Analysis of Organelle SSRs in Hypomethylated Regions of the Oil Palm Genome and Identification of Informative Chloroplast SSRs

The Malaysian Palm Oil Board (MPOB) successfully generated over 400,000 genomic sequences from four oil palm samples (dura, tenera, pisifera and oleifera) through the sequencing of hypomethylated genespace of the oil palm genome using the GeneThresher™ technology. This preferentially selected regions of the genome that encode genes and their regulatory regions. The sequences represent approximately 95% of the functional genes in oil palm. A small percentage of organelle genome was detected in the hypomethylated sequences. As such, analysis was performed to identify the SSRs in the chloroplast and mitochondria sequences. Our analysis revealed 42 SSRs, of which, 13 SSRs were identified as chloroplast, 13 as mitochondrial and 16 common in both the chloroplast and mitochondria. We report here our efforts in exploiting the chloroplast SSRs (cpSSRs). A total of 11 pairs of SSR primers were designed and confirmed as chloroplast via amplicon sequencing. The cpSSR primers are being tested on African oil palm germplasm materials.