The Genome Landscape Of Elaeis Guineensis: Development And Utility Of Chromosome-Specific Cytogenetic Markers

Identification of individual Elaeis guineensis (2n=32; Arecaceae) chromosomes facilitates further understanding of the genome as well as inheritance of specific agronomic traits in oil palm. While chromosome morphology shows a range of lengths and arm ratios, these do not identify most chromosomes; a tertiary-constriction was noted on the largest chromosome. Here, the first E. guineensis reference karyotype with a combination of physical FISH-mapping of repetitive DNA and single copy sequence (EgOligoFISH) was developed. The individual 16 pairs of E. guineensis chromosomes could be distinguished using probes from a combination of repetitive DNA (5S rDNA, 18S rDNA) and single copy DNA derived from massive pools of oligonucleotides. Analysis of repetitive DNA from raw Illumina sequence data revealed that, aside from the structural component of repetitive DNA (telomere and rDNAs) and abundance of transposable element superfamily (including copia-like Eg9CEN), no newly identified repetitive DNA could distinguish individual E. guineensis chromosomes. Exploration of various approaches in developing robust FISH-based chromosome-specific markers from single copy sequence resulted in three sets of massive oligonucleotide (oligo)-based probes (EgOligoFISH; OPAQUE, PPAQUE, and QPAQUE) that are able to identify 16 oil palm chromosomes via fluorescent in situ hybridisation (FISH). Simultaneous in situ hybridization of all three pre-labelled oligo-probes successfully identify about 2/3 of the oil palm chromosomes. The assessment of E. guineensis derived massive oligo-probes (EgOligoFISH) on other Arecaceae species was informative. A conserved physical localization of the EgOligoFISH on another Elaeis species; E. oleifera permits the first proposed E. oleifera FISH-karyotype established in this study. The integration of information obtained from in silico, as well as physical FISH-mapping of EgOligoFISH on E. oleifera mitotic chromosomes, successfully established E. oleifera standard karyotype for the first time. As intergeneric markers, the EgOligoFISH probes allowed comparison of chromosome organization in coconut (Cocos nucifera) and date palm (Pheonix dactylifera) chromosomes.