Diversity in African oil palm by reduced representation genome sequencing

Single Nucleotide Polymorphism (SNP) markers were developed in oil palm using high throughput sequencing of reduced representation libraries in a set of progenies selected for contrasting phenotypes. Twenty four samples from 12 progenies (Dura X Pisifera) with contrasting bunch numbers (12 high and 12 average) were analyzed by sequencing of size selected insert libraries generated by restriction enzyme digestion. From each library approximately 14 million sequence reads were obtained (paired end, 100 bp). From the individual reads, fragment sequences were reconstructed by combining forward and reverse reads. These fragment sequences were then searched within each library and among the 24 libraries for similar sequences. Aligning the matching sequences revealed those derived from individual loci and allowed the identification of SNPs. A total of 161,400 bi-allelic loci (SNP pairs) and 57,833 loci with three alleles (triplets) were retained.