Journal of Oil Palm Research Vol. 25  2013 August p.  180-187

Exploiting synteny between oil palm and rice to find markers more closely linked to selected trait

Author(s): JAYANTHI, N.* ; ROZANA, R.* ; TING, N.C.* ; LESLIE OOI, C.L.* ; LOW, E.T.L.* ; RAJINDER Singh*

The African oil palm (Elaeis guineensis) and rice (Oryza sativa) are important economic crops. The rice genome has been more extensively characterised and studied compared to oil palm. GBrowse, a bioinformatics tool for visualising genomic and other sequences along a reference genome was applied in this study. Herein, we report the use of model organism Oryza sativa as a reference genome to map 75 463 genomic E. guineensis sequences. A subset of 328 oil palm sequences that aligned well to the 12 rice chromosomes was shortlisted for further analysis. Of these 328 genomic sequences, 261 contained microsatellite motifs and were apt for primer design. A total of 208 Simple Sequence Repeats (SSR) were selected to screen for polymorphism in a subset of palms from a selfed Nigerian tenera mapping population (T128), whereby, 67 SSR were found to be polymorphic. Thirty-eight of the polymorphic markers were mapped onto the genetic map. In comparison to the 12 rice chromosomes, six SSR from the oil palm linkage group 1 (LG1), containing the shell gene (SH) locus were identified on chromosomes 2 and 5 of rice. The order of these six SSR on linkage group 1 was mostly similar to that in chromosomes 2 and 5 of rice. The study provided evidence on synteny between oil palm and rice and facilitated the mapping of a marker closer to SH locus.

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Author Information
* Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia

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