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

Additional files

Additional file 1:

Alignment of oil palm genetic maps developed for intraspecific (P2) and interspecific (OxG) crosses using common markers. The P2 bi-parental integrated (DP), dura parental (D) and pisifera parental (P) maps are shown on the left and OxG bi-parental integrated (OT), E. oleifera parental (O) and tenera parental (T) maps on the right. The integrated map of P2 and OxG is shown at the centre, labeled DPxOT/T. Haldane genetic distance (cM) is indicated by the ruler on the left of the map. Common markers that co-mapped across D, P, DP, DPxOT/T and T are indicated in red. Nomenclature for markers is: SNPM (SNP), mEgCIR (genomic SSR from [8,23], sEg (E. guineensis EST-SSR), sMg (E. guineensis genomic-SSR), sMo (E. oleifera genomic-SSR), sPSc (SSR developed from E. guineensis scaffold data). Markers showing distorted segregation are marked by *representing significance, viz.,*p < 0.1,**p < 0.05,***p < 0.01,****p < 0.005,*****p < 0.001 and ******p < 0.0005.

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Open Data

Additional file 2:

Information on P2 (D, P and DP) and OxG (O, T and OT) genetic maps as well as the cross-population integrated map (DPxOT/T).

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Open Data

Additional file 3:

A closer view of comparative linkage groups (LGs) of dura (D), pisifera (P), E. oleifera (O) and tenera (T) plotted with Circos [[60]]. LGs 1 – 16 are scaled in Haldane genetic distance (cM) and represented by different color coded lines.

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Additional file 4:

Comparative linkage groups (LGs) between the current maps and previously published oil palm maps. The P2 integrated map (DP) and OxG integrated map (OT/T) are aligned with maps developed by Billotte et al. [8], Singh et al. [9], Ting et al. [17] and Seng et al. [24] based on common RFLP and SSR markers.

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