Genome-wide SSR marker development in oil palm by Illumina HiSeq for parental selection

Next-generation sequencing is a new technique for plant genome sequencing at a large scale that is faster and cheaper than previous sequencing technologies. The present work reports the development of new polymorphic simple sequence repeat (SSR) markers in oil palm (Elaeis guineensis Jacq.) using Illumina HiSeq sequencing data. More than 39 Gb (total 39,086,646,904 bases) was generated from the selected oil palm clone, D4. After de novo assembly, a total of 130,840 potential SSRs were identified. For SSR validation, 144 out of 762 SSR primer pairs were designed, including tri-nucleotide motifs, from the D4 contigs. Using 11 lines from three different clones of oil palm, 61 SSR primers revealed polymorphic alleles and high average polymorphic information content (PIC) values. Cluster analysis separated all oil palm plants into three clusters: clones A, B and C. These identified genome-wide SSR markers will enrich current genomic resources of the oil palm crop.