1
|
Xue F, Zhang J, Wu D, Sun S, Fu M, Wang J, Searle I, Gao H, Liang W. m 6A demethylase OsALKBH5 is required for double-strand break formation and repair by affecting mRNA stability in rice meiosis. THE NEW PHYTOLOGIST 2024. [PMID: 39044689 DOI: 10.1111/nph.19976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024]
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent messenger RNA (mRNA) modification in eukaryotes and plays critical roles in the regulation of gene expression. m6A is a reversible RNA modification that is deposited by methyltransferases (writers) and removed by demethylases (erasers). The function of m6A erasers in plants is highly diversified and their roles in cereal crops, especially in reproductive development essential for crop yield, are largely unknown. Here, we demonstrate that rice OsALKBH5 acts as an m6A demethylase required for the normal progression of male meiosis. OsALKBH5 is a nucleo-cytoplasmic protein, highly enriched in rice anthers during meiosis, that associates with P-bodies and exon junction complexes, suggesting that it is involved in regulating mRNA processing and abundance. Mutations of OsALKBH5 cause reduced double-strand break (DSB) formation, severe defects in DSB repair, and delayed meiotic progression, leading to complete male sterility. Transcriptome analysis and m6A profiling indicate that OsALKBH5-mediated m6A demethylation stabilizes the mRNA level of multiple meiotic genes directly or indirectly, including several genes that regulate DSB formation and repair. Our study reveals the indispensable role of m6A metabolism in post-transcriptional regulation of meiotic progression in rice.
Collapse
Affiliation(s)
- Feiyang Xue
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Wu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiyu Sun
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Iain Searle
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| |
Collapse
|
2
|
Cseh A, Lenykó-Thegze A, Makai D, Szabados F, Hamow KÁ, Gulyás Z, Kiss T, Karsai I, Moncsek B, Mihók E, Sepsi A. Meiotic instability and irregular chromosome pairing underpin heat-induced infertility in bread wheat carrying the Rht-B1b or Rht-D1b Green Revolution genes. THE NEW PHYTOLOGIST 2024; 241:180-196. [PMID: 37691304 DOI: 10.1111/nph.19256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023]
Abstract
Mutations in the Rht-B1a and Rht-D1a genes of wheat (Triticum aestivum; resulting in Rht-B1b and Rht-D1b alleles) cause gibberellin-insensitive dwarfism and are one of the most important elements of increased yield introduced during the 'Green Revolution'. We measured the effects of a short period of heat imposed during the early reproductive stage on near-isogenic lines carrying Rht-B1b or Rht-D1b alleles, with respect to the wild-type (WT). The temperature shift caused a significant fertility loss within the ears of Rht-B1b and Rht-D1b wheats, greater than that observed for the WT. Defects in chromosome synapsis, reduced homologous recombination and a high frequency of chromosome mis-segregation were associated with reduced fertility. The transcription of TaGA3ox gene involved in the final stage of gibberellic acid (GA) biosynthesis was activated and ultra-performance liquid chromatography-tandem mass spectrometry identified GA1 as the dominant bioactive GA in developing ears, but levels were unaffected by the elevated temperature. Rht-B1b and Rht-D1b mutants were inclined to meiotic errors under optimal temperatures and showed a higher susceptibility to heat than their tall counterparts. Identification and introduction of new dwarfing alleles into modern breeding programmes is invaluable in the development of climate-resilient wheat varieties.
Collapse
Affiliation(s)
- András Cseh
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Andrea Lenykó-Thegze
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Diána Makai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Fanni Szabados
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Kamirán Áron Hamow
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Zsolt Gulyás
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Tibor Kiss
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eszterházy tér 1, Eger, 3300, Hungary
| | - Ildikó Karsai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Blanka Moncsek
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Edit Mihók
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Adél Sepsi
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| |
Collapse
|
3
|
Cook TM, Isenegger D, Dutta S, Sahab S, Kay P, Aboobucker SI, Biswas E, Heerschap S, Nikolau BJ, Dong L, Lübberstedt T. Overcoming roadblocks for in vitro nurseries in plants: induction of meiosis. FRONTIERS IN PLANT SCIENCE 2023; 14:1204813. [PMID: 37332695 PMCID: PMC10272530 DOI: 10.3389/fpls.2023.1204813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023]
Abstract
Efforts to increase genetic gains in breeding programs of flowering plants depend on making genetic crosses. Time to flowering, which can take months to decades depending on the species, can be a limiting factor in such breeding programs. It has been proposed that the rate of genetic gain can be increased by reducing the time between generations by circumventing flowering through the in vitro induction of meiosis. In this review, we assess technologies and approaches that may offer a path towards meiosis induction, the largest current bottleneck for in vitro plant breeding. Studies in non-plant, eukaryotic organisms indicate that the in vitro switch from mitotic cell division to meiosis is inefficient and occurs at very low rates. Yet, this has been achieved with mammalian cells by the manipulation of a limited number of genes. Therefore, to experimentally identify factors that switch mitosis to meiosis in plants, it is necessary to develop a high-throughput system to evaluate a large number of candidate genes and treatments, each using large numbers of cells, few of which may gain the ability to induce meiosis.
Collapse
Affiliation(s)
- Tanner M. Cook
- Iowa State University, Department of Agronomy, Ames, IA, United States
| | - Daniel Isenegger
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | - Somak Dutta
- Iowa State University, Department of Statistics, Ames, IA, United States
| | - Sareena Sahab
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | - Pippa Kay
- Agriculture Victoria, Agribio, La Trobe University, Melbourne, VIC, Australia
| | | | - Eva Biswas
- Iowa State University, Department of Statistics, Ames, IA, United States
| | - Seth Heerschap
- Iowa State University, Department of Electrical and Computer Engineering, Ames, IA, United States
| | - Basil J. Nikolau
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Ames, IA, United States
| | - Liang Dong
- Iowa State University, Department of Electrical and Computer Engineering, Ames, IA, United States
| | | |
Collapse
|
4
|
Misra CS, Sousa AGG, Barros PM, Kermanov A, Becker JD. Cell-type-specific alternative splicing in the Arabidopsis germline. PLANT PHYSIOLOGY 2023; 192:85-101. [PMID: 36515615 PMCID: PMC10152659 DOI: 10.1093/plphys/kiac574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 05/03/2023]
Abstract
During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.
Collapse
Affiliation(s)
- Chandra Shekhar Misra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Anton Kermanov
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| |
Collapse
|
5
|
Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, Kagale S. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:209-224. [PMID: 36710629 DOI: 10.1111/tpj.16125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.
Collapse
Affiliation(s)
- Yunfei Jiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Arun S K Shunmugam
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan W Kirzinger
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Ehsan Sari
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Kevin Rozwadowski
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK, S7N 0X2, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| |
Collapse
|
6
|
Cheng J, Xu L, Bergér V, Bruckmann A, Yang C, Schubert V, Grasser KD, Schnittger A, Zheng B, Jiang H. H3K9 demethylases IBM1 and JMJ27 are required for male meiosis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 235:2252-2269. [PMID: 35638341 DOI: 10.1111/nph.18286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Dimethylation of histone H3 lysine 9 (H3K9me2), a crucial modification for heterochromatin formation and transcriptional silencing, is essential for proper meiotic prophase progression in mammals. We analyzed meiotic defects and generated genome-wide profiles of H3K9me2 and transcriptomes for the mutants of H3K9 demethylases. Moreover, we also identified proteins interacting with H3K9 demethylases. H3K9me2 is usually found at transposable elements and repetitive sequences but is absent from the bodies of protein-coding genes. In this study, we show that the Arabidopsis thaliana H3K9 demethylases IBM1 and JMJ27 cooperatively regulate crossover formation and chromosome segregation. They protect thousands of protein-coding genes from ectopic H3K9me2, including genes essential for meiotic prophase progression. In addition to removing H3K9me2, IBM1 and JMJ27 interact with the Precocious Dissociation of Sisters 5 (PDS5) cohesin complex cofactors. The pds5 mutant shared similar transcriptional alterations with ibm1 jmj27, including meiosis-essential genes, yet without affecting H3K9me2 levels. Hence, PDS5s, together with IBM1 and JMJ27, regulate male meiosis and gene expression independently of H3K9 demethylation. These findings uncover a novel role of H3K9me2 removal in meiosis and a new function of H3K9 demethylases and cohesin cofactors in meiotic transcriptional regulation.
Collapse
Affiliation(s)
- Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Valentin Bergér
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Regensburg, 93053, Germany
| | - Astrid Bruckmann
- Department of Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, 93053, Germany
| | - Chao Yang
- Department of Developmental Biology, University of Hamburg, Hamburg, 20146, Germany
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Regensburg, 93053, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, 20146, Germany
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| |
Collapse
|
7
|
Kong L, Zhuo Y, Xu J, Meng X, Wang Y, Zhao W, Lai H, Chen J, Wang J. Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera. BMC Genomics 2022; 23:596. [PMID: 35974339 PMCID: PMC9380326 DOI: 10.1186/s12864-022-08836-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. RESULTS These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. CONCLUSIONS This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.
Collapse
Affiliation(s)
- Lingshan Kong
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China.,School of Horticulture, Hainan University, 570228, Haikou, P. R. China
| | - Yanjing Zhuo
- School of Public Administration, Hainan University, 570228, Haikou, P. R. China
| | - Jieru Xu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Xiangxu Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Yue Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Wenxiu Zhao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Hanggui Lai
- School of Tropical Crops, Hainan University, 570228, Haikou, P. R. China
| | - Jinhui Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China. .,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China.
| | - Jian Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China. .,School of Horticulture, Hainan University, 570228, Haikou, P. R. China.
| |
Collapse
|
8
|
Han Y, Hu M, Ma X, Yan G, Wang C, Jiang S, Lai J, Zhang M. Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1394-1410. [PMID: 35607822 PMCID: PMC10360140 DOI: 10.1111/jipb.13276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.
Collapse
Affiliation(s)
- Yingjia Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuxu Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ge Yan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
9
|
Morgan C, Nayak A, Hosoya N, Smith GR, Lambing C. Meiotic chromosome organization and its role in recombination and cancer. Curr Top Dev Biol 2022; 151:91-126. [PMID: 36681479 PMCID: PMC10022578 DOI: 10.1016/bs.ctdb.2022.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomes adopt specific conformations to regulate various cellular processes. A well-documented chromosome configuration is the highly compacted chromosome structure during metaphase. More regional chromatin conformations have also been reported, including topologically associated domains encompassing mega-bases of DNA and local chromatin loops formed by kilo-bases of DNA. In this review, we discuss the changes in chromatin conformation taking place between somatic and meiotic cells, with a special focus on the establishment of a proteinaceous structure, called the chromosome axis, at the beginning of meiosis. The chromosome axis is essential to support key meiotic processes such as chromosome pairing, homologous recombination, and balanced chromosome segregation to transition from a diploid to a haploid stage. We review the role of the chromosome axis in meiotic chromatin organization and provide a detailed description of its protein composition. We also review the conserved and distinct roles between species of axis proteins in meiotic recombination, which is a major factor contributing to the creation of genetic diversity and genome evolution. Finally, we discuss situations where the chromosome axis is deregulated and evaluate the effects on genome integrity and the consequences from protein deregulation in meiocytes exposed to heat stress, and aberrant expression of genes encoding axis proteins in mammalian somatic cells associated with certain types of cancers.
Collapse
Affiliation(s)
| | - Aditya Nayak
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zürich, Switzerland
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christophe Lambing
- Plant Science Department, Rothamsted Research, Harpenden, United Kingdom.
| |
Collapse
|
10
|
Schreiber M, Gao Y, Koch N, Fuchs J, Heckmann S, Himmelbach A, Börner A, Özkan H, Maurer A, Stein N, Mascher M, Dreissig S. Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye. Mol Biol Evol 2022; 39:msac131. [PMID: 35687854 PMCID: PMC9218680 DOI: 10.1093/molbev/msac131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analysing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analysed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harbouring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected for during domestication to achieve more homogeneous populations for agricultural use.
Collapse
Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, 35037 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Yixuan Gao
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Natalie Koch
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Hakan Özkan
- Faculty of Agriculture, Department of Field Crops, University of Cukurova, 01330 Adana, Turkey
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Steven Dreissig
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| |
Collapse
|
11
|
Cross A, Li JB, Waugh R, Golicz AA, Pourkheirandish M. Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1263-1277. [PMID: 35192007 PMCID: PMC9033732 DOI: 10.1007/s00122-022-04029-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/04/2022] [Indexed: 05/31/2023]
Abstract
KEY MESSAGE Grain disarticulation in wild progenitor of wheat and barley evolved through a local duplication event followed by neo-functionalization resulting from changes in location of gene expression. One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene duplication.
Collapse
Affiliation(s)
- Arthur Cross
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - John B Li
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - Robbie Waugh
- Division of Plant Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Agnieszka A Golicz
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia.
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany.
| | | |
Collapse
|
12
|
Lewandowska D, Orr J, Schreiber M, Colas I, Ramsay L, Zhang R, Waugh R. The proteome of developing barley anthers during meiotic prophase I. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1464-1482. [PMID: 34758083 PMCID: PMC8890616 DOI: 10.1093/jxb/erab494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/08/2021] [Indexed: 05/11/2023]
Abstract
Flowering plants reproduce sexually by combining a haploid male and female gametophyte during fertilization. Male gametophytes are localized in the anthers, each containing reproductive (meiocyte) and non-reproductive tissue necessary for anther development and maturation. Meiosis, where chromosomes pair and exchange their genetic material during a process called recombination, is one of the most important and sensitive stages in breeding, ensuring genetic diversity. Most anther development studies have focused on transcript variation, but very few have been correlated with protein abundance. Taking advantage of a recently published barley anther transcriptomic (BAnTr) dataset and a newly developed sensitive mass spectrometry-based approach to analyse the barley anther proteome, we conducted high-resolution mass spectrometry analysis of barley anthers, collected at six time points and representing their development from pre-meiosis to metaphase. Each time point was carefully staged using immunocytology, providing a robust and accurate staging mirroring our previous BAnTr dataset. We identified >6100 non-redundant proteins including 82 known and putative meiotic proteins. Although the protein abundance was relatively stable throughout prophase I, we were able to quantify the dynamic variation of 336 proteins. We present the first quantitative comparative proteomics study of barley anther development during meiotic prophase I when the important process of homologous recombination is taking place.
Collapse
Affiliation(s)
- Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Research Precinct, Glen Osmond, SA 5064, Australia
- Correspondence:
| |
Collapse
|
13
|
Schreiber M, Orr J, Barakate A, Waugh R. Barley (Hordeum Vulgare) Anther and Meiocyte RNA Sequencing: Mapping Sequencing Reads and Downstream Data Analyses. Methods Mol Biol 2022; 2484:291-311. [PMID: 35461459 DOI: 10.1007/978-1-0716-2253-7_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA sequencing (RNA-seq) data is by now the most common method to study differential gene expression. Here we present a pipeline from RNA-seq generation to analysis with examples based on our own barley anther and meiocyte transcriptome. The bioinformatics pipeline will give everyone, from a beginner to a more experienced user, the possibility to analyze their datasets and identify significantly differentially expressed genes. It also allows differential alternative splicing analysis which will become increasingly common due to the high regulatory impact on the gene expression. We describe use of the Galaxy interface for RNA-seq read quantification and the 3D RNA-seq app for the downstream data analysis.
Collapse
Affiliation(s)
- Miriam Schreiber
- Division of Plant Sciences, The University of Dundee, James Hutton Institute, Dundee, UK
| | - Jamie Orr
- Cell and Molecular Sciences, James Hutton Institute, Dundee, UK
| | | | - Robbie Waugh
- Division of Plant Sciences, The University of Dundee, James Hutton Institute, Dundee, UK.
- Cell and Molecular Sciences, James Hutton Institute, Dundee, UK.
| |
Collapse
|
14
|
Barakate A, Arrieta M, Macaulay M, Vivera S, Davidson D, Stephens J, Orr J, Schreiber M, Ramsay L, Halpin C, Waugh R. Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers. FRONTIERS IN PLANT SCIENCE 2021; 12:745070. [PMID: 34659314 PMCID: PMC8515186 DOI: 10.3389/fpls.2021.745070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helicase 1 (RTEL1) DNA helicase was previously shown to enforce the number of meiotic COs in Caenorhabditis elegans but its function in plants has been studied only in the vegetative phase. Here, we characterised barley RTEL1 gene structure and expression using RNA-seq data previously obtained from vegetative and reproductive organs and tissues. Using RNAi, we downregulated RTEL1 expression specifically in reproductive tissues and analysed its impact on recombination using a barley 50k iSelect SNP Array. Unlike in C. elegans, in a population segregating for RTEL1 downregulated by RNAi, high resolution genome-wide genetic analysis revealed a significant increase of COs at distal chromosomal regions of barley without a change in their total number. Our data reveal the important role of RTEL1 helicase in plant meiosis and control of recombination.
Collapse
Affiliation(s)
- Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Vivera
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Waite Campus, Adelaide, SA, Australia
| |
Collapse
|
15
|
Böwer F, Schnittger A. How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants. Annu Rev Genet 2021; 55:427-452. [PMID: 34530640 DOI: 10.1146/annurev-genet-112618-043553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the major cell fate transitions in eukaryotes is entry into meiosis. While in single-celled yeast this decision is triggered by nutrient starvation, in multicellular eukaryotes, such as plants, it is under developmental control. In contrast to animals, plants have only a short germline and instruct cells to become meiocytes in reproductive organs late in development. This situation argues for a fundamentally different mechanism of how plants recruit meiocytes, and consistently, none of the regulators known to control meiotic entry in yeast and animals are present in plants. In recent years, several factors involved in meiotic entry have been identified, especially in the model plant Arabidopsis, and pieces of a regulatory network of germline control in plants are emerging. However, the corresponding studies also show that the mechanisms of meiotic entry control are diversified in flowering plants, calling for further analyses in different plant species. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Franziska Böwer
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
| | - Arp Schnittger
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
| |
Collapse
|
16
|
Gutiérrez Pinzón Y, González Kise JK, Rueda P, Ronceret A. The Formation of Bivalents and the Control of Plant Meiotic Recombination. FRONTIERS IN PLANT SCIENCE 2021; 12:717423. [PMID: 34557215 PMCID: PMC8453087 DOI: 10.3389/fpls.2021.717423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/13/2021] [Indexed: 06/06/2023]
Abstract
During the first meiotic division, the segregation of homologous chromosomes depends on the physical association of the recombined homologous DNA molecules. The physical tension due to the sites of crossing-overs (COs) is essential for the meiotic spindle to segregate the connected homologous chromosomes to the opposite poles of the cell. This equilibrated partition of homologous chromosomes allows the first meiotic reductional division. Thus, the segregation of homologous chromosomes is dependent on their recombination. In this review, we will detail the recent advances in the knowledge of the mechanisms of recombination and bivalent formation in plants. In plants, the absence of meiotic checkpoints allows observation of subsequent meiotic events in absence of meiotic recombination or defective meiotic chromosomal axis formation such as univalent formation instead of bivalents. Recent discoveries, mainly made in Arabidopsis, rice, and maize, have highlighted the link between the machinery of double-strand break (DSB) formation and elements of the chromosomal axis. We will also discuss the implications of what we know about the mechanisms regulating the number and spacing of COs (obligate CO, CO homeostasis, and interference) in model and crop plants.
Collapse
|
17
|
Gasparis S, Przyborowski M, Nadolska-Orczyk A. Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development. Int J Mol Sci 2021; 22:5087. [PMID: 34064912 PMCID: PMC8150791 DOI: 10.3390/ijms22105087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNA molecules with gene regulatory functions in plant development and the stress response. Although the number of lncRNAs identified in plants is rapidly increasing, very little is known about their role in barley development. In this study, we performed global identification of barley lncRNAs based on 53 RNAseq libraries derived from nine different barley tissues and organs. In total, 17,250 lncRNAs derived from 10,883 loci were identified, including 8954 novel lncRNAs. Differential expression of lncRNAs was observed in the developing shoot apices and grains, the two organs that have a direct influence on the final yield. The regulatory interaction of differentially expressed lncRNAs with the potential target genes was evaluated. We identified 176 cis-acting lncRNAs in shoot apices and 424 in grains, while the number of trans-acting lncRNAs in these organs was 1736 and 540, respectively. The potential target protein-coding genes were identified, and their biological function was annotated using MapMan ontology. This is the first insight into the roles of lncRNAs in barley development on the genome-wide scale, and our results provide a solid background for future functional studies.
Collapse
Affiliation(s)
- Sebastian Gasparis
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute—National Research Institute, 05-870 Błonie, Radzików, Poland; (M.P.); (A.N.-O.)
| | | | | |
Collapse
|
18
|
Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
Collapse
Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| |
Collapse
|