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Development and validation of a high-density SNP genotyping array for African Oil Palm

Kwong, Qi Bin; Teh, Chee Keng; Ong, Ai Ling; Heng, Huey Ying; Lee, Heng Leng; Mohamed, Mohaimi; Low, Joel Zi-Bin; Apparow, Sukganah; Chew, Fook Tim; Mayes, Sean; Kulaveerasingam, Harikrishna; Tammi, Martti; Appleton, David Ross

Development and validation of a high-density SNP genotyping array for African Oil Palm Thumbnail


Qi Bin Kwong

Chee Keng Teh

Ai Ling Ong

Huey Ying Heng

Heng Leng Lee

Mohaimi Mohamed

Joel Zi-Bin Low

Sukganah Apparow

Fook Tim Chew

Associate Professor

Harikrishna Kulaveerasingam

Martti Tammi

David Ross Appleton


High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50) when compared with the semi-wild populations (19.5 kb at r2 = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F%variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.

Journal Article Type Article
Acceptance Date Apr 17, 2016
Online Publication Date Apr 22, 2016
Publication Date Aug 1, 2016
Deposit Date Sep 4, 2017
Publicly Available Date Sep 4, 2017
Journal Molecular Plant
Print ISSN 1674-2052
Electronic ISSN 1752-9867
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 9
Issue 8
Keywords oil palm, whole-genome SNP array, genome-wide association study, genomic selection, genetic fixation,
genome-wide linkage disequilibrium
Public URL
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