Tree Genetics & Genomes

, 14:31 | Cite as

Mapping QTL for leaf area in oil palm using genotyping by sequencing

  • Bin Bai
  • Ying Jun Zhang
  • Le Wang
  • May Lee
  • Rahmadsyah
  • Bao Qing Ye
  • Yuzer Alfiko
  • Sigit Purwantomo
  • Antonius Suwanto
  • Gen Hua Yue
Original Article
Part of the following topical collections:
  1. Complex Traits


Leaf area is an important parameter in oil palm breeding as it is positively correlated with oil yield. However, measurement of leaf area is tedious and also destructive. In the present study, a breeding population with 145 palms derived from a cross between Deli Dura and Avros Pisifera was used to construct a high-density linkage map and identify quantitative trait loci (QTL) for leaf area in oil palm. Using genotyping by sequencing, a linkage map containing 2413 SNPs was constructed. The total length of the linkage map was 1161.89 cM, with an average marker spacing of 0.48 cM. Based on the continuous phenotyping of leaf area from 2010 to 2015, two suggestive QTL for leaf area were mapped on chromosomes (Chr) 3 and 9. The allelic effects of the QTL associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method. The QTL on Chr 9 explained 13.3% of phenotypic variation for leaf area. A candidate gene, ARC5, within the narrow interval of QTL on Chr 9 was identified. The gene was significantly higher expressed in leaf than root and fruit of oil palm. This high-quality and SNP-based map supplies a base to fine map QTL for agronomic traits in oil palm, and the markers closely linked to the stable QTL may be used in marker-assisted selection in oil palm breeding.


Oil palm SNP RAD-seq QTL mapping Leaf area 



This research has been financially supported by Wilmar International and the internal fund of the Temasek Life Sciences Laboratory, Singapore. We thank staff members of the R&D Department of Wilmar International Plantation for technical support.

Authors’ contributions

GHY designed and supervised this study. BB performed SNP development, linkage map construction, and drafted the manuscript. YJZ assisted with DNA extraction, data analysis and gene expression study. LW conducted in RAD-seq data analysis and SNP calling. ML prepared DNA samples and carried out genotyping using microchip. BQY edited the paper. Rahmadsyah, CHL, YA, SP and AS managed the plants and recorded the traits in the field. GHY finalized the manuscript, and all authors read and approved the final manuscript.

Compliance with ethical standards

Competing interests

The authors BB, YJZ, LW, ML, BQY, and GHY declare no competing financial interests. But the authors R, YA, SP and AS have financial competing interests due to they are employees of Wilmar International and Wilmar International funded this study.

Data archiving statement

The RAD-seq datasets supporting the conclusions of this article are available in the DDBJ database, accession number (BioProject Accession: PRJDB5817). Other data related to this paper are available in Supplementary Materials, Additional Tables S1, S2 and S3, as well as Additional Fig. S1.

Supplementary material

11295_2018_1245_MOESM1_ESM.xlsx (283 kb)
Additional Table S1 All the RAD-seq markers and micro-chip array markers used in this study, with flanking sequences, linkage map and physical position. (XLSX 282 kb)
11295_2018_1245_MOESM2_ESM.docx (13 kb)
Additional Table S2 Descriptive statistics of leaf area in the mapping population of Deli Dura × Avros Pisifera (DOCX 13 kb)
11295_2018_1245_MOESM3_ESM.docx (15 kb)
Additional Table S3 Summary of annotated genes within QTL region on Chr 9 for leaf area in oil palm genome (DOCX 14 kb)
11295_2018_1245_MOESM4_ESM.jpg (38 kb)
Additional Figure S1 Distribution of leaf area value (average across four periods) in the mapping population of Deli Dura × Avros Pisifera (JPEG 38 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingaporeSingapore
  2. 2.Wheat Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
  3. 3.Institute of Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
  4. 4.R & D DepartmentWilmar International PlantationPalembangIndonesia
  5. 5.Biotech LabWilmar InternationalJakartaIndonesia
  6. 6.Bogor Agricultural UniversityBogorIndonesia
  7. 7.Department of Biological SciencesNational University of SingaporeSingaporeSingapore
  8. 8.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore

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