny. Components of this network have now been elucidated and provide a unique opportunity for comparing strategies that were developed in the animal and plant kingdoms, which underlie the logic of stem cell behaviour.
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34
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Kajala K, Ramakrishna P, Fisher A, C. Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants. ANNALS OF BOTANY 2014; 113:1083-1105. [PMID: 24825294 PMCID: PMC4030820 DOI: 10.1093/aob/mcu065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development. SCOPE This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. CONCLUSIONS Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
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Affiliation(s)
- Kaisa Kajala
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Adam Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dominique C. Bergmann
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
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35
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Sozzani R, Iyer-Pascuzzi A. Postembryonic control of root meristem growth and development. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:7-12. [PMID: 24507488 DOI: 10.1016/j.pbi.2013.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 10/10/2013] [Indexed: 05/08/2023]
Abstract
Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size.
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Affiliation(s)
- Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anjali Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States.
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36
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Venglat P, Xiang D, Wang E, Datla R. Genomics of seed development: Challenges and opportunities for genetic improvement of seed traits in crop plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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