Beyond population genetics: natural epigenetic variation in wild cherry (Prunus avium)

Tree Genetics and Genomes

Volumn 11, Issue 5, 2015, Pages

  Avramidou, Evangellia V ^a   Ganopoulos, Ioannis V ^a,b   Doulis, Andreas G ^c   Tsaftaris, Athanasios S ^a,b   Aravanopoulos, Filippos A ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

^c INSTITUTE OF TECHNOLOGY OF AGRICULTURAL PRODUCTS   (Greece)

Author keywords

Epigenetic diversity; MSAP markers; Natural populations; Wild cherry

Indexed keywords

EID: 84941365133     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-015-0921-7     Document Type: Article

References (43)

1. Aravanopoulos FA (2014) Genomics of trees. In: Ramawat KG, Merillon JM, Ahuja MR (eds) Tree biotechnology. CRC Press, Boca Raton, pp 514–557
2. Arzate-Mejía RG, Valle-García D, Recillas-Targa F (2011) Signaling epigenetics: novel insights on cell signaling and epigenetic regulation. IUBMB life 63:881–895
3. Avramidou E, Ganopoulos IV, Aravanopoulos FA (2010) DNA fingerprinting of elite Greek wild cherry (Prunus avium L.) genotypes using microsatellite markers. Forestry 83:527–533
4. Avramidou EV, Doulis AG, Aravanopoulos FA (2015) Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L. Gene 162:180–187
5. Bonduriansky R, Crean AJ, Day T (2012) The implications of nongenetic inheritance for evolution in changing environments. Evol Appl 5:192–201
6. Bossdorf O, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Lett 11:106–115
7. Cara NS, Marfil CF, Masuelli RW (2013) Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum. Ecol Evol 3:3764–3779
8. Cervera MT, Ruiz-Garcia L, Martinez-Zapater J (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552
9. Chwedorzewska K, Bednarek P (2012) Genetic and epigenetic variation in a cosmopolitan grass Poa annua from Antarctic and Polish populations. Pol Polar Res 33:63–80
10. Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
11. Ganopoulos I, Aravanopoulos FA, Argiriou A, Kalivas A, Tsaftaris A (2011) Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellite-based markers. Tree Genet Genomes 7:1299–1313
12. Ganopoulos IV, Aravanopoulos FA, Tsaftaris A (2012a) Genetic differentiation and gene flow between wild and cultivated Prunus avium: an analysis of molecular genetic evidence at a regional scale. Plant Biosyst 147:678–685
13. Ganopoulos I, Aravanopoulos F, Argiriou A, Tsaftaris A (2012b) Genome and population dynamics under selection and neutrality: an example of S-allele diversity in wild cherry (Prunus avium L.). Tree Genet Genomes 8:1181–1190
14. Grativol C, Hemerly AS, Ferreira PCG (2012) Genetic and epigenetic regulation of stress responses in natural plant populations. BBA Gene Regul Mech 1819:176–185
15. Herrera CM, Bazaga P (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol 187:867–876
16. Herrera CM, Medrano M, Bazaga P (2013) Epigenetic differentiation persists after male gametogenesis in natural populations of the perennial herb Helleborus foetidus (Ranunculaceae). PLoS One 8:e70730
17. Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol Evol 19:309–314
18. Li Y, Shan X, Liu X, Hu L, Guo W, Liu B (2008) Utility of the methylation-sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species (Hordeum brevisubulatum). Ecol Res 23:927–930
19. Lira-Medeiros 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:e10326
20. Ma K, Song Y, Yang X, Zhang Z, Zhang D (2013) Variation in genomic methylation in natural populations of Chinese white poplar. PLoS One 8:e63977
21. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
22. Mariette S, Tavaud M, Arunyawat U, Capdeville G, Millan M, Salin F (2010) Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. BMC Genet 11:77
23. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
24. Okhovat M, Berrio A, Ophir AG, Lysak N, Phelps SM (2014) Balancing selection promotes epigenetic variation in prairie vole spatial memory circuit. Department, Oxford University Press, 2001 Evans Road, Cary, NC 27513, USA, pp E326–E326
25. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539
26. Penn SCP, Siemens DH (2010) Ecological genomics—changing perspectives on Darwin’s basic concerns. Mol Ecol 19:3025–3030
27. Potter D (2011) Prunus. Wild crop relatives: genomic and breeding resources. Springer Berlin Heidelberg, pp 129–145
28. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91
29. Renn SCP, Siemens DH (2010) Ecological genomics—changing perspectives on Darwin’s basic concerns. Mol Ecol 19:3025–3030
30. Reyna-López GE, Ruiz-Herrera J (2004) Specificity of DNA methylation changes during fungal dimorphism and its relationship to polyamines. Curr Microbiol 48:118–123
31. Richards EJ (2006) Opinion—inherited epigenetic variation—revisiting soft inheritance. Nat Rev Genet 7:395–U392
32. Richards CL, Schrey AW, Pigliucci M (2012) Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol Lett 15:1016–1025
33. Rico L, Ogaya R, Barbeta A, Penuelas J (2014) Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change. Plant Biol 16:419–427
34. Rinehart TA (2004) AFLP analysis using GeneMapper® software and an Excel® macro that aligns and converts output to binary. Biotechniques 37:186–187
35. Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14:1163–1175
36. Schmitz RJ, Ecker JR (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci 17:149–154
37. Schrey AW, Alvarez M, Foust CM, Kilvitis HJ, Lee JD, Liebl AL, Martin LB, Richards CL, Robertson M (2013) Ecological epigenetics: beyond MS-AFLP. Integr Compar Biol 53:340–350
38. Schulz B, Eckstein RL, Durka W (2013) Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies. Mol Ecol Res 13:642–653
39. Schulz B, Eckstein RL, Durka W (2014) Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb. Mol Ecol 23:3523–3537
40. Shan XH, Li YD, Liu XM, Wu Y, Zhang MZ, Guo WL, Liu B, Yuan YP (2011) Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP. Genet Mol Res 11:2749–2759
41. Vekemans X, Beauwens T, Lemaire M, Roldán‐Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151
42. Wenzel MA, Piertney SB (2014) Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica). Mol Ecol 23:4256–4273
43. Xiong LZ, Xu CG, Maroof MAS, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Molec Gen Genet 261:439–446