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Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

  • Berend K, Haynes K, MacKenzie CM (2019) Common garden experiments as a dynamic tool for ecological studies of alpine plants and communities in northeastern north America. Rhodora 121:174–212

    Google Scholar 

  • Berli FJ, Alonso R, Bressan-Smith R, Bottini R (2013) UV-B impairs growth and gas exchange in grapevines grown in high altitude. Physiol Plant 149:127–140

    CAS  PubMed  Google Scholar 

  • Camadro EL (2012) Relevance of the genetic structure of natural populations, and sampling and classification approaches for conservation and use of wild crop relatives: potato as an example. Botany 90(11):1065–1072

    Google Scholar 

  • Cara N, Marfil CF, Masuelli RW (2013) Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum. Ecol Evol 3:3764–3779

    PubMed  PubMed Central  Google Scholar 

  • Castonguay E, Angers B (2012) The key role of epigenetics in the persistence of asexual lineages. Genet Res Int 2012:1–9

    Google Scholar 

  • Coneva V, Chitwood DH (2018) Genetic and developmental basis for increased leaf thickness in the Arabidopsis cvi ecotype. Front Plant Sci 9:1–10.

    Google Scholar 

  • Cooper HF, Grady KC, Cowan JA, Best RJ, Allan GJ, Whitham TG (2019) Genotypic variation in phenological plasticity: Reciprocal common gardens reveal adaptive responses to warmer springs but not to fall frost. Glob Change Biol 25:187–200

    Google Scholar 

  • Correll D (1962) The potato and its wild relatives. Texas Research Foundation, Renner, TX

  • Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K et al. (2014) Mapping the epigenetic basis of complex traits. Science 343:1145–1148

    CAS  PubMed  Google Scholar 

  • Crisp PA, Ganguly D, Eichten SR, Borevitz JO, Pogson BJ (2016) Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Sci Adv 2:1–14.

    Google Scholar 

  • Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157–161

    CAS  PubMed  Google Scholar 

  • Donelson JM, Salinas S, Munday PL, Shama LN (2017) Transgenerational plasticity and climate change experiments: Where do we go from here? Glob Change Biol 24:13–34

    Google Scholar 

  • Dubin MJ, Zhang P, Meng D, Remigereau M-S, Osborne EJ, Casale FP et al. (2015) DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. Elife 4:e05255

    PubMed  PubMed Central  Google Scholar 

  • Erazzú LE, Camadro EL, Clausen AM (2009) Persistence over time, overlapping distribution and molecular indications of interspecific hybridization in wild potato populations of Northwest Argentina. Euphytica 168:249–262

    Google Scholar 

  • FAO UN (2018) FAOstat. http://www.fao.org/faostat/en/#data/QC. Accessed 29 Dec 2018.

  • Fulneček J, Kovařík A (2014) How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? BMC Genet 15:1–9

    Google Scholar 

  • Gao L, Geng Y, Li B, Chen J, Yang J (2010) Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: Implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant Cell Environ 33:1820–1827

    CAS  PubMed  Google Scholar 

  • Garnier E, Laurent G, Bellmann A, Debain S, Berthelier P, Ducout B, Roumet C, Navas ML (2001) Consistency of species ranking based on functional leaf traits. N Phytologist 152:69–83

    Google Scholar 

  • Godoy O, Valladares F, Castro‐Díez P (2012) The relative importance for plant invasiveness of trait means, and their plasticity and integration in a multivariate framework. N Phytologist 195:912–922

    Google Scholar 

  • González APR, Preite V, Verhoeven KJF, Latzel V (2018) Transgenerational effects and epigenetic memory in the clonal plant Trifolium repens. Front Plant Sci 9:1–11

    Google Scholar 

  • Hawkes JG (1954) The ecology of wild potato species and its bearing on the origin of potato cultivation. J d’Agriculture Traditionnelle et de Botanique Appliquée 1:356–358

    Google Scholar 

  • Hawkes JG, Hjerting JP (1969) The potatoes of Argentina, Brazil, Paraguay and Uruguay. A biosystematic study. Clarendon Press, Oxford, UK

    Google Scholar 

  • Herrera CM, Bazaga P (2011) Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Mol Ecol 20:1675–1688

    CAS  PubMed  Google Scholar 

  • Hijmans RJ, Spooner DM, Salas AR, Guarino L, de la Cruz J (2002) Atlas of wild potatoes. International Plant Genetic Resources Institute, Rome

  • Hiatt D, Flory SL (2020) Populations of a widespread invader and co‐occurring native species vary in phenotypic plasticity. N Phytologist 225:584–594

    CAS  Google Scholar 

  • Ibañez VN, Berli FJ, Masuelli RW, Bottini RA, Marfil CF (2017) 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 and Wittm collected from an elevational gradient. Plant Sci 261:60–68

    PubMed  Google Scholar 

  • IPCC (2014) Climate Change 2014: Synthesis report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, In: Core Writing Team, RK Pachauri, LA Meyer (eds). IPCC, Geneva, Switzerland, p 151

  • Jansky SH, Simon R, Spooner DM (2006) A test of taxonomic predictivity: resistance to white mold in wild relatives of cultivated potato. Crop Sci 46:2561–2570

    Google Scholar 

  • Jansky SH, Simon R, Spooner DM (2009) A test of taxonomic predictivity: resistance to the colorado potato beetle in wild relatives of cultivated potato. J Economic Entomol 102:422–431

    CAS  Google Scholar 

  • Kassambara A, Mundt F (2017) Factoextra: extract and visualize the results of multivariate data analyses. R package version 1.0.5.

  • Kelly M (2019) Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes. Philos Trans R Soc B 374:20180176

    Google Scholar 

  • Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot, Vreugdenhil D, Keurentjes JJB (2015) Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. Plant Cell 27:337–348

    CAS  PubMed  PubMed Central  Google Scholar 

  • Latzel V, Allan E, Bortolini Silveira A, Colot V, Fischer M, Bossdorf O (2013) Epigenetic diversity increases the productivity and stability of plant populations. Nat Commun 4:1–7

    Google Scholar 

  • Le S, Julie J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25:1–18

    Google Scholar 

  • Lira-Madeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE 5:1–8

    Google Scholar 

  • Marfil CF, Camadro EL, Masuelli RW (2009) Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii. BMC Plant Biol 9:1–16.

    Google Scholar 

  • Marfil CF, Asurmendi S, Masuelli RW (2012) Changes in micro RNA expression in a wild tuber-bearing Solanum species induced by 5-Azacytidine treatment. Plant Cell Rep 31:1449–1461

    CAS  PubMed  Google Scholar 

  • Marfil CF, Masuelli RW (2014) Reproductive ecology and genetic variability in natural populations of the wild potato, Solanum kurtzianum. Plant Biol 16:485–494

    CAS  PubMed  Google Scholar 

  • Marfil CF, Hidalgo V, Masuelli RW (2015) In situ conservation of wild potato germplasm in Argentina: example and possibilities. Glob Ecol Conserv 3:461–476

    Google Scholar 

  • Marfil CF, Duarte P, Masuelli RW (2018) Phenotypic and epigenetic variation induced in newly synthesized allopolyploids and autopolyploids of potato. Scientia Horticulturae 234:101–109

    Google Scholar 

  • Masuelli RW, Camadro EL, Erazzú LE, Bedogni MC, Marfil CF (2009) Homoploid hybridization in the origin and evolution of wild diploid potato species. Plant Syst Evol 277:143–151

    Google Scholar 

  • McGregor CE, van Treuren R, Hoekstra R, van Hintum TJL (2002) Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation. TAG. Theor Appl Genet 104:146–156

    CAS  PubMed  Google Scholar 

  • Medrano M, Herrera CM, Bazaga P (2014) Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb. Mol Ecol 23:4926–4938

    CAS  PubMed  Google Scholar 

  • Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M (2010) Plant phenotypic plasticity in a changing climate. Trends plant Sci 15:684–692

    CAS  PubMed  Google Scholar 

  • Nicotra AB, Segal DL, Hoyle GL, Schrey AW, Verhoeven KJF, Richards CL (2015) Adaptive plasticity and epigenetic variation in response to warming in an Alpine plant. Ecol Evolution 5:634–647

    Google Scholar 

  • O’Dea RE, Noble DW, Johnson SL, Hesselson D, Nakagawa S (2016) The role of non-genetic inheritance in evolutionary rescue: epigenetic buffering, heritable bet hedging and epigenetic traps. Environ Epigenetics 2:1–12.

    Google Scholar 

  • Oksanen J,(2015) Multivariate analysis of ecological communities in R: vegan tutorial. R Documentation. 1:11–12

  • Peppe DJ, Royer DL, Cariglino B, Oliver SY, Newman S, Leight E et al. (2011) Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applications. N Phytologist 190:724–739

    Google Scholar 

  • Pimpinelli S, Piacentini L (2019) Environmental change and the evolution of genomes: Transposable elements as translators of phenotypic plasticity into genotypic variability. Funct Ecol 00:1–14

    Google Scholar 

  • Preite V, Snoek LB, Oplaat C, Biere A, Van Der Putten WH, Verhoeven KJF (2015) The epigenetic footprint of poleward range-expanding plants in apomictic dandelions. Mol Ecol 24:4406–4418

    CAS  PubMed  Google Scholar 

  • R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria

  • Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colomé-Tatché M et al. (2017) Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett 20:1576–1590

    PubMed  Google Scholar 

  • Richards EJ (2006) Inherited epigenetic variation revisiting soft inheritance. Nat Rev Genet 7:395–401

    CAS  PubMed  Google Scholar 

  • Schulz B, Eckstein RL, Durka W (2013) Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies. Mol Ecol Resour 13:642–653

    CAS  PubMed  Google Scholar 

  • Schulz E, Tohge T, Zuther E, Fernie AR, Hincha DK (2015) Natural variation in flavonol and anthocyanin metabolism during cold acclimation in Arabidopsis thaliana accessions. Plant Cell Environ 38:1658–1672

    CAS  PubMed  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical taxonomy. The principles and practice of numerical classification. WH Freeman and Company, San Francisco, USA

    Google Scholar 

  • Spooner DM (2009) DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am J Bot 96:1177–1189

    CAS  PubMed  Google Scholar 

  • Spooner DM, Jansky SH, Simon R (2009) Tests of taxonomic and biogeographic predictivity: resistance to disease and insect pests in wild relatives of cultivated potato. Crop Sci 49:1367–1376

    Google Scholar 

  • Tricker PJ, Gibbings JG, Rodríguez López CM, Hadley P, Wilkinson MJ (2012) Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development. J Exp Bot 63:3799–3813

    CAS  PubMed  PubMed Central  Google Scholar 

  • Valladares F, Sanchez-Gomez D, Zavala M (2006) Quantitative estimation of phenotypic plasticity: bridging the gap between the evolutionary concept and its ecological applications. J Ecol 94:1103–1116

    Google Scholar 

  • Verhoeven KJF, Jansen JJ, van Dijk PJ, Biere A (2010) Stress-induced DNA methylation changes and their heritability in asexual dandelions. N Phytologist 185:1108–1118

    CAS  Google Scholar 

  • Verhoeven KJF, Preite V (2014) Epigenetic variation in asexually reproducing organisms. Evolution 68:644–655

    PubMed  Google Scholar 

  • Verhoeven KJF, Von Holdt BM, Sork VL (2016) Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol 25:1631–1638

    PubMed  Google Scholar 

  • Wei N, Cronn R, Liston A, Ashman TL (2019) Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments. N Phytologist 221:2286–2297

    Google Scholar 

  • Wright IJ, Dong N, Maire V, Prentice IC, Westoby M, Díaz S et al. (2017) Global climatic drivers of leaf size. Science 357:917–921

    CAS  PubMed  Google Scholar 

  • Zhang YY, Fischer M, Colot V, Bossdorf O (2013) Epigenetic variation creates potential for evolution of plant phenotypic plasticity. N Phytologist 197:314–322

    CAS  Google Scholar 


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