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Koh E, Goh W, Julca I, Villanueva E, Mutwil M. PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1592-1603. [PMID: 38050352 DOI: 10.1111/tpj.16566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.
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Affiliation(s)
- Eugene Koh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - William Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Erielle Villanueva
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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Lou H, Huang Y, Zhu Z, Xu Q. Cloning and Expression Analysis of Onion (Allium cepa L.) MADS-Box Genes and Regulation Mechanism of Cytoplasmic Male Sterility. Biochem Genet 2023; 61:2116-2134. [PMID: 36947296 DOI: 10.1007/s10528-023-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
Flower organ development is one of the most important processes in plant life. However, onion CMS (cytoplasmic male sterility) shows an abnormal development of floral organs. The regulation of MADS-box transcription factors is important for flower development. To further understand the role of MADS-box transcription factors in the regulation of cytoplasmic male sterility onions. We cloned the full-length cDNA of five MADS-box transcription factors from the flowers of onion using RACE (rapid amplification of cDNA ends) technology. We used bioinformatics methods for sequence analysis and phylogenetic analysis. Real-time quantitative PCR was used to detect the expression patterns of these genes in different onion organs. The relative expression levels of five flower development genes were compared in CMS onions and wild onions. The results showed that the full-length cDNA sequences of the cloned MADS-box genes AcFUL, AcDEF, AcPI, AcAG, and AcSEP3 belonged to A, B, C, and E MADS-box genes, respectively. A phylogenetic tree construction analysis was performed on its sequence. Analysis of MADS-box gene expression in wild onion and CMS onion showed that the formation of CMS onion was caused by down-regulation of AcDEF, AcPI, and AcAG gene expression, up-regulation of AcSEP3 gene expression, and no correlation with AcFUL gene expression. This work laid the foundation for further study of the molecular mechanism of onion flower development and the molecular mechanism of CMS onion male sterility.
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Affiliation(s)
- Hu Lou
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuntong Huang
- Medical Laboratory College of Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China
- Industrial College of Biomedicine and Health Industry, Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China
| | - Zhengjie Zhu
- Agriculture and Food Engineering College, Baise University, Baise, 533000, Guangxi, China
| | - Qijiang Xu
- Medical Laboratory College of Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China.
- Industrial College of Biomedicine and Health Industry, Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China.
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Mingmanit Y, Boonsrangsom T, Sujipuli K, Ratanasut K, Inthima P. Pollen viabilities and gene expression profiles across Musa genomes. AOB PLANTS 2023; 15:plad052. [PMID: 37564880 PMCID: PMC10411045 DOI: 10.1093/aobpla/plad052] [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: 02/03/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Banana (Musa spp.) is a major global economic fruit crop. However, cross-pollination from other Musa cultivars grown in nearby plantations results in seeded fruit that exceeds market demand. This study investigated pollen viability and germination and examined the expression profiles of pollen development-related genes across seven Musa genomes (AA, BB, AAA, BBB, AAB, ABB and ABBB). Twenty-three Musa cultivars were assessed for pollen viability using lacto-aceto-orcein and triphenyltetrazolium chloride staining methods. Results revealed that pollen viability obtained from both methods was significantly different among all the studied cultivars. Cultivars carrying BB (diploid) genomes had higher viability percentages than AA (diploid), AAA, BBB, AAB and ABB (triploid) and ABBB (tetraploid) genomes. Germination of the studied cultivars was also investigated on pollen culture medium, with results showing significant differences between the pollen of each cultivar. The best germinating cultivar was TKM (11.0 %), carrying BB genome. Expression profiles of pollen development-related genes by RT-qPCR indicated that both TPD1A and MYB80 genes were highly expressed in triploid Musa genomes but the PTC1 gene showed down-regulated expression, resulting in non-viable pollen. Pollen viability, pollen germination and pollen development-related genes differed across Musa cultivars. This knowledge will be useful for the selection of male parents for Musa cross-breeding programs. Pollen viability should also be considered when planning Musa production to avoid seeded fruit.
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Affiliation(s)
- Yonlada Mingmanit
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Thanita Boonsrangsom
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Kawee Sujipuli
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Kumrop Ratanasut
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Phithak Inthima
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Plant Tissue Culture Research Unit, Department of Biology, Faculty of Science, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
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Tidy AC, Ferjentsikova I, Vizcay-Barrena G, Liu B, Yin W, Higgins JD, Xu J, Zhang D, Geelen D, Wilson ZA. Sporophytic control of pollen meiotic progression is mediated by tapetum expression of ABORTED MICROSPORES. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5543-5558. [PMID: 35617147 PMCID: PMC9467646 DOI: 10.1093/jxb/erac225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Pollen development is dependent on the tapetum, a sporophytic anther cell layer surrounding the microspores that functions in pollen wall formation but is also essential for meiosis-associated development. There is clear evidence of crosstalk and co-regulation between the tapetum and microspores, but how this is achieved is currently not characterized. ABORTED MICROSPORES (AMS), a tapetum transcription factor, is important for pollen wall formation, but also has an undefined role in early pollen development. We conducted a detailed investigation of chromosome behaviour, cytokinesis, radial microtubule array (RMA) organization, and callose formation in the ams mutant. Early meiosis initiates normally in ams, shows delayed progression after the pachytene stage, and then fails during late meiosis, with disorganized RMA, defective cytokinesis, abnormal callose formation, and microspore degeneration, alongside abnormal tapetum development. Here, we show that selected meiosis-associated genes are directly repressed by AMS, and that AMS is essential for late meiosis progression. Our findings indicate that AMS has a dual function in tapetum-meiocyte crosstalk by playing an important regulatory role during late meiosis, in addition to its previously characterized role in pollen wall formation. AMS is critical for RMA organization, callose deposition, and therefore cytokinesis, and is involved in the crosstalk between the gametophyte and sporophytic tissues, which enables synchronous development of tapetum and microspores.
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Affiliation(s)
| | | | - Gema Vizcay-Barrena
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Bing Liu
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Wenzhe Yin
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jie Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Danny Geelen
- Department of Plant Production, Ghent University, geb. A, Gent, Belgium
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Borghi M, Perez de Souza L, Tohge T, Mi J, Melandri G, Proost S, Martins MCM, Al-Babili S, Bouwmeester HJ, Fernie AR. High-energy-level metabolism and transport occur at the transition from closed to open flowers. PLANT PHYSIOLOGY 2022; 190:319-339. [PMID: 35640120 PMCID: PMC9434183 DOI: 10.1093/plphys/kiac253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
During the maturation phase of flower development, the onset of anthesis visibly marks the transition from buds to open flowers, during which petals stretch out, nectar secretion commences, and pollination occurs. Analysis of the metabolic changes occurring during this developmental transition has primarily focused on specific classes of metabolites, such as pigments and scent emission, and far less on the whole network of primary and secondary metabolites. To investigate the metabolic changes occurring at anthesis, we performed multi-platform metabolomics alongside RNA sequencing in individual florets harvested from the main inflorescence of Arabidopsis (Arabidopsis thaliana) ecotype Col-0. To trace metabolic fluxes at the level of the whole inflorescence and individual florets, we further integrated these studies with radiolabeled experiments. These extensive analyses revealed high-energy-level metabolism and transport of carbohydrates and amino acids, supporting intense metabolic rearrangements occurring at the time of this floral transition. These comprehensive data are discussed in the context of our current understanding of the metabolic shifts underlying flower opening. We envision that this analysis will facilitate the introgression of floral metabolic traits promoting pollination in crop species for which a comprehensive knowledge of flower metabolism is still limited.
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Affiliation(s)
- Monica Borghi
- Department of Biology, Utah State University, Logan, Utah 84321-5305, USA
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | | | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Jianing Mi
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
- INRAE, University of Bordeaux, UMR BFP, Villenave d’Ornon 33140, France
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven 3000, Belgium
| | - Marina C M Martins
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- In Press—Consultoria e Comunicação Científica, São Paulo 05089-030, Brazil
| | - Salim Al-Babili
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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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.
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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:
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Zogopoulos VL, Saxami G, Malatras A, Angelopoulou A, Jen CH, Duddy WJ, Daras G, Hatzopoulos P, Westhead DR, Michalopoulos I. Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. iScience 2021; 24:102848. [PMID: 34381973 PMCID: PMC8334378 DOI: 10.1016/j.isci.2021.102848] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/23/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions.
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Affiliation(s)
- Vasileios L. Zogopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - Georgia Saxami
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - Apostolos Malatras
- Center for Research in Myology, Sorbonne Université, Paris 75013, France
| | - Antonia Angelopoulou
- Department of Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Chih-Hung Jen
- Cold Spring Biotech Corp, Da Hu Science Park, New Taipei City, Taiwan
| | - William J. Duddy
- Center for Research in Myology, Sorbonne Université, Paris 75013, France
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT52 1SJ, UK
| | - Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | | | - David R. Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
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Jeong J, Park S, Im JH, Yi H. Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene. BMC Genomics 2021; 22:22. [PMID: 33407107 PMCID: PMC7789250 DOI: 10.1186/s12864-020-07345-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Background The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results As a first step to understand regulation and molecular functions of Group III subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13–1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13–1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions Sixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) in BoGH3.13–1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07345-9.
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Affiliation(s)
- Jiseong Jeong
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sunhee Park
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jeong Hui Im
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hankuil Yi
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Malik A, Gul A, Amir R, Munir F, Babar MM, Bakhtiar SM, Hayat MQ, Paracha RZ, Khalid Z, Alipour H. Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113. Front Genet 2020; 11:609668. [PMID: 33381153 PMCID: PMC7767997 DOI: 10.3389/fgene.2020.609668] [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: 09/23/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.
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Affiliation(s)
- Afsheen Malik
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Department of Biosciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zoya Khalid
- Computational Biology Research Lab, Department of Computer Science, National University of Computer and Emerging Sciences-FAST, Islamabad, Pakistan
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
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Jiao Z, Zhu X, Li H, Liu Z, Huang X, Wu N, An J, Li J, Zhang J, Jiang Y, Li Q, Qi Z, Niu J. Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility. PeerJ 2020; 8:e10275. [PMID: 33194433 PMCID: PMC7605228 DOI: 10.7717/peerj.10275] [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: 06/19/2020] [Accepted: 10/08/2020] [Indexed: 11/20/2022] Open
Abstract
A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
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Affiliation(s)
- Zhixin Jiao
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Xinxin Zhu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zhitao Liu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China.,Sichuan Academy of Agricultural Sciences, Crop Research Institue, Chengdu, Sichuan, China
| | - Xinyi Huang
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Nan Wu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Junhang An
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Jing Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Yumei Jiang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Qiaoyun Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zengjun Qi
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Jishan Niu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
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11
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Hu C, Sheng O, Dong T, Yang Q, Dou T, Li C, He W, Gao H, Yi G, Deng G, Bi F. Overexpression of MaTPD1A impairs fruit and pollen development by modulating some regulators in Musa itinerans. BMC PLANT BIOLOGY 2020; 20:402. [PMID: 32867686 PMCID: PMC7461258 DOI: 10.1186/s12870-020-02623-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Pollen formation and development is important for crop fertility and is a key factor for hybrid development. Previous reports have indicated that Arabidopsis thaliana TAPETUM DETERMINANT1 (AtTPD1) and its rice (Oryza sativa) homolog, OsTPD1-like (OsTDL1A), are required for cell specialization and greatly affect pollen formation and development. Little is known about the role of the TPD1 homolog in banana pollen development. RESULTS Here, we report the identification and characterization of TPD1 homologs in diploid banana (Musa itinerans) and examine their role in pollen development by overexpressing the closest homolog, MaTPD1A. MaTPD1A exhibits high expression in stamen and localizes in the plasma membrane. MaTPD1A-overexpressing plants produce no pollen grains and smaller and seedless fruit compared to wild-type plants. Transcriptome analysis showed that in plant hormone, starch and sucrose metabolism, and linolenic acid metabolism-related pathways were affected by overexpression of MaTPD1A, and the expression of several key regulators, such as PTC1 and MYB80, which are known to affect anther development, is affected in MaTPD1A-overexpressing lines. CONCLUSIONS Our results indicate that MaTPD1A plays an important role in pollen formation and fruit development in diploid banana, possibly by affecting the expression of some key regulators of pollen development.
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Affiliation(s)
- Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China.
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China.
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
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12
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Lu JY, Xiong SX, Yin W, Teng XD, Lou Y, Zhu J, Zhang C, Gu JN, Wilson ZA, Yang ZN. MS1, a direct target of MS188, regulates the expression of key sporophytic pollen coat protein genes in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4877-4889. [PMID: 32374882 PMCID: PMC7410184 DOI: 10.1093/jxb/eraa219] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 05/04/2023]
Abstract
Sporophytic pollen coat proteins (sPCPs) derived from the anther tapetum are deposited into pollen wall cavities and function in pollen-stigma interactions, pollen hydration, and environmental protection. In Arabidopsis, 13 highly abundant proteins have been identified in pollen coat, including seven major glycine-rich proteins GRP14, 16, 17, 18, 19, 20, and GRP-oleosin; two caleosin-related family proteins (AT1G23240 and AT1G23250); three lipase proteins EXL4, EXL5 and EXL6, and ATA27/BGLU20. Here, we show that GRP14, 17, 18, 19, and EXL4 and EXL6 fused with green fluorescent protein (GFP) are translated in the tapetum and then accumulate in the anther locule following tapetum degeneration. The expression of these sPCPs is dependent on two essential tapetum transcription factors, MALE STERILE188 (MS188) and MALE STERILITY 1 (MS1). The majority of sPCP genes are up-regulated within 30 h after MS1 induction and could be restored by MS1 expression driven by the MS188 promoter in ms188, indicating that MS1 is sufficient to activate their expression; however, additional MS1 downstream factors appear to be required for high-level sPCP expression. Our ChIP, in vivo transactivation assay, and EMSA data indicate that MS188 directly activates MS1. Together, these results reveal a regulatory cascade whereby outer pollen wall formation is regulated by MS188 followed by synthesis of sPCPs controlled by MS1.
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Affiliation(s)
- Jie-Yang Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuang-Xi Xiong
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenzhe Yin
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
| | - Xiao-Dong Teng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yue Lou
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jun Zhu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Cheng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing-Nan Gu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
| | - Zhong-Nan Yang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Correspondence: or
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13
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Van den Broeck L, Gordon M, Inzé D, Williams C, Sozzani R. Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Front Genet 2020; 11:457. [PMID: 32547596 PMCID: PMC7270862 DOI: 10.3389/fgene.2020.00457] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/14/2020] [Indexed: 12/26/2022] Open
Abstract
Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.
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Affiliation(s)
- Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Max Gordon
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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14
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Guo J, Dong X, Li Y, Wang B. NaCl treatment markedly enhanced pollen viability and pollen preservation time of euhalophyte Suaeda salsa via up regulation of pollen development-related genes. JOURNAL OF PLANT RESEARCH 2020; 133:57-71. [PMID: 31654246 DOI: 10.1007/s10265-019-01148-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 10/02/2019] [Indexed: 05/27/2023]
Abstract
Vegetable growth of halophytes has significantly increased through moderate salinity. However, little is known about the reproductive traits of euhalophytes. Male reproduction is pivotal for fertilization and seed production and sensitive to abiotic stressors. The pollen viability and pollen longevity of Suaeda salsa treated with 0 and 200 mM of NaCl were evaluated. It was revealed that the pollen size of S. salsa treated with NaCl was significantly bigger than that in controls. Furthermore, the pollen viability of S. salsa plants treated with NaCl was also significantly higher than that of control after 8 h of the pollens were collected (from 10 to 27 h). The pollen viability of NaCl-treated plants in the field could be maintained for 8 h (from 07:00 to 15:00) in sunny days, which was 1 h longer than that of control plants (from 07:00 to 14:00). Meanwhile, the pollen preservation time of NaCl-treated plants was 16 h at room temperature, which was 8 h longer than that of control plants. Genes related to pollen development, such as SsPRK3, SsPRK4, and SsLRX, exhibited high expression in the flowers of NaCl-treated plants. This indicated that NaCl markedly improved the pollen viability and preservation time via the increased expression of pollen development-related genes, and this benefits the population establishment of halophytes such as S. salsa in saline regions.
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Affiliation(s)
- Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, Shandong, China
| | - Xinxiu Dong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, Shandong, China
| | - Ying Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, Shandong, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, 250014, Shandong, China.
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15
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Liu M, Li W, Zhao G, Fan X, Long H, Fan Y, Shi M, Tan X, Zhang L. New Insights of Salicylic Acid Into Stamen Abortion of Female Flowers in Tung Tree ( Vernicia fordii). Front Genet 2019; 10:316. [PMID: 31024626 PMCID: PMC6460477 DOI: 10.3389/fgene.2019.00316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/21/2019] [Indexed: 12/03/2022] Open
Abstract
Tung tree (Vernicia fordii), an economically important woody oil plant, is a monoecious and diclinous species with male and female flowers on the same inflorescence. The extremely low proportion of female flowers leads to low fruit yield in tung orchards. The female flower normally develops along with stamen abortion; otherwise sterile ovules will be produced. However, little knowledge is known about the molecular basis of the female flower development in tung tree. In this study, integrated analyses of morphological and cytological observations, endogenous phytohormone assay and RNA-seq were conducted to understand the molecular mechanism of the female flower development in tung tree. Cytological observation suggested that the abortion of stamens in female flowers (SFFs) belongs to the type of programmed cell death (PCD), which was caused by tapetum degeneration at microspore mother cell stage. A total of 1,366 differentially expressed genes (DEGs) were identified in female flowers by RNA-seq analysis, of which 279 (20.42%) DEGs were significantly enriched in phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Stage-specific transcript identification detected dynamically expressed genes of important transcription regulators in female flowers that may be involved in PCD and floral organ development. Gene expression patterns revealed that 17 anther and pollen development genes and 37 PCD-related genes might be involved in the abortion of SFF. Further analyses of phytohormone levels and co-expression networks suggested that salicylic acid (SA) accumulation could trigger PCD and inhibit the development of SFF in tung tree. This study provides new insights into the role of SA in regulating the abortion of SFF to develop normal female flowers.
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Affiliation(s)
- Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Guang Zhao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xiaoming Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yanru Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Mingwang Shi
- Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China.,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, China
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16
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Gupta C, Pereira A. Recent advances in gene function prediction using context-specific coexpression networks in plants. F1000Res 2019; 8:F1000 Faculty Rev-153. [PMID: 30800290 PMCID: PMC6364378 DOI: 10.12688/f1000research.17207.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
Predicting gene functions from genome sequence alone has been difficult, and the functions of a large fraction of plant genes remain unknown. However, leveraging the vast amount of currently available gene expression data has the potential to facilitate our understanding of plant gene functions, especially in determining complex traits. Gene coexpression networks-created by integrating multiple expression datasets-connect genes with similar patterns of expression across multiple conditions. Dense gene communities in such networks, commonly referred to as modules, often indicate that the member genes are functionally related. As such, these modules serve as tools for generating new testable hypotheses, including the prediction of gene function and importance. Recently, we have seen a paradigm shift from the traditional "global" to more defined, context-specific coexpression networks. Such coexpression networks imply genetic correlations in specific biological contexts such as during development or in response to a stress. In this short review, we highlight a few recent studies that attempt to fill the large gaps in our knowledge about cellular functions of plant genes using context-specific coexpression networks.
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Affiliation(s)
- Chirag Gupta
- Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Andy Pereira
- Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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17
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Yu H, Lu L, Jiao B, Liang C. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics 2019; 35:361-364. [PMID: 30032165 DOI: 10.1093/bioinformatics/bty642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2023] Open
Abstract
Motivation The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism. Results Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding. Availability and implementation The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp://47.94.193.106/pub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hua Yu
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- School of Computer and Information Engineering, NanTong Institute of Technology, Nantong, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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18
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Ganguly P, Saha S, Behera AP, Roy A, Datta AB, Chaudhuri S. RETRACTED: Interaction of AtHMGB15, an ARID-HMG family protein, with RING-H2 type E3 ubiquitin ligase AtATL79. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:32-43. [PMID: 30348326 DOI: 10.1016/j.plantsci.2018.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/28/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Payel Ganguly
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Sudip Saha
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Aditya Prasad Behera
- Department of Biochemistry, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Ajit Bikram Datta
- Department of Biochemistry, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, India.
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19
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Heng S, Gao J, Wei C, Chen F, Li X, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:455-466. [PMID: 29301015 PMCID: PMC5853284 DOI: 10.1093/jxb/erx443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/17/2017] [Indexed: 05/22/2023]
Abstract
Cytoplasmic male sterility (CMS) is primarily caused by chimeric genes located in the mitochondrial genomes. In Brassica juncea, orf288 has been identified as a CMS-associated gene in the hau CMS line; however, neither the specific abortive stage nor the molecular function of the gene have been determined. We therefore characterized the hau CMS line, and found that defective mitochondria affect the development of archesporial cells during the L2 stage, leading to male sterility. The expression level of the orf288 transcript was higher in the male-sterility line than in the fertility-restorer line, although no significant differences were apparent at the protein level. The toxicity region of ORF288 was found to be located near the N-terminus and repressed growth of Escherichia coli. However, transgenic expression of different portions of ORF288 indicated that the region that causes male sterility resides between amino acids 73 and 288, the expression of which in E. coli did not result in growth inhibition. Transcriptome analysis revealed a wide range of genes involved in anther development and mitochondrial function that were differentially expressed in the hau CMS line. This study provides new insights into the hau CMS mechanism by which orf288 affects the fertility of Brassica juncea.
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Affiliation(s)
- Shuangping Heng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chao Wei
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Fengyi Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xianwen Li
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
- Correspondence:
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20
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Heng S, Gao J, Wei C, Chen F, Li X, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea. JOURNAL OF EXPERIMENTAL BOTANY 2018. [PMID: 29301015 DOI: 10.5061/dryad.9s68p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cytoplasmic male sterility (CMS) is primarily caused by chimeric genes located in the mitochondrial genomes. In Brassica juncea, orf288 has been identified as a CMS-associated gene in the hau CMS line; however, neither the specific abortive stage nor the molecular function of the gene have been determined. We therefore characterized the hau CMS line, and found that defective mitochondria affect the development of archesporial cells during the L2 stage, leading to male sterility. The expression level of the orf288 transcript was higher in the male-sterility line than in the fertility-restorer line, although no significant differences were apparent at the protein level. The toxicity region of ORF288 was found to be located near the N-terminus and repressed growth of Escherichia coli. However, transgenic expression of different portions of ORF288 indicated that the region that causes male sterility resides between amino acids 73 and 288, the expression of which in E. coli did not result in growth inhibition. Transcriptome analysis revealed a wide range of genes involved in anther development and mitochondrial function that were differentially expressed in the hau CMS line. This study provides new insights into the hau CMS mechanism by which orf288 affects the fertility of Brassica juncea.
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Affiliation(s)
- Shuangping Heng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chao Wei
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Fengyi Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xianwen Li
- College of Life Science, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, P.R. China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, P.R. China
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21
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Lou Y, Zhou HS, Han Y, Zeng QY, Zhu J, Yang ZN. Positive regulation of AMS by TDF1 and the formation of a TDF1-AMS complex are required for anther development in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:378-391. [PMID: 28940573 DOI: 10.1111/nph.14790] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
Tapetum development and pollen production are regulated by a complex transcriptional network that consists of a group of tapetum-specific Arabidopsis transcription factors (TFs). Among these TFs, DEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION 1 (TDF1) encodes an R2R3 MYB factor, and ABORTED MICROSPORE (AMS) encodes a basic helix-loop-helix (bHLH) factor. However, knowledge regarding the regulatory role of TDF1 in anther development remains limited. Here, we discovered that TDF1 directly regulates AMS via an AACCT cis-element. We found the precocious AMS transcript and absence of AMS protein in ams-/- gpTDF1:AMS-FLAG lines, suggesting the timing of the TDF1-regulated AMS expression is a prerequisite for AMS functioning. We found that TDF1 interacts with AMS. Additionally, the TDF1-AMS complex additively promotes the expression of AMS-regulated genes, suggesting that TDF1 and AMS regulate the downstream genes through a feed-forward loop. EPXB5, encoding a beta-expansin family protein, is another direct target of TDF1, and it is highly expressed in the tapetum and pollen grains. The TDF1-AMS complex acts in concert to activate EXPB5 expression through a feed-forward loop. The identification of the regulatory pathway between TDF1 and AMS provides an interlocked feed-forward loop circuit that precisely regulates the transcriptional cascades that support anther development.
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Affiliation(s)
- Yue Lou
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Hai-Sheng Zhou
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Yu Han
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Qiu-Ye Zeng
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Jun Zhu
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
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22
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Lin H, Yu J, Pearce SP, Zhang D, Wilson ZA. RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1076-1091. [PMID: 29031031 DOI: 10.1111/tpj.13744] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1-4, ostdl1a, gamyb-2, tip2, udt1-1, tdr, eat1-1, ptc1 and mads3-4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2-9), while genes in Clade 3 are expressed later (stages 10-12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided (https://www.cpib.ac.uk/anther/riceindex.html) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.
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Affiliation(s)
- Hong Lin
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, UK
| | - Jing Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Simon P Pearce
- School of Mathematics, University of Manchester, Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, UK
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, UK
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23
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Yang C, Song J, Ferguson AC, Klisch D, Simpson K, Mo R, Taylor B, Mitsuda N, Wilson ZA. Transcription Factor MYB26 Is Key to Spatial Specificity in Anther Secondary Thickening Formation. PLANT PHYSIOLOGY 2017; 175:333-350. [PMID: 28724622 PMCID: PMC5580765 DOI: 10.1104/pp.17.00719] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/17/2017] [Indexed: 05/03/2023]
Abstract
Successful fertilization relies on the production and effective release of viable pollen. Failure of anther opening (dehiscence), results in male sterility, although the pollen may be fully functional. MYB26 regulates the formation of secondary thickening in the anther endothecium, which is critical for anther dehiscence and fertility. Here, we show that although the MYB26 transcript shows expression in multiple floral organs, the MYB26 protein is localized specifically to the anther endothecium nuclei and that it directly regulates two NAC domain genes, NST1 and NST2, which are critical for the induction of secondary thickening biosynthesis genes. However, there is a complex relationship of regulation between these genes and MYB26. Using DEX-inducible MYB26 lines and overexpression in the various mutant backgrounds, we have shown that MYB26 up-regulates both NST1 and NST2 expression. Surprisingly normal thickening and fertility rescue does not occur in the absence of MYB26, even with constitutively induced NST1 and NST2, suggesting an additional essential role for MYB26 in this regulation. Combined overexpression of NST1 and NST2 in myb26 facilitates limited ectopic thickening in the anther epidermis, but not in the endothecium, and thus fails to rescue dehiscence. Therefore, by a series of regulatory controls through MYB26, NST1, NST2, secondary thickening is formed specifically within the endothecium; this specificity is essential for anther opening.
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Affiliation(s)
- Caiyun Yang
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Jie Song
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Alison C Ferguson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Kim Simpson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Rui Mo
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Benjamin Taylor
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST). Üentral 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, United Kingdom
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24
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Li SF, Zhang GJ, Zhang XJ, Yuan JH, Deng CL, Gao WJ. Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis). BMC PLANT BIOLOGY 2017; 17:143. [PMID: 28830346 PMCID: PMC5567890 DOI: 10.1186/s12870-017-1091-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/14/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. RESULTS De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development. CONCLUSIONS Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003 China
| | - Xue-Jin Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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25
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Ferguson AC, Pearce S, Band LR, Yang C, Ferjentsikova I, King J, Yuan Z, Zhang D, Wilson ZA. Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis. THE NEW PHYTOLOGIST 2017; 213:778-790. [PMID: 27787905 PMCID: PMC5215365 DOI: 10.1111/nph.14200] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 08/03/2016] [Indexed: 05/19/2023]
Abstract
Viable pollen is essential for plant reproduction and crop yield. Its production requires coordinated expression at specific stages during anther development, involving early meiosis-associated events and late pollen wall formation. The ABORTED MICROSPORES (AMS) transcription factor is a master regulator of sporopollenin biosynthesis, secretion and pollen wall formation in Arabidopsis. Here we show that it has complex regulation and additional essential roles earlier in pollen formation. An inducible-AMS reporter was created for functional rescue, protein expression pattern analysis, and to distinguish between direct and indirect targets. Mathematical modelling was used to create regulatory networks based on wild-type RNA and protein expression. Dual activity of AMS was defined by biphasic protein expression in anther tapetal cells, with an initial peak around pollen meiosis and then later during pollen wall development. Direct AMS-regulated targets exhibit temporal regulation, indicating that additional factors are associated with their regulation. We demonstrate that AMS biphasic expression is essential for pollen development, and defines distinct functional activities during early and late pollen development. Mathematical modelling suggests that AMS may competitively form a protein complex with other tapetum-expressed transcription factors, and that biphasic regulation is due to repression of upstream regulators and promotion of AMS protein degradation.
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Affiliation(s)
- Alison C. Ferguson
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - Simon Pearce
- Faculty of BiologyUniversity of ManchesterMichael Smith Building, Oxford RoadManchesterM13 9PLUK
- School of MathematicsUniversity of ManchesterAlan Turing Building, Oxford RoadManchesterM13 9PLUK
| | - Leah R. Band
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- School of Mathematical SciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Caiyun Yang
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - Ivana Ferjentsikova
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - John King
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- School of Mathematical SciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental SciencesShanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and HealthSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental SciencesShanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and HealthSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Zoe A. Wilson
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
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26
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Krishnan A, Gupta C, Ambavaram MMR, Pereira A. RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:1640. [PMID: 28979289 PMCID: PMC5611544 DOI: 10.3389/fpls.2017.01640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/06/2017] [Indexed: 05/22/2023]
Abstract
Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.
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Affiliation(s)
- Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
| | - Chirag Gupta
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
| | | | - Andy Pereira
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
- *Correspondence: Andy Pereira,
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27
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Liu H, Tan M, Yu H, Li L, Zhou F, Yang M, Zhou T, Zhao Y. Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2016; 16:250. [PMID: 27832742 PMCID: PMC5105256 DOI: 10.1186/s12870-016-0934-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L.) is a globally important oilseed crop with highly-valued oil. Strong hybrid vigor is frequently observed within this crop, which can be exploited by the means of genic male sterility (GMS). We have previously developed a dominant GMS (DGMS) line W1098A that has great potential for the breeding of F1 hybrids. Although it has been genetically and anatomically characterized, the underlying molecular mechanism for male sterility remains unclear and therefore limits the full utilization of such GMS line. In this study, RNA-seq based transcriptome profiling was carried out in two near-isogenic DGMS lines (W1098A and its fertile counterpart, W1098B) to identify differentially expressed genes (DEGs) related to male sterility. RESULTS A total of 1,502 significant DEGs were detected, among which 751 were up-regulated and 751 were down-regulated in sterile flower buds. A number of DEGs were implicated in both ethylene and JA synthesis & signaling pathway; the expression of which were either up- or down-regulated in the sterile buds, respectively. Moreover, the majority of NAC and WRKY transcription factors implicated from the DEGs were up-regulated in sterile buds. By querying the Plant Male Reproduction Database, 49 sesame homologous genes were obtained; several of these encode transcription factors (bHLH089, MYB99, and AMS) that showed reduced expression in sterile buds, thus implying the possible role in specifying or determining tapetal fate and development. The predicted effect of allelic variants on the function of their corresponding DEGs highlighted several Insertions/Deletions (InDels), which might be responsible for the phenotype of sterility/fertility in DGMS lines. CONCLUSION The present comparative transcriptome study suggested that both hormone signaling pathway and transcription factors control the male sterility of DGMS in sesame. The results also revealed that several InDels located in DEGs prone to cause loss of function, which might contribute to male sterility. These findings provide valuable genomic resources for a deeper insight into the molecular mechanism underlying DGMS.
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Affiliation(s)
- Hongyan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Haijuan Yu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Liang Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Fang Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Minmin Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Ting Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Yingzhong Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
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28
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Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:490-504. [PMID: 27401965 DOI: 10.1111/tpj.13261] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 05/21/2023]
Abstract
Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
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Affiliation(s)
- Ryan S Austin
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Shu Hiu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ting Ting Wang
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jim Fan
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Curtis Foong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Robert Breit
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Alan Moses
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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29
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Dekkers BJW, Pearce SP, van Bolderen-Veldkamp RPM, Holdsworth MJ, Bentsink L. Dormant and after-Ripened Arabidopsis thaliana Seeds are Distinguished by Early Transcriptional Differences in the Imbibed State. FRONTIERS IN PLANT SCIENCE 2016; 7:1323. [PMID: 27625677 PMCID: PMC5003841 DOI: 10.3389/fpls.2016.01323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/18/2016] [Indexed: 05/22/2023]
Abstract
Seed dormancy is a genetically controlled block preventing the germination of imbibed seeds in favorable conditions. It requires a period of dry storage (after-ripening) or certain environmental conditions to be overcome. Dormancy is an important seed trait, which is under selective pressure, to control the seasonal timing of seed germination. Dormant and non-dormant (after-ripened) seeds are characterized by large sets of differentially expressed genes. However, little information is available concerning the temporal and spatial transcriptional changes during early stages of rehydration in dormant and non-dormant seeds. We employed genome-wide transcriptome analysis on seeds of the model plant Arabidopsis thaliana to investigate transcriptional changes in dry seeds upon rehydration. We analyzed gene expression of dormant and after-ripened seeds of the Cvi accession over four time points and two seed compartments (the embryo and surrounding single cell layer endosperm), during the first 24 h after sowing. This work provides a global view of gene expression changes in dormant and non-dormant seeds with temporal and spatial detail, and these may be visualized via a web accessible tool (http://www.wageningenseedlab.nl/resources). A large proportion of transcripts change similarly in both dormant and non-dormant seeds upon rehydration, however, the first differences in transcript abundances become visible shortly after the initiation of imbibition, indicating that changes induced by after-ripening are detected and responded to rapidly upon rehydration. We identified several gene expression profiles which contribute to differential gene expression between dormant and non-dormant samples. Genes with enhanced expression in the endosperm of dormant seeds were overrepresented for stress-related Gene Ontology categories, suggesting a protective role for the endosperm against biotic and abiotic stress to support persistence of the dormant seed in its environment.
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Affiliation(s)
- Bas J. W. Dekkers
- Department of Molecular Plant Physiology, Utrecht UniversityUtrecht, Netherlands
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Simon P. Pearce
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK
- School of Mathematics, University of ManchesterManchester, UK
| | - R. P. M. van Bolderen-Veldkamp
- Department of Molecular Plant Physiology, Utrecht UniversityUtrecht, Netherlands
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Michael J. Holdsworth
- Division of Plant and Crop Science, School of Biosciences, University of NottinghamLeicestershire, UK
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
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Xie Y, Zhang W, Wang Y, Xu L, Zhu X, Muleke EM, Liu L. Comprehensive transcriptome-based characterization of differentially expressed genes involved in microsporogenesis of radish CMS line and its maintainer. Funct Integr Genomics 2016; 16:529-43. [DOI: 10.1007/s10142-016-0504-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 11/29/2022]
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Walbot V, Egger RL. Pre-Meiotic Anther Development: Cell Fate Specification and Differentiation. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:365-95. [PMID: 26735065 DOI: 10.1146/annurev-arplant-043015-111804] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Research into anther ontogeny has been an active and developing field, transitioning from a strictly lineage-based view of cellular differentiation events to a more complex understanding of cell fate specification. Here we describe the modern interpretation of pre-meiotic anther development, from the earliest cell specifications within the anther lobes through SPL/NZZ-, MSP1-, and MEL1-dependent pathways as well as the initial setup of the abaxial and adaxial axes and outgrowth of the anther lobes. We then continue with a look at the known information regarding further differentiation of the somatic layers of the anther (the epidermis, endothecium, middle layer, and tapetum), with an emphasis on male-sterile mutants identified as defective in somatic cell specification. We also describe the differences in developmental stages among species and use this information to discuss molecular studies that have analyzed transcriptome, proteome, and small-RNA information in the anther.
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Affiliation(s)
- Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
| | - Rachel L Egger
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
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Zhao N, Xu X, Wamboldt Y, Mackenzie SA, Yang X, Hu Z, Yang J, Zhang M. MutS HOMOLOG1 silencing mediates ORF220 substoichiometric shifting and causes male sterility in Brassica juncea. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:435-44. [PMID: 26516127 PMCID: PMC4682445 DOI: 10.1093/jxb/erv480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cytoplasmic male sterility (CMS) has consistently been associated with the expression of mitochondrial open reading frames (ORFs) that arise from genomic rearrangements. Spontaneous fertility reversion in CMS has been observed in several cases, but a clear understanding of fertility reversion controlled by nuclear genetic influences has been lacking. Here, we identified spontaneous fertile revertant lines for Brassica juncea CMS cytoplasm in which the mitochondrial genome has undergone substoichiometric shifting (SSS) to suppress ORF220 copy number. We placed ORF220, with or without a mitochondrial targeting presequence, under the control of the CaMV35S and AP3 promoters in Arabidopsis to confirm that ORF220 causes male sterility when mitochondrially localized. We found that copy number of the ORF220 gene was altered under conditions that suppress MSH1, a nuclear gene that controls illegitimate recombination in plant mitochondria. MSH1-RNAi lines with increased ORF220 copy number were male sterile compared with wild type. We found that a wide range of genes involved in anther development were up- and down-regulated in revertant and MSH1-RNAi lines, respectively. The system that we have developed offers valuable future insight into the interplay of MSH1 and SSS in CMS induction and fertility reversion as a mediator of nuclear-mitochondrial crosstalk.
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Affiliation(s)
- Na Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Xu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Yashitola Wamboldt
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588-0660, USA
| | - Sally A Mackenzie
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588-0660, USA
| | - Xiaodong Yang
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588-0660, USA.
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China. Key laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China. Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Jinghua Yang
- Key laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China. Key laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China. Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China. Key laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China. Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
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