Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L.

Gene

Volumn 562, Issue 2, 2015, Pages 180-187

  Avramidou, Evangelia V ^a,b   Doulis, Andreas G ^b   Aravanopoulos, Filippos A ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b INSTITUTE OF TECHNOLOGY OF AGRICULTURAL PRODUCTS   (Greece)

Author keywords

AFLP; Cypress; DNA cytosine methylation; Epigenetics; Inheritance; MSAP

Indexed keywords

CYTOSINE; DNA; GENOMIC DNA;

ADAPTATION; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CONIFER; CONTROLLED STUDY; CORRELATION ANALYSIS; CUPRESSUS; CUPRESSUS SEMPERVIRENS; DNA METHYLATION; EPIGENETIC INHERITANCE; EPIGENETICS; EXTRACHROMOSOMAL INHERITANCE; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC INHERITANCE; GENETIC REGULATION; GENETIC VARIABILITY; INHERITANCE; METHYLATION SENSITIVE AMPLIFIED POLYMORPHISM; NONHUMAN; PARENT; PHENOTYPIC PLASTICITY; PLANT BREEDING; PLANT EVOLUTION; PLANT GENOME; PLANT GROWTH; PRIORITY JOURNAL; PROGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS;

CUPRESSUS; CUPRESSUS SEMPERVIRENS;

CUPRESSUS; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; SEQUENCE ANALYSIS, DNA;

EID: 84925601847     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.02.068     Document Type: Article

References (44)

1. Abid G., Muhoviski Y., Jacquemin J.-M., Mingeot D., Sassi K., Toussaint A., Baudoin J.-P. Changes in DNA-methylation during zygotic embryogenesis in interspecific hybrids of beans (Phaseolus ssp.). Plant Cell, Tis. and Org. Cult. 2011, 105:383-393.
2. Aravanopoulos F. Biochemical evidence for maternal effects in Salix exigua (Nutt.). Proc. IUFRO XIX World Congress, S2.01-05 Session on Biotechnology, Montreal 1990, 121-130.
3. Autran D., Baroux C., Raissig M.T., Lenormand T., Wittig M., Grob S., Steimer A., Barann M., Klostermeier U.C., Leblanc O. Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 2011, 145:707-719.
4. Ba Q., Zhang G., Niu N., Ma S., Wang J. Cytoplasmic effects on DNA methylation between male sterile lines and the maintainer in wheat (Triticum aestivum L.). Gene 2014, 549:192-197.
5. Chagné D., Lalanne C., Madur D., Kumar S., Frigério J.-M., Krier C., Decroocq S., Savouré A., Bou-Dagher-Kharrat M., Bertocchi E. A high density genetic map of maritime pine based on AFLPs. Ann. For. Sci. 2002, 59:627-636.
6. Eichten S.R., Swanson-Wagner R.A., Schnable J.C., Waters A.J., Hermanson P.J., Liu S., Yeh C.-T., Jia Y., Gendler K., Freeling M. Heritable epigenetic variation among maize inbreds. PLoS Genet. 2011, 7:e1002372.
7. Fujimoto R., Sasaki T., Ishikawa R., Osabe K., Kawanabe T., Dennis E.S. Molecular mechanisms of epigenetic variation in plants. Int. J. Mol. Sci. 2012, 13:9900-9922.
8. Gomez A., Aravanopoulos F.A., Bueno M.A., Alia R. Linkage of random amplified polymorphic DNA markers in Pinus halepensis Mill. Silvae Genet. 2002, 51:196-200.
9. Huff D.R., Peakall R., Smouse P.E. RAPD variation within and among natural populations of outcrossing buffalograss [Buchloe dactyloides (Nutt.) Engelm.]. Theor. Appl. Genet. 1993, 86:927-934.
10. Kakutani T. Epi-alleles in plants: inheritance of epigenetic information over generations. Plant Cell Physiol. 2002, 43:1106-1111.
11. Kovar A., Koukalova B., Bezde M., Opatrn Z. Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor. Appl. Genet. 1997, 95:301-306.
12. Kuang H., Richardson T., Carson S., Wilcox P., Bongarten B. Genetic analysis of inbreeding depression in plus tree 850.55 of Pinus radiata D. Don. I. Genetic map with distorted markers. Theor. Appl. Genet. 1999, 98:697-703.
13. Kunkel T.A. DNA replication fidelity. J. Biol. Chem. 2004, 279:16895-16898.
14. Lerceteau E., Szmidt A.E. Properties of AFLP markers in inheritance and genetic diversity studies of Pinus sylvestris L. Heredity 1999, 82:252-260.
15. Li A., Song W.-Q., Chen C.-B., Zhou Y.-N., Qi L.-W., Wang C.-G. DNA methylation status is associated with the formation of heterosis in Larix kaempferi intraspecific hybrids. Mol. Breed. 2013, 31:463-475.
16. Lira-Medeiros C.F., Parisod C., Fernandes R.A., Mata C.S., Cardoso M.A., Ferreira P.C.G. Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 2010, 5:e10326.
17. Long Y., Xia W., Li R., Wang J., Shao M., Feng J., King G.J., Meng J. Epigenetic QTL mapping in Brassica napus. Genetics 2011, 189:1093-1102.
18. Ma K., Song Y., Jiang X., Zhang Z., Li B., Zhang D. Photosynthetic response to genome methylation affects the growth of Chinese white poplar. Tree Genet. Genomes 2012, 8:1407-1421.
19. Ma K., Song Y., Yang X., Zhang Z., Zhang D. Variation in genomic methylation in natural populations of Chinese white poplar. PLoS One 2013, 8:e63977.
20. Manescu C., Hamamouch N., Maios C., Harfouche A., Doulis A.G., Aravanopoulos F.A. Linkage mapping of the Mediterranean cypress, Cupressus sempervirens, based on molecular and morphological markers. Genet. Mol. Res. 2011, 10:1891-1909.
21. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27:209-220.
22. Mukai Y., Suyama Y., Tsumura Y., Kawahara T., Yoshimaru H., Kondo T., Tomaru N., Kuramoto N., Murai M. A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci. Theor. Appl. Genet. 1995, 90:835-840.
23. Nikaido A.M., Ujino T., Iwata H., Yoshimura K., Yoshimura H., Suyama Y., Murai M., Nagasaka K., Tsumura Y. AFLP and CAPS linkage maps of Cryptomeria japonica. Theor. Appl. Genet. 2000, 100:825-831.
24. Nystedt B., Street N.R., Wetterbom A., Zuccolo A., Lin Y.-C., Scofield D.G., Vezzi F., Delhomme N., Giacomello S., Alexeyenko A. The Norway spruce genome sequence and conifer genome evolution. Nature 2013, 497:579-584.
25. Peakall R.O.D., Smouse P.E. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 2006, 6:288-295.
26. Peng H., Jiang G., Zhang J., Zhang W., Zhai W. DNA methylation polymorphism and stability in Chinese indica hybrid rice. Sci. China Life Sci. 2013, 56:1097-1106.
27. Remington D.L., Whetten R.W., Liu B.H., O'malley D.M. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor. Appl. Genet. 1999, 98:1279-1292.
28. Ribeiro M.M., Mariette S., Vendramin G.G., Szmidt A.E., Plomion C., Kremer A. Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data. Mol. Ecol. 2002, 11:869-877.
29. Richards E.J. Inherited epigenetic variation - revisiting soft inheritance. Nat. Rev. Genet. 2006, 7:395-401.
30. Sáez-Laguna E., Guevara M.-Á., Díaz L.-M., Sánchez-Gómez D., Collada C., Aranda I., Cervera M.-T. Epigenetic variability in the genetically uniform forest tree species Pinus pinea L. PLoS One 2014, 9:e103145.
31. Salmon A., Clotault J., Jenczewski E., Chable V., Manzanares-Dauleux M.J. Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Sci. 2008, 174:61-70.
32. Schmitz R.J., He Y., Valdés-López O., Khan S.M., Joshi T., Urich M.A., Nery J.R., Diers B., Xu D., Stacey G. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013, 23:1663-1674.
33. Schrey A.W., Alvarez M., Foust C.M., Kilvitis H.J., Lee J.D., Liebl A.L., Martin L.B., Richards C.L., Robertson M. Ecological epigenetics: beyond MS-AFLP. Integr. Comp. Biol. 2013, 53:340-350.
34. Schulz B., Eckstein R.L., Durka W. Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies. Mol. Ecol. Resour. 2013, 13:642-653.
35. Takamiya T., Hosobuchi S., Noguchi T., Asai K., Nakamura E., Habu Y., Paterson A.H., Iijima H., Murakami Y., Okuizumi H. Inheritance and alteration of genome methylation in F1 hybrid rice. Electrophoresis 2008, 29:4088-4095.
36. Tang X.-M., Tao X., Wang Y., Ma D.-W., Li D., Yang H., Ma X.-R. Analysis of DNA methylation of perennial ryegrass under drought using the methylation-sensitive amplification polymorphism (MSAP) technique. Mol. Gen. Genomics. 2014, 1-10.
37. Vekemans X., Beauwens T., Lemaire M., Roldán-Ruiz I. 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. 2002, 11:139-151.
38. Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Hornes M., Friters A., Pot J., Paleman J., Kuiper M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23:4407-4414.
39. Xiong L.Z., Xu C.G., Maroof M.A.S., Zhang Q. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol. Gen. Genet. 1999, 261:439-446.
40. Yang C., Huang Y., Tang Z., Lu L., Liu L. Analysis of DNA methylation variation in sibling tobacco (Nicotiana tabacum) cultivars. Afr. J. Biotechnol. 2013, 10:874-881.
41. Yin T.M., Wang X.R., Andersson B., Lerceteau-Köhler E. Nearly complete genetic maps of Pinus sylvestris L. (Scots pine) constructed by AFLP marker analysis in a full-sib family. Theor. Appl. Genet. 2003, 106:1075-1083.
42. Zhang M.S., Yan H.Y., Zhao N., Lin X.Y., Pang J.S., Xu K.Z., Liu L.X., Liu B. Endosperm-specific hypomethylation, and meiotic inheritance and variation of DNA methylation level and pattern in sorghum (Sorghum bicolor L.) inter-strain hybrids. Theor. Appl. Genet. 2007, 115:195-207.
43. Zhao X., Chai Y., Liu B. Epigenetic inheritance and variation of DNA methylation level and pattern in maize intra-specific hybrids. Plant Sci. 2007, 172:930-938.
44. Zhao Y., Yu S., Xing C., Fan S., Song M. Analysis of DNA methylation in cotton hybrids and their parents. Mol. Biol. 2008, 42:169-178.