Abstract
Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.
Highlights
Elaeis oleifera is a species in the oil palm genus along with the commercial Elaeis guineensis and occurs naturally in South-Central America, from Honduras to Colombia and in the Amazon region [1]
The GeneThresherTM library is a comprehensive collection of gene sequences of oil palm obtained from sequencing of the hypomethylated region of the oil palm genome using methylation filtration technology [17]
The clear advantage is that the simple sequence repeat (SSR) locus may point to a gene of interest and show high levels of polymorphism associated with being genomic-based SSR markers
Summary
Elaeis oleifera is a species in the oil palm genus along with the commercial Elaeis guineensis and occurs naturally in South-Central America, from Honduras to Colombia and in the Amazon region [1] This American species is seen as a promising genetic resource for oil palm improvement and is currently used in oil palm hybrid (E. guineensis × E. oleifera) breeding programs. Among all the available molecular markers, simple sequence repeats (SSR) are still among the most favored, due to their many desirable attributes, which include hypervariability, wide genomic distribution, co-dominant inheritance, a multi-allelic nature and chromosome specific location. They are assayed using PCR [6]. E. guineensis-based SSR markers have been used to construct genetic maps [8,9], and are actively used to characterize germplasm collections [1]
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