Oil palm (Elaeis guineensis) is the most economically important plantation crop in Malaysia. It is a diploid (2n=32), outcrossing species with a genome size of 1800 Mb. As a perennial crop, oil palm has a long breeding cycle of about 10 years. Hence, construction of a genetic linkage map is of great value in oil palm breeding and improvement programmes. A mapping population consisting of 60 individuals derived from a cross between Ulu Remis Deli dura (female parent) and Nigerian pisifera (male parent) was used in this study. A total of 27,117 SNPs were obtained through genotyping-by-sequencing. The physical positions of these SNPs were distributed across the scaffolds of the oil palm Pisifera 8 (P8) reference genome build. The number of SNPs were reduced to 15,419 after removal of SNPs with more than 10% missing data. Further filtering based on non-informative markers resulted in the identification of 1,203 high quality SNPs, which were then used in the construction of a genetic linkage map. The linkage map was constructed using maximum likehood (ML) mapping algorithm in the JoinMap 4.1 software. The consensus map contained 589 SNPs markers and were mapped into 16 linkage groups. The length of the individual linkage groups ranged from 11.6 to 135.0 cM. The total length of the map was 1776.5 cM with an average marker density of 3.0 cM and 7 to 50 markers per linkage group. Linkage position of these SNPs on the consensus map represents a good estimation in most cases with their physical position on the P8 scaffolds and EG8 pseudomolecules. Genetic linkage map constructed in this study is useful for identifying QTLs and candidate genes associated with important agronomic traits.
