1
|
Ibañez VN, van Antro M, Peña-Ponton C, Milanovic-Ivanovic S, Wagemaker CAM, Gawehns F, Verhoeven KJF. Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage. J Evol Biol 2023; 36:663-674. [PMID: 36810811 DOI: 10.1111/jeb.14162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/08/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.
Collapse
Affiliation(s)
- Verónica Noé Ibañez
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Université Paris Diderot, Gif sur Yvette, France.,Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Morgane van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Slavica Milanovic-Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | | | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| |
Collapse
|
2
|
Ibañez VN, Quadrana L. Shaping inheritance: how distinct reproductive strategies influence DNA methylation memory in plants. Curr Opin Genet Dev 2023; 78:102018. [PMID: 36525825 DOI: 10.1016/j.gde.2022.102018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
DNA methylation is a major epigenetic mark involved in the silencing of genes and transposable elements (TEs). DNA methylation varies significantly across the plant life cycle, but is efficiently reinforced during reproduction, ensuring stable silencing of TEs. Plants are remarkably flexible in their mode of reproduction and numerous species, including crops, can propagate asexually, skipping one or more of these critical reinforcement steps. In this review, we summarize recent advances in the characterization of DNA methylation inheritance in sexual and asexual plants. We argue that because most epigenetic reinforcement appears to occur during seed formation, methylomes of asexual seeds should resemble that of their sexual counterparts. Conversely, clonally propagated plants are expected to be hypomethylated and undergo frequent stochastic epigenetic changes. Last, we provide insights on how the use of nonmodel organisms will advance our understanding of epigenetic inheritance in plants.
Collapse
Affiliation(s)
- Verónica Noé Ibañez
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Université Paris Diderot, 91190 Gif sur Yvette, France. https://twitter.com/veronik_noe
| | - Leandro Quadrana
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Université Paris Diderot, 91190 Gif sur Yvette, France.
| |
Collapse
|
3
|
Gantuz M, Morales A, Bertoldi MV, Ibañez VN, Duarte PF, Marfil CF, Masuelli RW. Hybridization and polyploidization effects on LTR-retrotransposon activation in potato genome. J Plant Res 2022; 135:81-92. [PMID: 34674075 DOI: 10.1007/s10265-021-01354-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Hybridization and polyploidization are major forces in plant evolution and potatoes are not an exception. It is proposed that the proliferation of Long Terminal Repeat-retrotransposons (LTR-RT) is related to genome reorganization caused by hybridization and/or polyploidization. The main purpose of the present work was to evaluate the effect of interspecific hybridization and polyploidization on the activation of LTR-RT. We evaluated the proliferation of putative active LTR-RT in a diploid hybrid between the cultivated potato Solanum tuberosum and the wild diploid potato species S. kurtzianum, allotetraploid lines derived from this interspecific hybrid and S. kurtzianum autotetraploid lines (ktz-autotetraploid) using the S-SAP (sequence-specific amplified polymorphism) technique and normalized copy number determination by qPCR. Twenty-nine LTR-RT copies were activated in the hybrid and present in the allotetraploid lines. Major LTR-RT activity was detected in Copia-27, Copia-12, Copia-14 and, Gypsy-22. According to our results, LTR-RT copies were activated principally in the hybrid, there was no activation in allotetraploid lines and only one copy was activated in the autotetraploid.
Collapse
Affiliation(s)
- Magdalena Gantuz
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina.
| | - Andrés Morales
- Instituto Nacional de Tecnología Agropecuaria (INTA), Luján de Cuyo, Mendoza, Argentina
| | - María Victoria Bertoldi
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina
| | - Verónica Noé Ibañez
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina
| | - Paola Fernanda Duarte
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina
| | - Carlos Federico Marfil
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Universidad Nacional de Cuyo, A. Brown 500 (M5528AHB) Chacras de Coria, Mendoza, Argentina.
| |
Collapse
|
4
|
Ibañez VN, Kozub PC, González CV, Jerez DN, Masuelli RW, Berli FJ, Marfil CF. Response to water deficit of semi-desert wild potato Solanum kurtzianum genotypes collected from different altitudes. Plant Sci 2021; 308:110911. [PMID: 34034868 DOI: 10.1016/j.plantsci.2021.110911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Drought-sensitive crops are threatened as a consequence of limited available water due to climate change. The cultivated potato (Solanum tuberosum) is susceptible to drought and within its wild relative species, Solanum kurtzianum is the Argentinian wild potato species best adapted to arid conditions. However, its physiological responses to water deficit (WD) are still missing. Within the distribution of S. kurtzianum, genotypes could be adapted to differential precipitation regimes. The aim of this work was to evaluate responses of three S. kurtzianum genotypes collected at 1100 (G1), 1900 (G2) and 2100 m a.s.l. (G3) to moderate and severe WD. Treatments were imposed since flowering and lasted 36 days. Yield components, morpho-physiological and biochemical responses; and phenotypic plasticity were evaluated. The three genotypes presented mechanisms to tolerate both WD treatments. G1 presented the lowest yield reduction under moderate WD, mainly through a rapid stomatal closure and a modest vegetative growth. The differences among genotypes suggest that local adaptation is taking place within its natural habitat. Also, G2 presented environmentally induced shifts in plasticity for stomatal length and carotenoids, suggesting that phenotypic plasticity has a role in acclimation of plants to WD until selection works.
Collapse
Affiliation(s)
- Verónica Noé Ibañez
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina.
| | - Perla Carolina Kozub
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina
| | - Carina Verónica González
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Contreras 1300, Mendoza, Argentina
| | - Damián Nicolás Jerez
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina
| | - Federico Javier Berli
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina
| | - Carlos Federico Marfil
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5505, Chacras de Coria, Mendoza, Argentina
| |
Collapse
|
5
|
Ibañez VN, Masuelli RW, Marfil CF. Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens. Heredity (Edinb) 2021; 126:50-62. [PMID: 32801346 PMCID: PMC7853039 DOI: 10.1038/s41437-020-00355-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 11/08/2022] Open
Abstract
DNA methylation can be environmentally modulated and plays a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) were assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability was positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.
Collapse
Affiliation(s)
- Verónica Noé Ibañez
- IBAM (Instituto de Biología Agrícola de Mendoza), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- IBAM (Instituto de Biología Agrícola de Mendoza), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Carlos Federico Marfil
- IBAM (Instituto de Biología Agrícola de Mendoza), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina.
| |
Collapse
|
6
|
Ibañez VN, Berli FJ, Masuelli RW, Bottini RA, Marfil CF. Influence of altitude and enhanced ultraviolet-B radiation on tuber production, seed viability, leaf pigments and morphology in the wild potato species Solanum kurtzianum Bitter & Wittm collected from an elevational gradient. Plant Sci 2017; 261:60-68. [PMID: 28554694 DOI: 10.1016/j.plantsci.2017.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/23/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Climate change could lead to an upward shift in plant distribution, exposing populations to higher levels of ultraviolet (UV)-B radiation. In the framework of an in situ strategy for conserving potato wild relatives, we evaluated the effect of high UV-B levels on natural population of Solanum kurtzianum. The hypothesis is that plants from naturally higher altitudes are more adapted to increased UV-B radiation. Two populations from low and high altitudes were field supplemented using UV-B-lamps (+UV-B) or excluded from it with plastic filters. Additionally, to assess in which extent the plant responses to these artificial experimental conditions are reproducible in natural conditions, three genotypes were cultivated in two mountain experimental gardens (EG) at different elevations. +UV-B treatment induced changes in leaf morphology and increases in phenolic compounds in both populations, indicating plant adaptation, since chlorophylls and reproductive structures were not negatively affected. These results indicate that this environmental factor may not limit the displacement of populations towards sites with higher UV-B levels. Meanwhile, in higher-altitude EG a tubers yield reduction, mainly through a decreased tuber number and a bigger accumulation of phenolic compounds than in +UV-B treatment were observed, suggesting that UV-B is not the only factor involved in plants adaptation to high altitude environments.
Collapse
Affiliation(s)
- V N Ibañez
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - F J Berli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - R W Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - R A Bottini
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - C F Marfil
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina.
| |
Collapse
|