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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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Pasten MC, Carballo J, Gallardo J, Zappacosta D, Selva JP, Rodrigo JM, Echenique V, Garbus I. A combined transcriptome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula. FRONTIERS IN PLANT SCIENCE 2022; 13:1012682. [PMID: 36247597 PMCID: PMC9563718 DOI: 10.3389/fpls.2022.1012682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/14/2022] [Indexed: 06/06/2023]
Abstract
Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass typically established in semi-arid regions, with good adaptability to dry conditions and sandy soils. This polymorphic complex includes both sexual and apomictic cytotypes, with different ploidy levels (2x-8x). Diploids are known to be sexual, while most polyploids are facultative apomicts, and full apomicts have also been reported. Plant breeding studies throughout the years have focused on achieving the introgression of apomixis into species of agricultural relevance, but, given the complexity of the trait, a deeper understanding of the molecular basis of regulatory mechanisms of apomixis is still required. Apomixis is thought to be associated with silencing or disruption of the sexual pathway, and studies have shown it is influenced by epigenetic mechanisms. In a previous study, we explored the role of miRNA-mRNA interactions using two contrasting E. curvula phenotypes. Here, the sexual OTA-S, the facultative Don Walter and the obligate apomictic Tanganyika cDNA and sRNA libraries were inquired, searching for miRNA discovery and miRNA expression regulation of genes related to the reproductive mode. This allowed for the characterization of seven miRNAs and the validation of their miRNA-target interactions. Interestingly, a kinesin gene was found to be repressed in the apomictic cultivar Tanganyika, targeted by a novel miRNA that was found to be overexpressed in this genotype, suggestive of an involvement in the reproductive mode expression. Our work provided additional evidence of the contribution of the epigenetic regulation of the apomictic pathway.
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Affiliation(s)
- María Cielo Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - José Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Jimena Gallardo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Juan Manuel Rodrigo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Ingrid Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
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Epigenetic Modifications in Plant Development and Reproduction. EPIGENOMES 2021; 5:epigenomes5040025. [PMID: 34968249 PMCID: PMC8715465 DOI: 10.3390/epigenomes5040025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 01/27/2023] Open
Abstract
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many ‘epigenomes’. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review.
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Carballo J, Zappacosta D, Selva JP, Caccamo M, Echenique V. Eragrostis curvula, a Model Species for Diplosporous Apomixis. PLANTS (BASEL, SWITZERLAND) 2021; 10:1818. [PMID: 34579351 PMCID: PMC8472828 DOI: 10.3390/plants10091818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Eragrostis curvula (Schrad.) Ness is a grass with a particular apomictic embryo sac development called Eragrostis type. Apomixis is a type of asexual reproduction that produces seeds without fertilization in which the resulting progeny is genetically identical to the mother plant and with the potential to fix the hybrid vigour from more than one generation, among other advantages. The absence of meiosis and the occurrence of only two rounds of mitosis instead of three during embryo sac development make this model unique and suitable to be transferred to economically important crops. Throughout this review, we highlight the advances in the knowledge of apomixis in E. curvula using different techniques such as cytoembryology, DNA methylation analyses, small-RNA-seq, RNA-seq, genome assembly, and genotyping by sequencing. The main bulk of evidence points out that apomixis is inherited as a single Mendelian factor, and it is regulated by genetic and epigenetic mechanisms controlled by a complex network. With all this information, we propose a model of the mechanisms involved in diplosporous apomixis in this grass. All the genetic and epigenetic resources generated in E. curvula to study the reproductive mode changed its status from an orphan to a well-characterised species.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca 8000, Argentina
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), San Juan 670, Bahía Blanca 8000, Argentina
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, Bahía Blanca 8000, Argentina; (J.C.); (J.P.S.); (V.E.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, Bahía Blanca 8000, Argentina
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Carballo J, Zappacosta D, Marconi G, Gallardo J, Di Marsico M, Gallo CA, Caccamo M, Albertini E, Echenique V. Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050946. [PMID: 34068493 PMCID: PMC8150776 DOI: 10.3390/plants10050946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 05/05/2023]
Abstract
DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Gianpiero Marconi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Jimena Gallardo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Cristian A. Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
- Correspondence: (E.A.); (V.E.); Tel.: +39-075-585-6206 (E.A.); +54-291-486-1124 (V.E.)
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
- Correspondence: (E.A.); (V.E.); Tel.: +39-075-585-6206 (E.A.); +54-291-486-1124 (V.E.)
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Soliman M, Podio M, Marconi G, Di Marsico M, Ortiz JPA, Albertini E, Delgado L. Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040793. [PMID: 33920644 PMCID: PMC8072704 DOI: 10.3390/plants10040793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Apomixis seems to emerge from the deregulation of preexisting genes involved in sexuality by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families presented a wide apospory expressivity variation. To locate methylation changes associated with apomixis expressivity, we compare relative DNA methylation levels, at CG, CHG, and CHH contexts, between full-sib P. rufum diploid genotypes presenting differential apospory expressivity. The survey was performed using a methylation content-sensitive enzyme ddRAD (MCSeEd) strategy on samples at premeiosis/meiosis and postmeiosis stages. Based on the relative methylation level, principal component analysis and heatmaps, clearly discriminate samples with contrasting apospory expressivity. Differential methylated contigs (DMCs) showed 14% of homology to known transcripts of Paspalum notatum reproductive transcriptome, and almost half of them were also differentially expressed between apomictic and sexual samples. DMCs showed homologies to genes involved in flower growth, development, and apomixis. Moreover, a high proportion of DMCs aligned on genomic regions associated with apomixis in Setaria italica. Several stage-specific differential methylated sequences were identified as associated with apospory expressivity, which could guide future functional gene characterization in relation to apomixis success at diploid and tetraploid levels.
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Affiliation(s)
- Mariano Soliman
- CONICET-UNR/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario, Zavalla S2123, Argentina; (M.S.); (M.P.); (J.P.A.O.)
| | - Maricel Podio
- CONICET-UNR/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario, Zavalla S2123, Argentina; (M.S.); (M.P.); (J.P.A.O.)
| | - Gianpiero Marconi
- Department Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Marco Di Marsico
- Department Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Juan Pablo A. Ortiz
- CONICET-UNR/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario, Zavalla S2123, Argentina; (M.S.); (M.P.); (J.P.A.O.)
| | - Emidio Albertini
- Department Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Luciana Delgado
- CONICET-UNR/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario, Zavalla S2123, Argentina; (M.S.); (M.P.); (J.P.A.O.)
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Ortiz JPA, Pupilli F, Acuña CA, Leblanc O, Pessino SC. How to Become an Apomixis Model: The Multifaceted Case of Paspalum. Genes (Basel) 2020; 11:E974. [PMID: 32839398 PMCID: PMC7564465 DOI: 10.3390/genes11090974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
In the past decades, the grasses of the Paspalum genus have emerged as a versatile model allowing evolutionary, genetic, molecular, and developmental studies on apomixis as well as successful breeding applications. The rise of such an archetypal system progressed through integrative phases, which were essential to draw conclusions based on solid standards. Here, we review the steps adopted in Paspalum to establish the current body of knowledge on apomixis and provide model breeding programs for other agronomically important apomictic crops. In particular, we discuss the need for previous detailed cytoembryological and cytogenetic germplasm characterization; the establishment of sexual and apomictic materials of identical ploidy level; the development of segregating populations useful for inheritance analysis, positional mapping, and epigenetic control studies; the development of omics data resources; the identification of key molecular pathways via comparative gene expression studies; the accurate molecular characterization of genomic loci governing apomixis; the in-depth functional analysis of selected candidate genes in apomictic and model species; the successful building of a sexual/apomictic combined breeding scheme.
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Affiliation(s)
- Juan Pablo A. Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA Zavalla, Argentina;
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources (IBBR-CNR), 06128 Perugia, Italy;
| | - Carlos A. Acuña
- Instituto de Botánica del Nordeste (IBONE), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, 3400 Corrientes, Argentina;
| | - Olivier Leblanc
- UMR DIADE, IRD, Univ. Montpellier, 34090 Montpellier, France;
| | - Silvina C. Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA Zavalla, Argentina;
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Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions. Genes (Basel) 2020; 11:genes11090969. [PMID: 32825586 PMCID: PMC7564825 DOI: 10.3390/genes11090969] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
Eragrostis curvula presents mainly facultative genotypes that reproduce by diplosporous apomixis, retaining a percentage of sexual pistils that increase under drought and other stressful situations, indicating that some regulators activated by stress could be affecting the apomixis/sexual switch. Water stress experiments were performed in order to associate the increase in sexual embryo sacs with the differential expression of genes in a facultative apomictic cultivar using cytoembryology and RNA sequencing. The percentage of sexual embryo sacs increased from 4 to 24% and 501 out of the 201,011 transcripts were differentially expressed (DE) between control and stressed plants. DE transcripts were compared with previous transcriptomes where apomictic and sexual genotypes were contrasted. The results point as candidates to transcripts related to methylation, ubiquitination, hormone and signal transduction pathways, transcription regulation and cell wall biosynthesis, some acting as a general response to stress and some that are specific to the reproductive mode. We suggest that a DNA glycosylase EcROS1-like could be demethylating, thus de-repressing a gene or genes involved in the sexuality pathways. Many of the other DE transcripts could be part of a complex mechanism that regulates apomixis and sexuality in this grass, the ones in the intersection between control/stress and apo/sex being the strongest candidates.
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Rathore P, Raina SN, Kumar S, Bhat V. Retro-Element Gypsy-163 Is Differentially Methylated in Reproductive Tissues of Apomictic and Sexual Plants of Cenchrus ciliaris. Front Genet 2020; 11:795. [PMID: 32849800 PMCID: PMC7387646 DOI: 10.3389/fgene.2020.00795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022] Open
Abstract
Apomixis, an asexual mode of reproduction through seeds, has immense scope for crop improvement due to its ability to fix hybrid vigor. In C. ciliaris, a predominantly apomictically reproducing range grass, apomixis is genetically controlled by an apospory-specific-genomic-region (ASGR) which is enriched with retrotransposons. Earlier studies showed insertional polymorphisms of a few ASGR-specific retrotransposons between apomictic and sexual plants of C. ciliaris. REs are mainly regulated at the transcriptional level through cytosine methylation. To understand the possible association of ASGR-specific retrotransposon to apomixis, the extent and pattern of differential methylation of Gy163 RE and its impact on transcription were investigated in two genotypes each of apomictic and sexual plants of C. ciliaris. We observed that Gy163 encodes for an integrase domain of RE Ty3-Gypsy, is differentially methylated between reproductive tissues of apomictic and sexual plants. However, leaf tissues did not exhibit differential methylation between apomictic and sexual plants. Among the three contexts (CG, CHG, and CHH) of cytosine methylation, the maximum variation was observed in CHH context in reproductive (at aposporous initial and mature embryo sac stages) tissues of apomictic plants implicating RdDM pathway in methylation of Gy163. Quantitative PCR analysis showed that Gy163 transcripts are expressed more in the reproductive tissues of apomictic plants compared to that in the sexual plants, which was negatively correlated with the methylation level. Thus, the study helps in understanding the role of RE present in ASGR in epigenetic regulation of apomictic mode of reproduction in C. ciliaris.
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Affiliation(s)
- Priyanka Rathore
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vishnu Bhat
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
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Schinkel CCF, Syngelaki E, Kirchheimer B, Dullinger S, Klatt S, Hörandl E. Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae). Int J Mol Sci 2020; 21:E3318. [PMID: 32392879 PMCID: PMC7247541 DOI: 10.3390/ijms21093318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
Abstract
Polyploidization and the shift to apomictic reproduction are connected to changes in DNA cytosine-methylation. Cytosine-methylation is further sensitive to environmental conditions. We, therefore, hypothesize that DNA methylation patterns would differentiate within species with geographical parthenogenesis, i.e., when diploid sexual and polyploid apomictic populations exhibit different spatial distributions. On natural populations of the alpine plant Ranunculus kuepferi, we tested differences in methylation patterns across two cytotypes (diploid, tetraploid) and three reproduction modes (sexual, mixed, apomictic), and their correlation to environmental data and geographical distributions. We used methylation-sensitive amplified fragment-length polymorphism (methylation-sensitive AFLPs) and scored three types of epiloci. Methylation patterns differed independently between cytotypes versus modes of reproduction and separated three distinct combined groups (2x sexual + mixed, 4x mixed, and 4x apomictic), with differentiation of 4x apomicts in all epiloci. We found no global spatial autocorrelation, but instead correlations to elevation and temperature gradients in 22 and 36 epiloci, respectively. Results suggest that methylation patterns in R. kuepferi were altered by cold conditions during postglacial recolonization of the Alps, and by the concomitant shift to facultative apomixis, and by polyploidization. Obligate apomictic tetraploids at the highest elevations established a distinct methylation profile. Methylation patterns reflect an ecological gradient rather than the geographical differentiation.
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Affiliation(s)
- Christoph C. F. Schinkel
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, 37073 Göttingen, Germany;
| | - Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, 37073 Göttingen, Germany;
| | - Bernhard Kirchheimer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (B.K.); (S.D.)
| | - Stefan Dullinger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (B.K.); (S.D.)
| | - Simone Klatt
- Section Safety and Environmental Protection, University of Goettingen, Humboldtallee 15, 37073 Göttingen, Germany;
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, 37073 Göttingen, Germany;
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11
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Garbus I, Selva JP, Pasten MC, Bellido AM, Carballo J, Albertini E, Echenique V. Characterization and discovery of miRNA and miRNA targets from apomictic and sexual genotypes of Eragrostis curvula. BMC Genomics 2019; 20:839. [PMID: 31718556 PMCID: PMC6852985 DOI: 10.1186/s12864-019-6169-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/02/2019] [Indexed: 01/01/2023] Open
Abstract
Background Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass found in semi-arid regions that is well adapted for growth in sandy soils and drought conditions. E. curvula constitutes a polymorphic complex that includes cytotypes with different ploidy levels (from 2x to 8x), where most polyploids are facultative apomicts, although both sexual reproduction and full apomixis have been reported in this species. Apomixis is thought to be associated with silencing of the sexual pathway, which would involve epigenetic mechanisms. However, a correlation between small RNAs and apomixis has not yet been conclusively established. Results Aiming to contribute to the elucidation of their role in the expression of apomixis, we constructed small RNA libraries from sexual and apomictic E. curvula genotypes via Illumina technology, characterized the small RNA populations, and conducted differential expression analysis by comparing these small RNAs with the E. curvula reference transcriptome. We found that the expression of two genes is repressed in the sexual genotype, which is associated with specific microRNA expression. Conclusion Our results support the hypothesis that in E. curvula the expression of apomixis leads to sexual repression.
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Affiliation(s)
- Ingrid Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina.
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - María Cielo Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Andrés Martín Bellido
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - José Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
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12
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Ortiz JPA, Leblanc O, Rohr C, Grisolia M, Siena LA, Podio M, Colono C, Azzaro C, Pessino SC. Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum. BMC Genomics 2019; 20:487. [PMID: 31195966 PMCID: PMC6567921 DOI: 10.1186/s12864-019-5881-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Background Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested that this trait could be modulated by epigenetic mechanisms involving small RNAs (sRNAs). Here we profiled floral sRNAs originated from apomictic and sexual Paspalum notatum genotypes in order to identify molecular pathways under epigenetic control that might be involved in the transition from sexuality to agamospermy. Results The mining of genes participating in sRNA-directed pathways from floral Paspalum transcriptomic resources showed these routes are functional during reproductive development, with several members differentially expressed in apomictic and sexual plants. Triplicate floral sRNA libraries derived from apomictic and a sexual genotypes were characterized by using high-throughput sequencing technology. EdgeR was apply to compare the number of sRNA reads between sexual and apomictic libraries that map over all Paspalum floral transcripts. A total of 1525 transcripts showed differential sRNA representation, including genes related to meiosis, plant hormone signaling, biomolecules transport, transcription control and cell cycle. Survey for miRNA precursors on transcriptome and genome references allowed the discovery of 124 entities, including 40 conserved and 8 novel ones. Fifty-six clusters were differentially represented in apomictic and sexual plants. All differentially expressed miRNAs were up-regulated in apomictic libraries but miR2275, which showed different family members with opposed representation. Examination of predicted miRNAs targets detected 374 potential candidates. Considering sRNA, miRNAs and target surveys together, 14 genes previously described as related with auxin metabolism, transport and signaling were detected, including AMINO ACID/AUXIN PERMEASE 15, IAA-AMIDO SYNTHETASE GH3–8, IAA30, miR160, miR167, miR164, miR319, ARF2, ARF8, ARF10, ARF12, AFB2, PROLIFERATING CELL FACTOR 6 and NITRATE TRANSPORTER 1.1. Conclusions This work provides a comprehensive survey of the sRNA differential representation in flowers of sexual and apomictic Paspalum notatum plants. An integration of the small RNA profiling data presented here and previous transcriptomic information suggests that sRNA-mediated regulation of auxin pathways is pivotal in promoting apomixis. These results will underlie future functional characterization of the molecular components mediating the switch from sexuality to apomixis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5881-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Olivier Leblanc
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Cristian Rohr
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Argentina
| | - Mauricio Grisolia
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Argentina
| | - Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Carolina Colono
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Celeste Azzaro
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina.
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Albertini E, Barcaccia G, Carman JG, Pupilli F. Did apomixis evolve from sex or was it the other way around? JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2951-2964. [PMID: 30854543 DOI: 10.1093/jxb/erz109] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/25/2019] [Indexed: 05/20/2023]
Abstract
In angiosperms, there are two pathways of reproduction through seeds: sexual, or amphimictic, and asexual, or apomictic. The essential feature of apomixis is that an embryo in an ovule is formed autonomously. It may form from a cell of the nucellus or integuments in an otherwise sexual ovule, a process referred to as adventitious embryony. Alternatively, the embryo may form by parthenogenesis from an unreduced egg that forms in an unreduced embryo sac. The latter may form from an ameiotic megasporocyte, in which case it is referred to as diplospory, or from a cell of the nucellus or integument, in which case it is referred to as apospory. Progeny of apomictic plants are generally identical to the mother plant. Apomixis has been seen over the years as either a gain- or loss-of-function over sexuality, implying that the latter is the default condition. Here, we consider an additional point of view, that apomixis may be anciently polyphenic with sex and that both reproductive phenisms involve anciently canalized components of complex molecular processes. This polyphenism viewpoint suggests that apomixis fails to occur in obligately sexual eukaryotes because genetic or epigenetic modifications have silenced the primitive sex apomixis switch and/or disrupted molecular capacities for apomixis. In eukaryotes where sex and apomixis are clearly polyphenic, apomixis exponentially drives clonal fecundity during reproductively favorable conditions, while stress induces sex for stress-tolerant spore or egg formation. The latter often guarantees species survival during environmentally harsh seasons.
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Affiliation(s)
- Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Gianni Barcaccia
- Laboratory of Genomics, Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova Legnaro, PD, Italy
| | - John G Carman
- Department of Plants, Soils and Climate, Utah State University, Logan, Utah, USA
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council (CNR), Perugia, Italy
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14
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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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15
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Ortiz JPA, Revale S, Siena LA, Podio M, Delgado L, Stein J, Leblanc O, Pessino SC. A reference floral transcriptome of sexual and apomictic Paspalum notatum. BMC Genomics 2017; 18:318. [PMID: 28431521 PMCID: PMC5399859 DOI: 10.1186/s12864-017-3700-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types. Raw data originated from floral samples collected from premeiosis to anthesis was assembled in three libraries: i) sexual (SEX), ii) apomictic (APO) and iii) global (SEX + APO). A group of physically-supported Paspalum mRNA and EST sequences matched with high level of confidence to both sexual and apomictic libraries. A preliminary trial allowed discovery of the whole set of putative alleles/paralogs corresponding to 23 previously identified apomixis-associated candidate genes. Moreover, a list of 3,732 transcripts and several co-expression and protein -protein interaction networks associated with apomixis were identified. CONCLUSIONS The use of the 454/Roche FLX+ transcriptome database will allow the detailed characterization of floral alleles/paralogs of apomixis candidate genes identified in prior and future work. Moreover, it was used to reveal additional candidate genes differentially represented in apomictic and sexual flowers. Gene ontology (GO) analyses of this set of transcripts indicated that the main molecular pathways altered in the apomictic genotype correspond to specific biological processes, like biotic and abiotic stress responses, growth, development, cell death and senescence. This data collection will be of interest to the plant reproduction research community and, particularly, to Paspalum breeding projects.
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Affiliation(s)
- Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Santiago Revale
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis, Provincia de Santa Fe, Rosario, 2000, Argentina.,Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Luciana Delgado
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Juliana Stein
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Olivier Leblanc
- UMR 232, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, 34394, France
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina.
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16
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Rodrigo JM, Zappacosta DC, Selva JP, Garbus I, Albertini E, Echenique V. Apomixis frequency under stress conditions in weeping lovegrass (Eragrostis curvula). PLoS One 2017; 12:e0175852. [PMID: 28419145 PMCID: PMC5395188 DOI: 10.1371/journal.pone.0175852] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/31/2017] [Indexed: 01/17/2023] Open
Abstract
To overcome environmental stress, plants develop physiological responses that are triggered by genetic or epigenetic changes, some of which involve DNA methylation. It has been proposed that apomixis, the formation of asexual seeds without meiosis, occurs through the temporal or spatial deregulation of the sexual process mediated by genetic and epigenetic factors influenced by the environment. Here, we explored whether there was a link between the occurrence of apomixis and various factors that generate stress, including drought stress, in vitro culture, and intraspecific hybridization. For this purpose, we monitored the embryo sacs of different weeping lovegrass (Eragrostis curvula [Schrad.] Nees) genotypes after the plants were subjected to these stress conditions. Progeny tests based on molecular markers and genome methylation status were analyzed following the stress treatment. When grown in the greenhouse, the cultivar Tanganyika INTA generated less than 2% of its progeny by sexual reproduction. Plants of this cultivar subjected to different stresses showed an increase of sexual embryo sacs, demonstrating an increased expression of sexuality compared to control plants. Plants of the cv. Tanganyika USDA did not demonstrate the ability to generate sexual embryo sacs under any conditions and is therefore classified as a fully apomictic cultivar. We found that this change in the prevalence of sexuality was correlated with genetic and epigenetic changes analyzed by MSAP and AFLPs profiles. Our results demonstrate that different stress conditions can alter the expression of sexual reproduction in facultative tetraploid apomictic cultivars and when the stress stops the reproductive mode shift back to the apomixis original level. These data together with previous observations allow us to generate a hypothetical model of the regulation of apomixis in weeping lovegrass in which the genetic/s region/s that condition apomixis, is/are affected by ploidy, and is/are subjected to epigenetic control.
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Affiliation(s)
- Juan Manuel Rodrigo
- CERZOS-CONICET, CCT-Bahía Blanca, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Diego Carlos Zappacosta
- CERZOS-CONICET, CCT-Bahía Blanca, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Juan Pablo Selva
- CERZOS-CONICET, CCT-Bahía Blanca, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Ingrid Garbus
- CERZOS-CONICET, CCT-Bahía Blanca, Bahía Blanca, Argentina
- Departamento de Ciencias de la Salud, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Viviana Echenique
- CERZOS-CONICET, CCT-Bahía Blanca, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
- * E-mail:
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Shah JN, Kirioukhova O, Pawar P, Tayyab M, Mateo JL, Johnston AJ. Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition. FRONTIERS IN PLANT SCIENCE 2016; 7:1539. [PMID: 27833618 PMCID: PMC5080521 DOI: 10.3389/fpls.2016.01539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/30/2016] [Indexed: 05/19/2023]
Abstract
Molecular dissection of apomixis - an asexual reproductive mode - is anticipated to solve the enigma of loss of meiotic sex, and to help fixing elite agronomic traits. The Brassicaceae genus Boechera comprises of both sexual and apomictic species, permitting comparative analyses of meiotic circumvention (apomeiosis) and parthenogenesis. Whereas previous studies reported local transcriptome changes during these events, it remained unclear whether global changes associated with hybridization, polyploidy and environmental adaptation that arose during evolution of Boechera might serve as (epi)genetic regulators of early development prior apomictic initiation. To identify these signatures during vegetative stages, we compared seedling RNA-seq transcriptomes of an obligate triploid apomict and a diploid sexual, both isolated from a drought-prone habitat. Uncovered were several genes differentially expressed between sexual and apomictic seedlings, including homologs of meiotic genes ASYNAPTIC 1 (ASY1) and MULTIPOLAR SPINDLE 1 (MPS1) that were down-regulated in apomicts. An intriguing class of apomict-specific deregulated genes included several NAC transcription factors, homologs of which are known to be transcriptionally reprogrammed during abiotic stress in other plants. Deregulation of both meiotic and stress-response genes during seedling stages might possibly be important in preparation for meiotic circumvention, as similar transcriptional alteration was discernible in apomeiotic floral buds too. Furthermore, we noted that the apomict showed better tolerance to osmotic stress in vitro than the sexual, in conjunction with significant upregulation of a subset of NAC genes. In support of the current model that DNA methylation epigenetically regulates stress, ploidy, hybridization and apomixis, we noted that ASY1, MPS1 and NAC019 homologs were deregulated in Boechera seedlings upon DNA demethylation, and ASY1 in particular seems to be repressed by global DNA methylation exclusively in the apomicts. Variability in stress and transcriptional response in a diploid apomict, which is geographically distinct from the triploid apomict, pinpoints both common and independent features of apomixis evolution. Our study provides a molecular frame-work to investigate how the adaptive traits associated with the evolutionary history of apomicts co-adapted with meiotic gene deregulation at early developmental stage, in order to predate meiotic recombination, which otherwise is thought to be favorable in stress and low-fitness conditions.
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Affiliation(s)
- Jubin N. Shah
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Olga Kirioukhova
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Pallavi Pawar
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Muhammad Tayyab
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Juan L. Mateo
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
| | - Amal J. Johnston
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
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