Karma-EgDEF1 methylation in Elaeis guineensis clonal mother palms that produced high mantling rates in the second clonal generation

Alwee SSRS, Roowi SH, Teng AK, Othman AZ (2010) Progress of oil palm tissue culture in Felda and its challenges, In: Proceedings of the International Society of Oil Palm Breeders (ISOPB) Seminar on Advances in Oil Palm Tissue Culture, Yogyakarta, Indonesia, pp 45–52

Bernstein DL, Kameswaran V, Le LJE, Sheaffer KL, Kaestner KH (2015) The BisPCR2 method for targeted bisulfite sequencing. Epigenetics Chromatin 8:27. https://doi.org/10.1186/s13072-015-0020-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Borges F, Donoghue MTA, LeBlanc C, Wear EE, Tanurdžić M, Berube B, Brooks A, Thompson WF, Hanley-Bowdoin L, Martienssen RA (2021) Loss of small-RNA-directed DNA methylation in the plant cell cycle promotes germline reprogramming and somaclonal variation. Curr Biol 31:591–600. https://doi.org/10.1016/j.cub.2020.10.098

Article  CAS  PubMed  Google Scholar 

Han Z, Crisp PA, Stelpflug S, Kaeppler SM, Li Q, Springer NM (2018) Heritable epigenomic changes to the maize methylome resulting from tissue culture. Genetics 209:983–995. https://doi.org/10.1534/genetics.118.300987

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hansen KD, Langmead B, Irizarry RA (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 13:R83. https://doi.org/10.1186/gb-2012-13-10-R83

Article  PubMed  PubMed Central  Google Scholar 

Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, Agbessi MDT, Sabot F, Garsmeur O, D’Hont A, Alwee SSRS, Rival A (2014) DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm. PLoS ONE 9:e91896. https://doi.org/10.1371/journal.pone.0091896

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Kim KD, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ (2019) Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. Plant Cell 31:2315–2331. https://doi.org/10.1105/tpc.19.00255

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kamstra JH, Sales LB, Aleström P, Legler J (2017) Differential DNA methylation at conserved non-genic elements and evidence for transgenerational inheritance following developmental exposure to mono (2-ethylhexyl) phthalate and 5-azacytidine in zebrafish. Epigenetics Chromatin 10:20. https://doi.org/10.1186/s13072-017-0126-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kawakatsu T, Nery JR, Castanon R, Ecker JR (2017) Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biol 18:171. https://doi.org/10.1186/s13059-017-1251-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572. https://doi.org/10.1093/bioinformatics/btr167

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar S (2018) Epigenetic memory of stress responses in plants. J Phytochemistry Biochem 2:e102

Google Scholar 

Kumar S, Seem K, Kumar S, Vinod KK, Chinnusamy V, Mohapatra T (2022) Pup1 QTL regulates gene expression through epigenetic modification of DNA under phosphate starvation stress in rice. Front Plant Sci 13:871890. https://doi.org/10.3389/fpls.2022.871890

Article  PubMed  PubMed Central  Google Scholar 

Latutrie M, Gourcilleau D, Pujol B (2019) Epigenetic variation for agronomic improvement: an opportunity for vegetatively propagated crops. Am J Bot 106:1281–1284. https://doi.org/10.1002/ajb2.1357

Article  PubMed  PubMed Central  Google Scholar 

Li J, Wang M, Li Y, Zhang Q, Lindsey K, Daniell H, Jin S, Zhang X (2019) Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process. Plant Biotechnol J 17:435–450. https://doi.org/10.1111/pbi.12988

Article  CAS  PubMed  Google Scholar 

Ong-Abdullah M, Ordway JM, Jiang N, Ooi S-E, Kok S-Y, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK, Malike FA, Bakar NAA, Marjuni M, Abdullah N, Yaakub Z, Amiruddin MD, Nookiah R, Singh R, Low E-TL, Chan K-L, Azizi N, Smith SW, Bacher B, Budiman MA, Van Brunt A, Wischmeyer C, Beil M, Hogan M, Lakey N, Lim C-C, Arulandoo X, Wong C-K, Choo C-N, Wong W-C, Kwan Y-Y, Alwee SSRS, Sambanthamurthi R, Martienssen RA (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525:533–539. https://doi.org/10.1038/nature15365

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ooi S-E, Sarpan N, Taranenko E, Feshah I, Nuraziyan A, Roowi SH, Burhan MN, Jayanthi N, Rahmah ARS, Teh O-K, Ong-Abdullah M, Tatarinova TV (2023) Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling. Plant Mol Biol 111:345–363. https://doi.org/10.1007/s11103-022-01330-4

Article  CAS  PubMed  Google Scholar 

Peraza-Echeverria S, Herrera-Valencia VA, Kay AJ (2001) Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 161:359–367. https://doi.org/10.1016/S0168-9452(01)00421-6

Article  CAS  PubMed  Google Scholar 

Soh AC, Wong G, Tan CC, Chew PS, Chong SP, Ho YW, Wong CK, Choo CN, Nor Azura H, Kumar K (2011) Commercial-scale propagation and planting of elite oil palm clones: Research and development towards realization. J Oil Palm Res 23:935–952

Google Scholar 

Stelpflug SC, Eichten SR, Hermanson PJ, Springer NM, Kaeppler SM (2014) Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize. Genetics 198:209–218. https://doi.org/10.1534/genetics.114.165480

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang G-L, Meyers BC, Jacobsen SE (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife 2:e00354. https://doi.org/10.7554/eLife.00354

Article  PubMed  PubMed Central  Google Scholar 

Suter L, Widmer A (2013) Environmental heat and salt stress induce transgenerational phenotypic changes in Arabidopsis thaliana. PLoS ONE 8:e60364. https://doi.org/10.1371/journal.pone.0060364

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tanurdžić M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 6:2880–2895. https://doi.org/10.1371/journal.pbio.0060302

Article  CAS  PubMed  Google Scholar 

Wibowo A, Becker C, Durr J, Price J, Spaepen S, Hilton S, Putra H, Papareddy R, Saintain Q, Harvey S, Bending GD, Schulze-Lefert P, Weigel D, Gutierrez-Marcos J (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci USA 115:E9145–E9152. https://doi.org/10.1073/pnas.1805371115

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wong G, Tan CC, Soh AC, Chong SP (1999) Clonal propagation of oil palm through tissue culture. Planter 75:221–230

Google Scholar 

Xu J, Tanino KK, Robinson SJ (2016) Stable epigenetic variants selected from an induced hypomethylated Fragaria vesca population. Front Plant Sci 7:1768. https://doi.org/10.3389/fpls.2016.01768

Article  PubMed  PubMed Central  Google Scholar 

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