Analysis of gene expression by EST from SSH library in dwarf oil palm

Abstract

Six subtracted cDNA libraries were constructed from PS1 and AG1 oil palm breeding lines using Suppression Subtractive Hybridisation (SSH) method. Six putative clones identified to be associated in dwarfism encodes for brassinosteroid biosynthesis-like protein (DWF1), brassinosteroid insensitive 1-associated receptor kinase 1 precursor (BRI1), late elongated hypocotyl protein (LHY), gibberellin receptor (GID1), sterol 24-methyltransferase 1 (SMT1) and E3 ubiquitin-protein ligase (E3Ub) were analysed. These candidate dwarfing genes are involved in various stages of brassinosteroids (BR), gibberellins (GA) biosynthesis and signaling pathways for plants growth and development. The expression levels of candidate genes were validated by quantitative Real-time PCR (qRT-PCR) by two reference genes, manganese superoxide dismutase (PD569) and predicted protein IFH-1 like (EA1332). Higher expression level of BRI1, LHY and SMT1 genes were observed in dwarf palms compared to standard palms with normalised fold-difference of 2.3285, 1.5620 and 4.9044, respectively. Statistical analysis of all potential transcripts showed further evidence of SMT1 as a potential molecular marker for the screening of dwarf palm planting materials with highly significant expression levels in dwarf palms compared to standard palms; however, the expression levels of BRI and LHY genes were statistically insignificant.