Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling

• Published in: Plant molecular biology Vol. 111; no. 4-5; pp. 345 - 363
• Main Authors: Ooi, Siew-Eng, Sarpan, Norashikin, Taranenko, Elizaveta, Feshah, Ishak, Nuraziyan, Azimi, Roowi, Siti Habsah, Burhan, Muhammad Nazmi, Jayanthi, Nagappan, Rahmah, Abdul Rahman Siti, Teh, Ooi-Kock, Ong-Abdullah, Meilina, Tatarinova, Tatiana V.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.03.2023; Springer; Springer Nature B.V
• Subjects: Analysis; Arecaceae - genetics; Biochemistry; Biomedical and Life Sciences; Clone Cells - metabolism; Cloning; DNA Methylation; Elaeis guineensis; Female; Genetic aspects; Humans; Life Sciences; Methylation; Mothers; mRNA; Phenotypes; Plant Pathology; Plant Sciences; RNA; RNA, Messenger - metabolism; Somaclonal variation; DNA methylation; sRNA cluster; Transposable element; Ortet; Karma-EgDEF1
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-022-01330-4

The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3′end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation. Key message Small RNA clusters derived from lncRNAs were differentially expressed in high mantling ortets, and hypomethylation of the 3′-end of Karma-EgDEF1 corresponded to previously identified hypomethylated regions in mantled clones.