Tree Genetics & Genomes

, 13:103 | Cite as

Multiple locus genome-wide association studies for important economic traits of oil palm

  • Maizura Ithnin
  • Yang Xu
  • Marhalil Marjuni
  • Norhalida Mohamed Serdari
  • Mohd Din Amiruddin
  • Eng-Ti Leslie Low
  • Yung-Chie Tan
  • Soon-Joo Yap
  • Leslie Cheng Li Ooi
  • Rajanaidu Nookiah
  • Rajinder Singh
  • Shizhong Xu
Original Article
Part of the following topical collections:
  1. Complex Traits


Palm oil has a balanced fatty acid composition and has no trans fat. As a result, its use in food has increased as food-labeling laws have changed to specify trans fat content. Increasing oil production is the main goal in oil palm breeding. Genetic mapping and genomic studies in palm trees are necessary to understand the genetic architecture of economic traits of importance for palm oil production. To help achieve this, we sampled 422 oil palms from MPOB (Malaysian Palm Oil Board)­Angola germplasm collection and measured 13 economic traits from these palms. Multi-locus genome-wide association studies (GWAS) were conducted using least absolute shrinkage and selection operator (LASSO) and genome-wide efficient mixed model analysis. We identified 19 quantitative trait loci (QTLs) for 8 traits. Of these, four Angola-specific QTLs associated with bunch components were detected on chromosomes 4, 8, and 11. These QTLs are potentially useful for introgression of desirable genes from the Angola palms to advanced breeding populations for improvement of bunch and oil yield traits. The majority of the QTLs were detected by LASSO-A, in which the p values of individual markers were calculated based on bootstrapped standard errors. Many of the detected QTLs are nearby known QTLs detected from linkage studies reported by other research groups. We also conducted genomic selection (GS) for the 13 traits and concluded that GS can be an effective tool for oil palm breeding. This is the first GWAS and GS study conducted on oil palm germplasm from Angola, and the results can be very useful in oil palm genetic studies and breeding.


BLUP Bootstrap sampling GWAS LASSO Mixed model Oil palm 



We acknowledge the Director General of MPOB for permission to publish the research findings. We thank the Breeding group for maintaining the Angola germplasm.

Funding information

We also acknowledge MPOB’s support through the DNA Chip Program (R000999000-RB01-J) in funding the SNP genotyping and bioinformatics efforts. The project was also supported by the US National Science Foundation Collaborative Research Grant 473 DBI-1458515 to SX.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Data archiving statement

All data are available at figshare (

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Maizura Ithnin
    • 1
  • Yang Xu
    • 2
  • Marhalil Marjuni
    • 1
  • Norhalida Mohamed Serdari
    • 1
  • Mohd Din Amiruddin
    • 1
  • Eng-Ti Leslie Low
    • 1
  • Yung-Chie Tan
    • 3
  • Soon-Joo Yap
    • 3
  • Leslie Cheng Li Ooi
    • 1
  • Rajanaidu Nookiah
    • 1
  • Rajinder Singh
    • 1
  • Shizhong Xu
    • 2
  1. 1.Advanced Biotechnology and Breeding CentreMalaysian Palm Oil Board (MPOB)Kuala LumpurMalaysia
  2. 2.Department of Botany and Plant SciencesUniversity of CaliforniaRiversideUSA
  3. 3.Department of Science and TechnologyCodon Genomics S/BSeri KembanganMalaysia

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