Genomic Characterization of E. oleifera Polymorphic Sites Based on Physical Mapping to the E. guineensis Genome

In this study we’ve aimed at discovering and characterizing molecular markers (MM) for Elaeis oleifera. To sample the genetic diversity of the species, we collected 552 leaf samples from 206 unique accessions. DNA was extracted and sent to DArT-Pty for DArTSeq development. More than 2 million reads per genotype was obtained and used to search for polymorphic sites including PAVs and SNPs. Marker characterization was performed based on physical mapping of the sequences to the public available E. guineensis reference genome (RG). Sequences were trimmed using FASTX-toolkit/FASTQC, and aligned to the RG using BWA-MEM. Variant calls were performed using SAMTools. Marker distribution, and co-localization with predicted gene models (PGM) was analyzed by dividing the RG into 130 5Mb intervals. We discovered a total of 17.412 PAVs and 2.370 SNPs with unique hits to the RG. The average number of PAVs/SNPs per chromosome was 1.088 and 148, respectively. Marker distribution however was quite uneven, with varying number of markers per interval. The number of PAVs/SNPs per interval varied between 33 and 352, 1 and 46, respectively. The average number of PAVs/SNPs and PMG per interval was 134, 18 and 267, respectively, demonstrating relatively good sampling/coverage of gene-enriched regions of the genome. The mean physical distance between adjacent PAVs is 38.7 kb while the mean physical distance between adjacent SNPs is 280.9 kb. The detailed information of the E. oleifera polymorphic sites provided here, is expected to help the designing of probes for target-enrichment and to select MM sets to be used for downstream applications such as genomic selection and association mapping.