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Le Lievre L, Chakkatu SP, Varghese S, Day RC, Pilkington SM, Brownfield L. RNA-seq analysis of synchronized developing pollen isolated from a single anther. Front Plant Sci 2023; 14:1121570. [PMID: 37077645 PMCID: PMC10106640 DOI: 10.3389/fpls.2023.1121570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Pollen development, from unicellular microspores to anthesis, is a complex process involving the coordinated specification, differentiation and functions of different cell types. Key to understanding this development is identifying the genes expressed at precise stages of development. However, transcriptomic studies on pollen prior to anthesis are complicated by the inaccessible nature of pollen developing in the anther and the resistant pollen wall. To assist with understanding gene expression during pollen development we have developed a protocol to perform RNA-Seq on pollen isolated from a single anther (SA RNA-Seq). The protocol involves removing pollen from a single anther for analysis and viewing the remaining pollen to determine the developmental stage. The isolated pollen is chemically lysed and mRNA isolated from the lysate using an oligo-dT column before library preparation. Here, we report on the development and testing of our method and the generation of a transcriptome for three stages of pollen development from Arabidopsis (Arabidopsis thaliana) and two stages from male kiwifruit (Actinidia chinensis). This protocol enables the transcriptome of precise developmental stages of pollen to be analyzed, and uses a small number of plants, potentially facilitating studies that require a range of treatments or the analysis of the first generation of transgenic plants.
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Affiliation(s)
- Liam Le Lievre
- Biochemistry Department, University of Otago, Dunedin, New Zealand
- The New Zealand Institute for Plant and Food Research, Lincoln, New Zealand
| | | | - Shiny Varghese
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Robert C. Day
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sarah M. Pilkington
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Lynette Brownfield
- Biochemistry Department, University of Otago, Dunedin, New Zealand
- *Correspondence: Lynette Brownfield,
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Winichayakul S, Macknight R, Le Lievre L, Beechey-Gradwell Z, Lee R, Cooney L, Xue H, Crowther T, Anderson P, Richardson K, Zou X, Maher D, Bryan G, Roberts N. Insight into the regulatory networks underlying the high lipid perennial ryegrass growth under different irradiances. PLoS One 2022; 17:e0275503. [PMID: 36227922 PMCID: PMC9560171 DOI: 10.1371/journal.pone.0275503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/18/2022] [Indexed: 11/19/2022] Open
Abstract
Under favourable conditions, perennial ryegrass (Lolium perenne) engineered to accumulated high lipid (HL) carbon sink in their leaves was previously shown to also enhance photosynthesis and growth. The greater aboveground biomass was found to be diminished in a dense canopy compared to spaced pots. Besides, the underlying genetic regulatory network linking between leaf lipid sinks and these physiological changes remains unknown. In this study, we demonstrated that the growth advantage was not displayed in HL Lolium grown in spaced pots under low lights. Under standard lights, analysis of differentiating transcripts in HL Lolium reveals that the plants had elevated transcripts involved in lipid metabolism, light capturing, photosynthesis, and sugar signalling while reduced expression of genes participating in sugar biosynthesis and transportation. The plants also had altered several transcripts involved in mitochondrial oxidative respiration and redox potential. Many of the above upregulated or downregulated transcript levels were found to be complemented by growing the plants under low light. Overall, this study emphasizes the importance of carbon and energy homeostatic regulatory mechanisms to overall productivity of the HL Lolium through photosynthesis, most of which are significantly impacted by low irradiances.
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Affiliation(s)
| | - Richard Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Liam Le Lievre
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Luke Cooney
- AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- AgResearch Ltd., Palmerston North, New Zealand
| | | | | | | | - Xiuying Zou
- AgResearch Ltd., Palmerston North, New Zealand
| | | | | | - Nick Roberts
- AgResearch Ltd., Palmerston North, New Zealand
- * E-mail: (SW); (NR)
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Tahir J, Crowhurst R, Deroles S, Hilario E, Deng C, Schaffer R, Le Lievre L, Brendolise C, Chagné D, Gardiner SE, Knaebel M, Catanach A, McCallum J, Datson P, Thomson S, Brownfield LR, Nardozza S, Pilkington SM. First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit. Front Genet 2022; 13:852161. [PMID: 35651931 PMCID: PMC9149279 DOI: 10.3389/fgene.2022.852161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Simon Deroles
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Robert Schaffer
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Liam Le Lievre
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Mareike Knaebel
- The New Zealand Institute for Plant and Food Research Limited, Manawatu Mail Centre, Palmerston North, New Zealand
| | - Andrew Catanach
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - John McCallum
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | | | - Simona Nardozza
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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Rossig C, Le Lievre L, Pilkington SM, Brownfield L. A simple and rapid method for imaging male meiotic cells in anthers of model and non-model plant species. Plant Reprod 2021; 34:37-46. [PMID: 33599868 DOI: 10.1007/s00497-021-00404-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
We describe a simple method to view meiotic cells in whole anthers from a range of plants. The method retains spatial organisation and enables simultaneous analysis of many meiotic cells. Understanding the process of male meiosis in flowering plants, and the role of genes involved in this process, offers potential for plant breeding, such as through increasing the level of genetic variation or the manipulation of ploidy levels in the gametes. A key to the characterisation of meiotic gene function and meiosis in non-model crop plants, is the analysis of cells undergoing meiosis, a task made difficult by the inaccessible nature of these cells. Here, we describe a simple and rapid method to analyse plant male meiosis in intact anthers in a range of plant species. This method allows analysis of numerous cells undergoing meiosis and, as meiotic cells stay within the anther, it retains information of the three-dimensional organisation and the location of organelles in meiotic cells. We show that the technique provides information on male meiosis by looking at the synchrony of meiotic progression between and within locules, and comparing wildtype and mutant plants through the chromosome separation stages in Arabidopsis thaliana. Additionally, we demonstrate that the protocol can be adopted to other plants with different floral morphology using Medicago truncatula as an example with small floral buds and the non-model plant kiwifruit (Actinidia chinensis) with larger buds and anthers.
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Affiliation(s)
- Claudia Rossig
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Liam Le Lievre
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sarah M Pilkington
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
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