Correlation between DNA methylation and expression of the MADS-box genes on mantled fruit of oil palm (Elaeis guineensis Jacq.) clonal plants.

Abstract

The presence of abnormal mantled fruit on large scale clonal production of oil palm had trully affected the oil productivity. Mantled phenotype is likely to be that of an epigenetic change involving DNA methylation and the MADS-box transcription factor genes which encoded floral organ homeotic transformation. We developed an Ultra Performance Liquid Chromatography (UPLC) to quantify the degree of methylation related to fruit abnormality and Quantitative Real-Time PCR (qPCR) to know the correlation between the expression of the MADS-box genes with mantled fruit abnormality. This study were consist of two experiments, the DNA methylation analysis and the MADS-box genes expression analysis. Materials used in this study were the young fruit of both normal and mantled with very heavy type of abnormality. Abnormal mantled fruit were grouped into two types, one is taken from inside (Abn m) and other is from outside the bunch (Abn). In gene expression analysis, cDNA used as the template for qPCR were obtained from the reverse transcription of the mRNA, while methylation analysis performed on total DNA genomic. The research for each gene and cDNA were conducted in two replications. The expression of the target genes were compared to EF1-α1 as the reference gene. Based on qPCR efficiency by comparing the target genes with the reference gene, from 11 genes that have been tested, i.e EgSQUA1, EgSQUA3, EgFUL, EgGLO1, EgGLO2, EgDEF1, EgAG2, EgAGA, EgAGL6, EgF-box and EgRING, only three genes are qualified for qPCR analysis, i.e EgAG2, EgAGA and EgAGL6. EgAG2 expression was not different in both mantled and normal fruit, while EgAGA expression was higher in mantled and EgAGL6 expression was significantly lower in outside-bunched mantled fruit (Abn). Nuclease S1 digestion and UPLC revealed the genome-wide increasing in DNA methylation on mantled fruit (18.33-19.55%) compared to its normal counterparts (5.67%). This increased in global DNA methylation showed by the significant decreased in EgAGL6 transcript level on mantled fruit. This gene is assumed to be involved in the development of mantled fruit.