Open Access Research article

High density SNP and SSR-based genetic maps of two independent oil palm hybrids

Ngoot-Chin Ting14, Johannes Jansen2, Sean Mayes3, Festo Massawe4, Ravigadevi Sambanthamurthi1, Leslie Cheng-Li Ooi1, Cheuk Weng Chin5, Xaviar Arulandoo6, Tzer-Ying Seng5, Sharifah Shahrul Rabiah Syed Alwee5, Maizura Ithnin1 and Rajinder Singh1*

Author Affiliations

1 Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia

2 Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, the Netherlands

3 Plant and Crop Sciences, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, Nottingham, UK

4 School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Nottingham, Malaysia

5 FELDA Agricultural Services Sdn. Bhd., 7th Floor, Balai Felda, Jalan Gurney 1, 54000 Kuala Lumpur, Malaysia

6 United Plantations Bhd., Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia

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BMC Genomics 2014, 15:309  doi:10.1186/1471-2164-15-309

Published: 27 April 2014



Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.


A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed.


The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.

Elaeis guineensis; E. oleifera; Interspecific; Intraspecific; Comparative mapping