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Islam MK, Mummadi ST, Liu S, Wei H. Regulation of regeneration in Arabidopsis thaliana. ABIOTECH 2023; 4:332-351. [PMID: 38106435 PMCID: PMC10721781 DOI: 10.1007/s42994-023-00121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023]
Abstract
We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs-WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1-were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00121-9.
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Affiliation(s)
- Md Khairul Islam
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sai Teja Mummadi
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Hairong Wei
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
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2
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Mahlandt A, Singh DK, Mercier R. Engineering apomixis in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:131. [PMID: 37199785 DOI: 10.1007/s00122-023-04357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/04/2023] [Indexed: 05/19/2023]
Abstract
Apomixis is an asexual mode of reproduction through seeds where progeny are clones of the mother plants. Naturally apomictic modes of reproduction are found in hundreds of plant genera distributed across more than 30 plant families, but are absent in major crop plants. Apomixis has the potential to be a breakthrough technology by allowing the propagation through seed of any genotype, including F1 hybrids. Here, we have summarized the recent progress toward synthetic apomixis, where combining targeted modifications of both the meiosis and fertilization processes leads to the production of clonal seeds at high frequencies. Despite some remaining challenges, the technology has approached a level of maturity that allows its consideration for application in the field.
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Affiliation(s)
- Alexander Mahlandt
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Dipesh Kumar Singh
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany.
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3
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Sayed HMB, Nassar S, Kaufholdt D, Beerhues L, Liu B, El-Awaad I. Biosynthesis of polyprenylated xanthones in Hypericum perforatum roots involves 4-prenyltransferase. PLANT PHYSIOLOGY 2023:kiad219. [PMID: 37061818 DOI: 10.1093/plphys/kiad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/24/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Polyprenylated xanthones are natural products with a multitude of biological and pharmacological activities. However, their biosynthetic pathway is not completely understood. In this study, metabolic profiling revealed the presence of 4-prenylated 1,3,5,6-tetrahydroxyxanthone derivatives in St. John's wort (Hypericum perforatum) root extracts. Transcriptomic data mining led to the detection of five variants of xanthone 4-prenyltransferase (HpPT4px) comprising four long variants (HpPT4px-v1 to HpPT4px-v4) and one short variant (HpPT4px-sh). The full-length sequences of all five variants were cloned and heterologously expressed in yeast (Saccharomyces cerevisiae). Microsomes containing HpPT4px-v2, HpPT4px-v4, and HpPT4px-sh catalyzed the addition of a prenyl group at the C-4 position of 1,3,5,6-tetrahydroxyxanthone, 1,3,5-trihydroxyxanthone, and 1,3,7-trihydroxyxanthone, whereas microsomes harboring HpPT4px-v1 and HpPT4px-v3 additionally accepted 1,3,6,7-tetrahydroxyxanthone. HpPT4px-v1 produced in Nicotiana benthamiana displayed the same activity as in yeast, while HpPT4px-sh was inactive. The kinetic parameters of HpPT4px-v1 and HpPT4px-sh chosen as representative variants indicated 1,3,5,6-tetrahydroxyxanthone as the preferred acceptor substrate, rationalizing that HpPT4px catalyzes the first prenylation step in the biosynthesis of polyprenylated xanthones in H. perforatum. Dimethylallyl pyrophosphate was the exclusive prenyl donor. Expression of the HpPT4px transcripts was highest in roots and leaves, raising the question of product translocation. C-terminal yellow fluorescent protein fusion of HpPT4px-v1 localized to the envelope of chloroplasts in N. benthamiana leaves, whereas short, truncated, and masked signal peptides led to the disruption of plastidial localization. These findings pave the way for a better understanding of the prenylation of xanthones in plants and the identification of additional xanthone-specific prenyltransferases.
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Affiliation(s)
- Hesham M B Sayed
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
| | - Sara Nassar
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, 11566 Cairo, Egypt
| | - David Kaufholdt
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, 38106 Braunschweig, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
| | - Islam El-Awaad
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106 Braunschweig, Germany
- Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, 38106 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
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4
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Niccolò T, Anderson AW, Emidio A. Apomixis: oh, what a tangled web we have! PLANTA 2023; 257:92. [PMID: 37000270 PMCID: PMC10066125 DOI: 10.1007/s00425-023-04124-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Apomixis is a complex evolutionary trait with many possible origins. Here we discuss various clues and causes, ultimately proposing a model harmonizing the three working hypotheses on the topic. Asexual reproduction through seeds, i.e., apomixis, is the holy grail of plant biology. Its implementation in modern breeding could be a game-changer for agriculture. It has the potential to generate clonal crops and maintain valuable complex genotypes and their associated heterotic traits without inbreeding depression. The genetic basis and origins of apomixis are still unclear. There are three central hypothesis for the development of apomixis that could be: i) a deviation from the sexual developmental program caused by an asynchronous development, ii) environmentally triggered through epigenetic regulations (a polyphenism of sex), iii) relying on one or more genes/alleles. Because of the ever-increasing complexity of the topic, the path toward a detailed understanding of the mechanisms underlying apomixis remains unclear. Here, we discuss the most recent advances in the evolution perspective of this multifaceted trait. We incorporated our understanding of the effect of endogenous effectors, such as small RNAs, epigenetic regulation, hormonal pathways, protein turnover, and cell wall modification in response to an upside stress. This can be either endogenous (hybridization or polyploidization) or exogenous environmental stress, mainly due to oxidative stress and the corresponding ROS (Reacting Oxygen Species) effectors. Finally, we graphically represented this tangled web.
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Affiliation(s)
- Terzaroli Niccolò
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Aaron W Anderson
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Fulbright Scholar From Department of Plant Sciences, University of California, Davis, USA
| | - Albertini Emidio
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Consorzio Interuniversitario per le Biotecnologie (CIB), Trieste, Italy
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5
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Comparative analysis of buds transcriptome and identification of two florigen gene AkFTs in Amorphophallus konjac. Sci Rep 2022; 12:6782. [PMID: 35473958 PMCID: PMC9043200 DOI: 10.1038/s41598-022-10817-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/13/2022] [Indexed: 11/15/2022] Open
Abstract
Leaves and flowers of Amorphophallus konjac do not develop simultaneously thus unique features can be elucidated through study of flowering transformation in A. konjac. In this study, transcriptome libraries of A. konjac leaf buds (LB) and flower buds (FB) were constructed followed by high-throughput sequencing. A total of 68,906 unigenes with an average length of 920 bp were obtained after library assembly. Out of these genes, 24,622 unigenes had annotation information. A total of 6859 differentially expressed genes (DEGs) were identified through differential expression analysis using LB as control. Notably, 2415 DEGs were upregulated whereas 4444 DEGs were downregulated in the two transcriptomes. Go and KEGG analysis showed that the DEGs belonged to 44 functional categories and were implicated in 98 metabolic pathways and 38 DEGs involved in plant hormone signal transduction. Several genes were mined that may be involved in A. konjac flower bud differentiation and flower organ development. Eight DEGs were selected for verification of RNA-seq results using qRT-PCR analysis. Two FLOWERING LOCUS T (FT) genes named AkFT1 and AkFT2 were identified though homologous analysis may be the florigen gene implicated in modulation of A. konjac flowering. These genes were significantly upregulated in flower buds compared with the expression levels on leaf buds. Overexpression of AkFT genes though heterologous expression in Arabidopsis showed that the transgenics flowered at a very early stage relative to wild type plants. These findings indicate that AkFT1 and AkFT2 function as regulation genes in A. konjac flowering development and the two genes may present similar functions during flowering transition.
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Hou W, Singh RK, Martins V, Tenllado F, Franklin G, Dias ACP. Transcriptional responses of Hypericum perforatum cells to Agrobacterium tumefaciens and differential gene expression in dark glands. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:936-947. [PMID: 34112313 DOI: 10.1071/fp20292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Hypericum perforatum L. (St. John's wort) is a well-known medicinal plant that possesses secondary metabolites with beneficial pharmacological properties. However, improvement in the production of secondary metabolites via genetic manipulation is a challenging task as H. perforatum remains recalcitrant to Agrobacterium tumefaciens-mediated transformation. Here, the transcripts of key genes involved in several plant defence responses (secondary metabolites, RNA silencing, reactive oxygen species (ROS) and specific defence genes) were investigated in H. perforatum suspension cells inoculated with A. tumefaciens by quantitative real-time PCR. Results indicated that key genes from the xanthone, hypericin and melatonin biosynthesis pathways, the ROS-detoxification enzyme HpAOX, as well as the defence genes Hyp-1 and HpPGIP, were all upregulated to rapidly respond to A. tumefaciens elicitation in H. perforatum. By contrast, expression levels of genes involved in hyperforin and flavonoid biosynthesis pathways were markedly downregulated upon A. tumefaciens elicitation. In addition, we compared the expression patterns of key genes in H. perforatum leaf tissues with and without dark glands, a major site of secondary metabolite production. Overall, we provide evidence for the upregulation of several phenylpropanoid pathway genes in response to elicitation by Agrobacterium, suggesting that production of secondary metabolites could modulate H. perforatum recalcitrance to A. tumefaciens-mediated transformation.
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Affiliation(s)
- Weina Hou
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal; and Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Rupesh K Singh
- Centro de Química de Vila Real (CQ-VR), UTAD, 5000-801, Vila Real, Portugal
| | - Viviana Martins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Francisco Tenllado
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain; and Corresponding authors. Emails: ;
| | - Gregory Franklin
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Alberto C P Dias
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, 4710-057, Braga, Portugal; and Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal; and Center of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal; and Corresponding authors. Emails: ;
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7
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Gao JJ, Wang B, Peng RH, Li ZJ, Xu J, Tian YS, Yao QH. Phytoremediation of multiple persistent pollutants co-contaminated soil by HhSSB transformed plant. ENVIRONMENTAL RESEARCH 2021; 197:110959. [PMID: 33722526 DOI: 10.1016/j.envres.2021.110959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/28/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
The high toxicity of persistent pollutants limits the phytoremediation of pollutants-contaminated soil. In this study, heterologous expressing Halorhodospira halophila single-stranded DNA binding protein gene (HhSSB) improves tolerance to 2,4,6-trinitrotoluene (TNT), 2,4,6-trichlorophenol (2,4,6-TCP), and thiocyanate (SCN-) in A. thaliana and tall fescue (Festuca arundinacea). The HhSSB transformed Arabidopsis, and tall fescue also exhibited enhanced phytoremediation of TNT, 2,4,6-TCP, and SCN- separately contaminated soil and co-contaminated soil compared to control plants. TNT assay was selected to explore the mechanism of how HhSSB enhances the phytoremediation of persistent pollutants. Our result indicates that HhSSB enhances the phytoremediation of TNT by enhancing the transformation of TNT in Arabidopsis. Moreover, transcriptomics and comet analysis revealed that HhSSB improves TNT tolerance through three pathways: strengthening the defense system, enhancing the ROS scavenging system, and reducing DNA damage. These results presented here would be particularly useful for further studies in the remediation of soil contaminated by organic and inorganic pollutants.
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Affiliation(s)
- Jian-Jie Gao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Bo Wang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Ri-He Peng
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Zhen-Jun Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Jing Xu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Yong-Sheng Tian
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Quan-Hong Yao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
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8
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A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum. BMC Genomics 2021; 22:185. [PMID: 33726667 PMCID: PMC7962388 DOI: 10.1186/s12864-021-07450-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 11/10/2022] Open
Abstract
Background Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of maternal seeds. Recently, reference floral transcriptomes were generated from sexual and apomictic biotypes of Paspalum notatum, one of the most well-known plant models for the study of apomixis. However, the transcriptome dynamics, the occurrence of apomixis vs. sexual expression heterochronicity across consecutive developmental steps and the orientation of transcription (sense/antisense) remain unexplored. Results We produced 24 Illumina TruSeq®/ Hiseq 1500 sense/antisense floral transcriptome libraries covering four developmental stages (premeiosis, meiosis, postmeiosis, and anthesis) in biological triplicates, from an obligate apomictic and a full sexual genotype. De novo assemblies with Trinity yielded 103,699 and 100,114 transcripts for the apomictic and sexual samples respectively. A global comparative analysis involving reads from all developmental stages revealed 19,352 differentially expressed sense transcripts, of which 13,205 (68%) and 6147 (32%) were up- and down-regulated in apomictic samples with respect to the sexual ones. Interestingly, 100 differentially expressed antisense transcripts were detected, 55 (55%) of them up- and 45 (45%) down-regulated in apomictic libraries. A stage-by-stage comparative analysis showed a higher number of differentially expressed candidates due to heterochronicity discrimination: the highest number of differential sense transcripts was detected at premeiosis (23,651), followed by meiosis (22,830), postmeiosis (19,100), and anthesis (17,962), while the highest number of differential antisense transcripts were detected at anthesis (495), followed by postmeiosis (164), meiosis (120) and premeiosis (115). Members of the AP2, ARF, MYB and WRKY transcription factor families, as well as the auxin, jasmonate and cytokinin plant hormone families appeared broadly deregulated. Moreover, the chronological expression profile of several well-characterized apomixis controllers was examined in detail. Conclusions This work provides a quantitative sense/antisense gene expression catalogue covering several subsequent reproductive developmental stages from premeiosis to anthesis for apomictic and sexual P. notatum, with potential to reveal heterochronic expression between reproductive types and discover sense/antisense mediated regulation. We detected a contrasting transcriptional and hormonal control in apomixis and sexuality as well as specific sense/antisense modulation occurring at the onset of parthenogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07450-3.
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Scheben A, Hojsgaard D. Can We Use Gene-Editing to Induce Apomixis in Sexual Plants? Genes (Basel) 2020; 11:E781. [PMID: 32664641 PMCID: PMC7397034 DOI: 10.3390/genes11070781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA;
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073 Goettingen, Germany
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10
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Karunarathne P, Reutemann AV, Schedler M, Glücksberg A, Martínez EJ, Honfi AI, Hojsgaard DH. Sexual modulation in a polyploid grass: a reproductive contest between environmentally inducible sexual and genetically dominant apomictic pathways. Sci Rep 2020; 10:8319. [PMID: 32433575 PMCID: PMC7239852 DOI: 10.1038/s41598-020-64982-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 04/25/2020] [Indexed: 12/24/2022] Open
Abstract
In systems alternating between sexual and asexual reproduction, sex increases under unfavorable environmental conditions. In plants producing sexual and asexual (apomictic) seeds, studies on the influence of environmental factors on sex are equivocal. We used Paspalum intermedium to study environmental effects on the expression of sexual and apomictic developments, and on resulting reproductive fitness variables. Flow cytometric and embryological analyses were performed to characterize ploidy and reproductive modes, and effects of local climatic conditions on sexual and apomictic ovule and seed frequencies were determined. Seed set and germination data were collected and used to estimate reproductive fitness. Frequencies of sexual and apomictic ovules and seeds were highly variable within and among populations. Apomictic development exhibited higher competitive ability but lower overall fitness. Frequencies of sexual reproduction in facultative apomictic plants increased at lower temperatures and wider mean diurnal temperature ranges. We identified a two-fold higher fitness advantage of sexuality and a Tug of War between factors intrinsic to apomixis and environmental stressors promoting sexuality which influence the distribution of sex in apomictic populations. This points toward a crucial role of local ecological conditions in promoting a reshuffling of genetic variability that may be shaping the adaptative landscape in apomictic P. intermedium plants.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany.
- Georg-August University School of Science, University of Goettingen, Goettingen, Germany.
| | - Anna V Reutemann
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Mara Schedler
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Adriana Glücksberg
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Eric J Martínez
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Ana I Honfi
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Rivadavia 2370, 3300, Posadas, Misiones, Argentina
| | - Diego H Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany.
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11
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Hojsgaard D. Apomixis Technology: Separating the Wheat from the Chaff. Genes (Basel) 2020; 11:E411. [PMID: 32290084 PMCID: PMC7231277 DOI: 10.3390/genes11040411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University of Göttingen, Untere Karspüle 2, D-37073-1 Göttingen, Germany
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Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation. Genes (Basel) 2020; 11:genes11030329. [PMID: 32245021 PMCID: PMC7140868 DOI: 10.3390/genes11030329] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.
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Tang Q, Xu Y, Deng C, Cheng C, Dai Z, Yang Z, Liu C, Su J. A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy. Int J Genomics 2019; 2019:4025747. [PMID: 31950027 PMCID: PMC6948294 DOI: 10.1155/2019/4025747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/21/2019] [Indexed: 01/27/2023] Open
Abstract
Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to "cell differentiation" and "cell cycle process," as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
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Basso A, Barcaccia G, Galla G. Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions. PLANTS (BASEL, SWITZERLAND) 2019; 8:E158. [PMID: 31181659 PMCID: PMC6631971 DOI: 10.3390/plants8060158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
The protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1-2 were found to be differentially expressed in ovules of apomictic Hypericum perforatum L. accessions. To gain further insight into the expression and regulation of these genes in the context of apomixis, we investigated genomic, transcriptional and functional aspects of the gene family in this species. The H. perforatum genome encodes for two IDN2-like and 7 FDM-like genes. Differential and heterochronic expression of FDM4-like genes was found in H. perforatum pistils. The involvement of these genes in reproduction and seed development is consistent with the observed reduction of the seed set and high variability in seed size in A. thaliana IDN2 and FDM-like knockout lines. Differential expression of IDN2-like and FDM-like genes in H. perforatum was predicted to affect the network of potential interactions between these proteins. Furthermore, pistil transcript levels are modulated by cytokinin and auxin but the effect operated by the two hormones depends on the reproductive phenotype.
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Affiliation(s)
- Andrea Basso
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
| | - Gianni Barcaccia
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
| | - Giulio Galla
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
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Galla G, Basso A, Grisan S, Bellucci M, Pupilli F, Barcaccia G. Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions. FRONTIERS IN PLANT SCIENCE 2019; 10:654. [PMID: 31178879 PMCID: PMC6543059 DOI: 10.3389/fpls.2019.00654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/01/2019] [Indexed: 05/09/2023]
Abstract
Hypericum perforatum L. (2n = 4x = 32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression variation in sexual and apomictic plants, by focusing on the ovule nucellus, which is the cellular domain primarily involved into the differentiation of meiocyte precursors and aposporous embryo sacs, at a pre-meiotic developmental stage. Gene expression analyses performed by RNAseq identified 396 differentially expressed genes and 1834 transcripts displaying phenotype-specific expression. Furthermore, the sequencing and assembly of the genome from a diploid sexual accession allowed the annotation of a 50 kb sequence portion located upstream the HAPPY locus and to address the extent to which single transcripts were assembled in multiple variants and their co-expression levels. About one third of identified DEGs and phenotype-specific transcripts were associated to transcript variants with alternative expression patterns. Additionally, considering DEGs and phenotype-specific transcript, the co-expression level was estimated in about two transcripts per locus. Our gene expression study shows massive differences in the expression of several genes encoding for transposable elements. Transcriptional differences in the ovule nucellus and pistil terminal developmental stages were also found for subset of genes encoding for potentially interacting proteins involved in pre-mRNA splicing. Furthermore, the sexual and aposporous ovule transcriptomes were characterized by differential expression in genes operating in RNA silencing, RNA-mediated DNA methylation (RdDM) and histone and chromatin modifications. These findings are consistent with a role of these processes in regulating cell fate determination in the ovule, as indicated by forward genetic studies in sexual model species. The association between aposporous apomixis, pre-mRNA splicing and DNA methylation mediated by sRNAs, which is supported by expression data and by the enrichment in GO terms related to these processes, is consistent with the massive differential expression of multiple transposon-related sequences observed in ovules collected from both sexual and aposporous apomictic accessions. Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with the modulation of key genes involved in the two interconnected processes: RNA splicing and RNA-directed DNA methylation.
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Affiliation(s)
- Giulio Galla
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
- *Correspondence: Giulio Galla,
| | - Andrea Basso
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
| | - Simone Grisan
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Michele Bellucci
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Gianni Barcaccia
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
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16
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Trends in herbgenomics. SCIENCE CHINA-LIFE SCIENCES 2018; 62:288-308. [PMID: 30128965 DOI: 10.1007/s11427-018-9352-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.
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Liang W, Zou X, Carballar-Lejarazú R, Wu L, Sun W, Yuan X, Wu S, Li P, Ding H, Ni L, Huang W, Zou S. Selection and evaluation of reference genes for qRT-PCR analysis in Euscaphis konishii Hayata based on transcriptome data. PLANT METHODS 2018; 14:42. [PMID: 29881443 PMCID: PMC5985561 DOI: 10.1186/s13007-018-0311-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/29/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Quantitative real-time reverse transcription-polymerase chain reaction has been widely used in gene expression analysis, however, to have reliable and accurate results, reference genes are necessary to normalize gene expression under different experimental conditions. Several reliable reference genes have been reported in plants of Traditional Chinese Medicine, but none have been identified for Euscaphis konishii Hayata. RESULTS In this study, 12 candidate reference genes, including 3 common housekeeping genes and 9 novel genes based on E. konishii Hayata transcriptome data were selected and analyzed in different tissues (root, branch, leaf, capsule and seed), capsule and seed development stages. Expression stability was calculated using geNorm and NormFinder, the minimal number of reference genes required for accurate normalization was calculated by Vn/Vn + 1 using geNorm. EkEEF-5A-1 and EkADF2 were the two most stable reference genes for all samples, while EkGSTU1 and EkGAPDH were the most stable reference genes for tissue samples. For seed development stages, EkGAPDH and EkEEF-5A-1 were the most stable genes, whereas EkGSTU1 and EkGAPDH were identified as the two most stable genes in the capsule development stages. Two reference genes were sufficient to normalize gene expression across all sample sets. CONCLUSION Results of this study revealed that suitable reference genes should be selected for different experimental samples, and not all the common reference genes are suitable for different tissue samples and/or experimental conditions. In this study, we present the first data of reference genes selection for E. konishii Hayata based on transcriptome data, our data will facilitate further studies in molecular biology and gene function on E. konishii Hayata and other closely related species.
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Affiliation(s)
- Wenxian Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Lingjiao Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weihong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueyuan Yuan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengfei Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Ding
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Ni
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Huang
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, China
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Selva JP, Siena L, Rodrigo JM, Garbus I, Zappacosta D, Romero JR, Ortiz JPA, Pessino SC, Leblanc O, Echenique V. Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula. Sci Rep 2017. [PMID: 29118334 DOI: 10.1038/fs41598-017-14898-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes. Quantitative expression analyses revealed contrasting expression patterns for the three genes in apomictic vs sexual plants. In situ hybridization corroborated these results for two candidates, EcAGO104 and EcDMT102, and revealed an unexpected ectopic pattern for the AGO gene during germ line differentiation in apomicts. Although our data partially support previous results obtained in sexual plant models, they suggest that rather than an RdDM breakdown in the ovule, altered localization of AtAGO9/ZmAGO104 expression is required for achieving diplospory in E. curvula. The differences in the RdDM machinery acquired during plant evolution might have promoted the emergence of the numerous apomictic paths observed in plants.
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Affiliation(s)
- J P Selva
- CERZOS-CONICET, CCT-Bahía Blanca, 8000, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - L Siena
- IICAR-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Parque Villarino, S2125ZAA, Zavalla, Argentina
| | - J M Rodrigo
- CERZOS-CONICET, CCT-Bahía Blanca, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - I Garbus
- Departamento de Ciencias de la Salud, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - D Zappacosta
- CERZOS-CONICET, CCT-Bahía Blanca, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - J R Romero
- CERZOS-CONICET, CCT-Bahía Blanca, 8000, Bahía Blanca, Argentina
| | - J P A Ortiz
- IICAR-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Parque Villarino, S2125ZAA, Zavalla, Argentina
| | - S C Pessino
- IICAR-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Parque Villarino, S2125ZAA, Zavalla, Argentina
| | - O Leblanc
- DIADE, IRD, Univ Montpellier, Montpellier, France.
| | - V Echenique
- CERZOS-CONICET, CCT-Bahía Blanca, 8000, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina.
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19
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Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula. Sci Rep 2017; 7:15092. [PMID: 29118334 PMCID: PMC5678148 DOI: 10.1038/s41598-017-14898-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 10/18/2017] [Indexed: 11/13/2022] Open
Abstract
Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes. Quantitative expression analyses revealed contrasting expression patterns for the three genes in apomictic vs sexual plants. In situ hybridization corroborated these results for two candidates, EcAGO104 and EcDMT102, and revealed an unexpected ectopic pattern for the AGO gene during germ line differentiation in apomicts. Although our data partially support previous results obtained in sexual plant models, they suggest that rather than an RdDM breakdown in the ovule, altered localization of AtAGO9/ZmAGO104 expression is required for achieving diplospory in E. curvula. The differences in the RdDM machinery acquired during plant evolution might have promoted the emergence of the numerous apomictic paths observed in plants.
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20
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De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes. PLoS One 2017; 12:e0185595. [PMID: 29091722 PMCID: PMC5665505 DOI: 10.1371/journal.pone.0185595] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
A long-standing goal in plant breeding has been the ability to confer apomixis to agriculturally relevant species, which would require a deeper comprehension of the molecular basis of apomictic regulatory mechanisms. Eragrostis curvula (Schrad.) Nees is a perennial grass that includes both sexual and apomictic cytotypes. The availability of a reference transcriptome for this species would constitute a very important tool toward the identification of genes controlling key steps of the apomictic pathway. Here, we used Roche/454 sequencing technologies to generate reads from inflorescences of E. curvula apomictic and sexual genotypes that were de novo assembled into a reference transcriptome. Near 90% of the 49568 assembled isotigs showed sequence similarity to sequences deposited in the public databases. A gene ontology analysis categorized 27448 isotigs into at least one of the three main GO categories. We identified 11475 SSRs, and several of them were assayed in E curvula germoplasm using SSR-based primers, providing a valuable set of molecular markers that could allow direct allele selection. The differential contribution to each library of the spliced forms of several transcripts revealed the existence of several isotigs produced via alternative splicing of single genes. The reference transcriptome presented and validated in this work will be useful for the identification of a wide range of gene(s) related to agronomic traits of E. curvula, including those controlling key steps of the apomictic pathway in this species, allowing the extrapolation of the findings to other plant species.
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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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22
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Landis JB, Soltis DE, Soltis PS. Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae). BMC Genomics 2017; 18:475. [PMID: 28645249 PMCID: PMC5481933 DOI: 10.1186/s12864-017-3868-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/16/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators. RESULTS Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly. Nuclear concatenation and species tree inference methods provide congruent topologies. The inferred evolutionary trajectory of flower size is from small flowers to larger flowers. We identified 4 to 10,368 transcripts that are differentially expressed during flower development, with many unigenes associated with cell wall modification and components of the auxin and gibberellin pathways. CONCLUSIONS Saltugilia is an excellent model for investigating covarying floral and pollinator evolution. Four candidate genes from model systems (BIG BROTHER, BIG PETAL, GASA, and LONGIFOLIA) show differential expression during development of flowers in Saltugilia, and four other genes (FLOWERING-PROMOTING FACTOR 1, PECTINESTERASE, POLYGALACTURONASE, and SUCROSE SYNTHASE) fit into hypothesized organ size pathways. Together, these gene sets provide a strong foundation for future functional studies to determine their roles in specifying interspecific differences in flower size.
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Affiliation(s)
- Jacob B. Landis
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Department of Botany and Plant Sciences, University of California Riverside, 4412 Boyce Hall, 3401 Watkins Drive, Riverside, CA 92521 USA
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Genetics Institute, University of Florida, Gainesville, FL 32610 USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Genetics Institute, University of Florida, Gainesville, FL 32610 USA
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23
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Tang Q, Zang G, Cheng C, Luan M, Dai Z, Xu Y, Yang Z, Zhao L, Su J. Diplosporous development in Boehmeria tricuspis: Insights from de novo transcriptome assembly and comprehensive expression profiling. Sci Rep 2017; 7:46043. [PMID: 28382950 PMCID: PMC5382578 DOI: 10.1038/srep46043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/07/2017] [Indexed: 01/05/2023] Open
Abstract
Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages. By classifying the transcripts into gene ontology categories of differentially expressed genes, we showed that differential plant hormone signal transduction, cell cycle regulation, and transcription factor regulation are possibly involved in apomictic development and/or a polyploidization response in B. tricuspis. Furthermore, we suggest that specific gene families are possibly related to apomixis and might have important effects on diplosporous floral development. These results make a notable contribution to our understanding of the molecular basis of diplosporous development in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Gonggu Zang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
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24
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Agapouda A, Booker A, Kiss T, Hohmann J, Heinrich M, Csupor D. Quality control of Hypericum perforatum L. analytical challenges and recent progress. J Pharm Pharmacol 2017; 71:15-37. [PMID: 28266019 DOI: 10.1111/jphp.12711] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/26/2017] [Indexed: 11/29/2022]
Abstract
Abstract
Objectives
The most widely applied qualitative and quantitative analytical methods in the quality control of Hypericum perforatum extracts will be reviewed, including routine analytical tools and most modern approaches.
Key findings
Biologically active components of H. perforatum are chemically diverse; therefore, different chromatographic and detection methods are required for the comprehensive analysis of St. John's wort extracts. Naphthodianthrones, phloroglucinols and flavonoids are the most widely analysed metabolites of this plant. For routine quality control, detection of major compounds belonging to these groups seems to be sufficient; however, closer characterization requires the detection of minor compounds as well.
Conclusions
TLC and HPTLC are basic methods in the routine analysis, whereas HPLC-DAD is the most widely applied method for quantitative analysis due to its versatility. LC-MS is gaining importance in pharmacokinetic studies due to its sensitivity. Modern approaches, such as DNA barcoding, NIRS and NMR metabolomics, may offer new possibilities for the more detailed characterization of secondary metabolite profile of H. perforatum extracts.
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Affiliation(s)
- Anastasia Agapouda
- Research Cluster “Biodiversity and Medicines”, Research Group “Pharmacognosy and Phytotherapy”, UCL School of Pharmacy, University of London, London, UK
| | - Anthony Booker
- Research Cluster “Biodiversity and Medicines”, Research Group “Pharmacognosy and Phytotherapy”, UCL School of Pharmacy, University of London, London, UK
- Division of Herbal and East Asian Medicine, Department of Life Sciences, University of Westminster, London, UK
| | - Tivadar Kiss
- Department of Pharmacognosy, University of Szeged, Szeged, Hungary
- Interdisciplinary Centre of Natural Products, University of Szeged, Szeged, Hungary
| | - Judit Hohmann
- Department of Pharmacognosy, University of Szeged, Szeged, Hungary
- Interdisciplinary Centre of Natural Products, University of Szeged, Szeged, Hungary
| | - Michael Heinrich
- Research Cluster “Biodiversity and Medicines”, Research Group “Pharmacognosy and Phytotherapy”, UCL School of Pharmacy, University of London, London, UK
| | - Dezső Csupor
- Department of Pharmacognosy, University of Szeged, Szeged, Hungary
- Interdisciplinary Centre of Natural Products, University of Szeged, Szeged, Hungary
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25
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Li W, Zhang L, Ding Z, Wang G, Zhang Y, Gong H, Chang T, Zhang Y. De novo sequencing and comparative transcriptome analysis of the male and hermaphroditic flowers provide insights into the regulation of flower formation in andromonoecious taihangia rupestris. BMC PLANT BIOLOGY 2017; 17:54. [PMID: 28241786 PMCID: PMC5329940 DOI: 10.1186/s12870-017-0990-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/31/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Taihangia rupestris, an andromonoecious plant species, bears both male and hermaphroditic flowers within the same individual. However, the establishment and development of male and hermaphroditic flowers in andromonoecious Taihangia remain poorly understood, due to the limited genetic and sequence information. To investigate the potential molecular mechanism in the regulation of Taihangia flower formation, we used de novo RNA sequencing to compare the transcriptome profiles of male and hermaphroditic flowers at early and late developmental stages. RESULTS Four cDNA libraries, including male floral bud, hermaphroditic floral bud, male flower, and hermaphroditic flower, were constructed and sequenced by using the Illumina RNA-Seq method. Totally, 84,596,426 qualified Illumina reads were obtained and then assembled into 59,064 unigenes, of which 24,753 unigenes were annotated in the NCBI non-redundant protein database. In addition, 12,214, 7,153, and 8,115 unigenes were assigned into 53 Gene Ontology (GO) functional groups, 25 Clusters of Orthologous Group (COG) categories, and 126 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. By pairwise comparison of unigene abundance between the samples, we identified 1,668 differential expressed genes (DEGs), including 176 transcription factors (TFs) between the male and hermaphroditic flowers. At the early developmental stage, we found 263 up-regulated genes and 436 down-regulated genes expressed in hermaphroditic floral buds, while 844 up-regulated genes and 314 down-regulated genes were detected in hermaphroditic flowers at the late developmental stage. GO and KEGG enrichment analyses showed that a large number of DEGs were associated with a wide range of functions, including cell cycle, epigenetic processes, flower development, and biosynthesis of unsaturated fatty acid pathway. Finally, real-time quantitative PCR was conducted to validate the DEGs identified in the present study. CONCLUSION In this study, transcriptome data of this rare andromonoecious Taihangia were reported for the first time. Comparative transcriptome analysis revealed the significant differences in gene expression profiles between male and hermaphroditic flowers at early and late developmental stages. The transcriptome data of Taihangia would be helpful to improve the understanding of the underlying molecular mechanisms in regulation of flower formation and unisexual flower establishment in andromonoecious plants.
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Affiliation(s)
- Weiguo Li
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Lihui Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
| | - Zhan Ding
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Guodong Wang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yandi Zhang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Hongmei Gong
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Tianjun Chang
- College of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000 Henan China
| | - Yanwen Zhang
- College of Life Science, Changchun Normal University, Changchun, 130032 Jilin China
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26
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Abstract
Apomixis, commonly defined as asexual reproduction through seed, is a reproductive trait that occurs in only a few minor crops, but would be highly valuable in major crops. Apomixis results in seed-derived progenies that are genetically identical to their maternal parent. The advantage of apomixis would lie in seed propagation of elite food, feed, and biofuel crops that are heterozygous such as hybrid corn and switchgrass or self-pollinating crops for which no commercial-scale hybrid production system is available. While hybrid plants often outperform parental lines in growth and higher yields, production of hybrid seed is accomplished through carefully controlled, labor intensive crosses. Both small farmers in developing countries who produce their own seed and commercial companies that market hybrid seed could benefit from the establishment of engineered apomixis in plants. In this chapter, we review what has been learned from studying natural apomicts and mutations in sexual plants leading to apomixis-like development, plus discuss how the components of apomixis could be successfully engineered in plants.
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Affiliation(s)
- Joann A Conner
- Horticulture Department, NESPAL/University of Georgia-Tifton Campus, 2356 Rainwater Road, Tifton, GA, 31794, USA.
| | - Peggy Ozias-Akins
- Horticulture Department, NESPAL/University of Georgia-Tifton Campus, 2356 Rainwater Road, Tifton, GA, 31794, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia-Tifton Campus, Tifton, GA, USA
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27
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Galla G, Zenoni S, Avesani L, Altschmied L, Rizzo P, Sharbel TF, Barcaccia G. Pistil Transcriptome Analysis to Disclose Genes and Gene Products Related to Aposporous Apomixis in Hypericum perforatum L. FRONTIERS IN PLANT SCIENCE 2017; 8:79. [PMID: 28203244 PMCID: PMC5285387 DOI: 10.3389/fpls.2017.00079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/13/2017] [Indexed: 05/19/2023]
Abstract
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell. Despite the importance of apomixis for breeding of crop plants and although much research has been conducted to study this process, the genetic control of apomixis is still not well understood. Hypericum perforatum is becoming an attractive model system for the study of aposporous apomixis. Here we report results from a global gene expression analysis of H. perforatum pistils collected from sexual and aposporous plant accessions for the purpose of identifying genes, biological processes and molecular functions associated with the aposporous apomixis pathway. Across two developmental stages corresponding to the expression of aposporous apomeiosis and parthenogenesis in ovules, a total of 224 and 973 unigenes were found to be significantly up- and down-regulated with a fold change ≥ 2 in at least one comparison, respectively. Differentially expressed genes were enriched for multiple gene ontology (GO) terms, including cell cycle, DNA metabolic process, and single-organism cellular process. For molecular functions, the highest scores were recorded for GO terms associated with DNA binding, DNA (cytosine-5-)-methyltransferase activity and heterocyclic compound binding. As deregulation of single components of the sexual developmental pathway is believed to be a trigger of the apomictic reproductive program, all genes involved in sporogenesis, gametogenesis and response to hormonal stimuli were analyzed in great detail. Overall, our data suggest that phenotypic expression of apospory is concomitant with the modulation of key genes involved in the sexual reproductive pathway. Furthermore, based on gene annotation and co-expression, we underline a putative role of hormones and key actors playing in the RNA-directed DNA methylation pathway in regulating the developmental changes occurring during aposporous apomixis in H. perforatum.
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Affiliation(s)
- Giulio Galla
- Laboratory of Genomics, Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaPadova, Italy
- *Correspondence: Giulio Galla
| | - Sara Zenoni
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Linda Avesani
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Lothar Altschmied
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Paride Rizzo
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Timothy F. Sharbel
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Gianni Barcaccia
- Laboratory of Genomics, Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaPadova, Italy
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28
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Hou W, Shakya P, Franklin G. A Perspective on Hypericum perforatum Genetic Transformation. FRONTIERS IN PLANT SCIENCE 2016; 7:879. [PMID: 27446112 PMCID: PMC4919345 DOI: 10.3389/fpls.2016.00879] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/03/2016] [Indexed: 05/22/2023]
Abstract
Hypericum perforatum (St John's wort) is a reservoir of diverse classes of biologically active and high value secondary metabolites, which captured the interest of both researchers and the pharmaceutical industry alike. Several studies and clinical trials have shown that H. perforatum extracts possess an astounding array of pharmacological properties. These properties include antidepressant, anti-inflammatory, antiviral, anti-cancer, and antibacterial activities; and are largely attributed to the naphtodianthrones and xanthones found in the genus. Hence, improving their production via genetic manipulation is an important strategy. In spite of the presence of contemporary genome editing tools, genetic improvement of this genus remains challenging without robust transformation methods in place. In the recent past, we found that H. perforatum remains recalcitrant to Agrobacterium tumefaciens mediated transformation partly due to the induction of plant defense responses coming into play. However, H. perforatum transformation is possible via a non-biological method, biolistic bombardment. Some research groups have observed the induction of hairy roots in H. perforatum after Agrobacterium rhizogenes co-cultivation. In this review, we aim at updating the available methods for regeneration and transformation of H. perforatum. In addition, we also propose a brief perspective on certain novel strategies to improve transformation efficiency in order to meet the demands of the pharmaceutical industry via metabolic engineering.
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Affiliation(s)
- Weina Hou
- Centre for the Research and Technology of Agro-Environment and Biological Sciences, University of MinhoBraga, Portugal
| | - Preeti Shakya
- Department of Integrative Plant Biology, Institute of Plant Genetics of the Polish Academy of SciencesPoznan, Poland
| | - Gregory Franklin
- Centre for the Research and Technology of Agro-Environment and Biological Sciences, University of MinhoBraga, Portugal
- Department of Integrative Plant Biology, Institute of Plant Genetics of the Polish Academy of SciencesPoznan, Poland
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29
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Klatt S, Hadacek F, Hodač L, Brinkmann G, Eilerts M, Hojsgaard D, Hörandl E. Photoperiod Extension Enhances Sexual Megaspore Formation and Triggers Metabolic Reprogramming in Facultative Apomictic Ranunculus auricomus. FRONTIERS IN PLANT SCIENCE 2016; 7:278. [PMID: 27014302 PMCID: PMC4781874 DOI: 10.3389/fpls.2016.00278;] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Meiosis, the key step of sexual reproduction, persists in facultative apomictic plants functional to some extent. However, it still remains unclear how and why proportions of reproductive pathways vary under different environmental stress conditions. We hypothesized that oxidative stress mediates alterations of developmental pathways. In apomictic plants we expected that megasporogenesis, the stage directly after meiosis, would be more affected than later stages of seed development. To simulate moderate stress conditions we subjected clone-mates of facultative apomictic Ranunculus auricomus to 10 h photoperiods, reflecting natural conditions, and extended ones (16.5 h). Reproduction mode was screened directly after megasporogenesis (microscope) and at seed stage (flow cytometric seed screening). Targeted metabolite profiles were performed with HPLC-DAD to explore if and which metabolic reprogramming was caused by the extended photoperiod. Prolonged photoperiods resulted in increased frequencies of sexual vs. aposporous initials directly after meiosis, but did not affect frequencies of sexual vs. asexual seed formation. Changes in secondary metabolite profiles under extended photoperiods affected all classes of compounds, and c. 20% of these changes separated the two treatments. Unexpectedly, the renowned antioxidant phenylpropanoids and flavonoids added more to clone-mate variation than to treatment differentiation. Among others, chlorophyll degradation products, non-assigned phenolic compounds and more lipophilic metabolites also contributed to the dissimilarity of the metabolic profiles of plants that had been exposed to the two different photoperiods. The hypothesis of moderate light stress effects was supported by increased proportions of sexual megaspore development at the expense of aposporous initial formation. The lack of effects at the seed stage confirms the basic assumption that only meiosis and sporogenesis would be sensitive to light stress. The concomitant change of secondary metabolite profiles, as a systemic response at this early developmental stage, supports the notion that oxidative stress could have affected megasporogenesis by causing the observed metabolic reprogramming. Hypotheses of genotype-specific responses to prolonged photoperiods are rejected.
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Affiliation(s)
- Simone Klatt
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Franz Hadacek
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Georg-August-University of Göttingen, Göttingen, Germany
| | - Ladislav Hodač
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Gina Brinkmann
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Marius Eilerts
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Diego Hojsgaard
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Elvira Hörandl
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
- *Correspondence: Elvira Hörandl,
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30
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Klatt S, Hadacek F, Hodač L, Brinkmann G, Eilerts M, Hojsgaard D, Hörandl E. Photoperiod Extension Enhances Sexual Megaspore Formation and Triggers Metabolic Reprogramming in Facultative Apomictic Ranunculus auricomus. FRONTIERS IN PLANT SCIENCE 2016; 7:278. [PMID: 27014302 PMCID: PMC4781874 DOI: 10.3389/fpls.2016.00278] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/21/2016] [Indexed: 05/20/2023]
Abstract
Meiosis, the key step of sexual reproduction, persists in facultative apomictic plants functional to some extent. However, it still remains unclear how and why proportions of reproductive pathways vary under different environmental stress conditions. We hypothesized that oxidative stress mediates alterations of developmental pathways. In apomictic plants we expected that megasporogenesis, the stage directly after meiosis, would be more affected than later stages of seed development. To simulate moderate stress conditions we subjected clone-mates of facultative apomictic Ranunculus auricomus to 10 h photoperiods, reflecting natural conditions, and extended ones (16.5 h). Reproduction mode was screened directly after megasporogenesis (microscope) and at seed stage (flow cytometric seed screening). Targeted metabolite profiles were performed with HPLC-DAD to explore if and which metabolic reprogramming was caused by the extended photoperiod. Prolonged photoperiods resulted in increased frequencies of sexual vs. aposporous initials directly after meiosis, but did not affect frequencies of sexual vs. asexual seed formation. Changes in secondary metabolite profiles under extended photoperiods affected all classes of compounds, and c. 20% of these changes separated the two treatments. Unexpectedly, the renowned antioxidant phenylpropanoids and flavonoids added more to clone-mate variation than to treatment differentiation. Among others, chlorophyll degradation products, non-assigned phenolic compounds and more lipophilic metabolites also contributed to the dissimilarity of the metabolic profiles of plants that had been exposed to the two different photoperiods. The hypothesis of moderate light stress effects was supported by increased proportions of sexual megaspore development at the expense of aposporous initial formation. The lack of effects at the seed stage confirms the basic assumption that only meiosis and sporogenesis would be sensitive to light stress. The concomitant change of secondary metabolite profiles, as a systemic response at this early developmental stage, supports the notion that oxidative stress could have affected megasporogenesis by causing the observed metabolic reprogramming. Hypotheses of genotype-specific responses to prolonged photoperiods are rejected.
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Affiliation(s)
- Simone Klatt
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Franz Hadacek
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Georg-August-University of Göttingen, Göttingen, Germany
| | - Ladislav Hodač
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Gina Brinkmann
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Marius Eilerts
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Diego Hojsgaard
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
| | - Elvira Hörandl
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Göttingen, Germany
- *Correspondence: Elvira Hörandl,
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