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DNA research : an international journal for rapid publication of reports on genes and genomes
Dec, 2016;23 (6): 527-533.

Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

Jingjing Jin, May Lee, Bin Bai, Yanwei Sun, Jing Qu, Yuzer Alfiko, Chin Huat Lim, Antonius Suwanto, Maria Sugiharti, Limsoon Wong, Jian Ye, Nam-Hai Chua, Gen Hua Yue
Author Information
  1. Jingjing Jin: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
  2. May Lee: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
  3. Bin Bai: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
  4. Yanwei Sun: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
  5. Jing Qu: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
  6. Rahmadsyah: R & D Department, Wilmar International Plantation, Palembang, Indonesia.
  7. Yuzer Alfiko: Biotech Lab, Wilmar International, Jakarta, Indonesia.
  8. Chin Huat Lim: R & D Department, Wilmar International Plantation, Palembang, Indonesia.
  9. Antonius Suwanto: Biotech Lab, Wilmar International, Jakarta, Indonesia.
  10. Maria Sugiharti: Biotech Lab, Wilmar International, Jakarta, Indonesia.
  11. Limsoon Wong: School of Computing, National University of Singapore, Singapore.
  12. Jian Ye: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.
  13. Nam-Hai Chua: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.
  14. Gen Hua Yue: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.
PMID: 27426468 DOI: 10.1093/dnares/dsw036

Abstract

Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.

Keywords

SNP breeding genome palm sequencing

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MeSH Term

Arecaceae
Genome, Plant
Linkage Disequilibrium
Polymorphism, Genetic
Journal Article

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