Optimal number of reference genes required for accurate and reliable normalization of gene expression data from each set of tissue culture lines as determined by geNorm software.

<p>Calculation of pairwise variation, V_n/n+1 was performed between the two sequential normalization factors (NF_n and NF_n+1) of reference genes across the same panel of samples. A cutoff value of 0.15 was used to determine whether the inclusion of an additional reference gene has a significant effect on the pairwise variation values.</p

Determination of the most stably expressed reference genes across MA2 and MA8 tissue culture lines using geNorm software.

<p>Average expression stability values (<i>M</i>) were calculated for each reference gene. The least stable genes with higher <i>M</i> values were excluded in a stepwise manner until the two most stable reference genes were obtained for the tested tissue culture lines.</p

Candidate reference genes for evaluation across oil palm tissue culture samples.

<p>Candidate reference genes for evaluation across oil palm tissue culture samples.</p

Ranking of oil palm candidate reference genes according to coefficient of variance (CV) and standard deviation (SD) using BestKeeper analysis.

<p>Ranking of oil palm candidate reference genes according to coefficient of variance (CV) and standard deviation (SD) using BestKeeper analysis.</p

Gene ontology classification of oil palm candidate reference genes at level 2 using Blast2GO.

<p>Gene ontology classification of oil palm candidate reference genes at level 2 using Blast2GO.</p

Mean Ct values of eight candidate reference genes across MA2 and MA8 tissue culture lines.

<p>The range of Ct values across the MA2 and MA8 tissue culture lines were exhibited in boxplot. Ct values of the candidate reference genes were widely distributed between 17 to 30 cycles. Lower and upper ends of the box represent 25th and 75 percentiles, respectively. Horizontal line inside the box is median. Whiskers below and above the box represent minimum and maximum values of the datasets, respectively. Asterisks represent the outliers.</p

Ranking of oil palm candidate reference genes using NormFinder analysis.

<p>Ranking of oil palm candidate reference genes using NormFinder analysis.</p

Expression profiling of PD00088 across oil palm leaf explants, callus and embryoids using RT-qPCR.

<p>Expression levels of PD00088 in leaf explants (W1, W3), callus and embryoids were normalized with PD000380, PD00569 or combination of both reference genes. Calculation of standard deviation on normalized gene expression level was done using geNorm v3.4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099774#pone.0099774-Vandesompele1" target="_blank">[19]</a>. The error bars represent ± standard deviation (SD).</p

PCR amplification efficiencies (Ex) and correlation coefficient (<i>R</i>²) values of oil palm candidate reference genes.

<p>PCR amplification efficiencies (Ex) and correlation coefficient (<i>R</i>²) values of oil palm candidate reference genes.</p

Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

<div><p>Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, <i>Arabidopsis thaliana</i>. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.</p></div