Construction of a high density linkage map in Oil Palm using SPET markers

A high-density genetic linkage map from a controlled cross of two oil palm (Elaeis guineensis) genotypes was constructed based on Single Primer Enrichment Technology (SPET) markers. A 5K panel of hybridization probes were used for this purpose which was derived from previously developed SNP primers in oil palm. Initially, 13,384 SNPs were detected which were reduced to 13,073 SNPs after filtering for only bi-allelic SNP. Around 75% of the markers were found to be monomorphic in the progeny, reducing the markers left for linkage mapping to 3,501. Using Lep-MAP3 software, a linkage map was constructed which contained initially 2,388 markers and had a total length of 1,370 cM. In many cases several adjacent SNP were located on the same locus, due to missing recombination events between them, leading to a total of 1,054 loci on the 16 LG. Nevertheless, the marker density of 1.74 markers per cM (0.57 cM/marker) should allow the detection of QTLs in the future. This study shows that cost efficient SPET markers are suitable for linkage map construction in oil palm and probably, also in other species.