title: Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.
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.
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.|School of Computing, National University of Singapore, Singapore.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Jin
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
authors.forename: May
authors.initials: M
authors.lastname: Lee
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
authors.forename: Bin
authors.initials: B
authors.lastname: Bai
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.|State key laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yanwei
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
authors.forename: Jing
authors.initials: J
authors.lastname: Qu
authors.affiliation: R & D Department, Wilmar International Plantation, Palembang, Indonesia.
authors.lastname: Rahmadsyah
authors.affiliation: Biotech Lab, Wilmar International, Jakarta, Indonesia.
authors.forename: Yuzer
authors.initials: Y
authors.lastname: Alfiko
authors.affiliation: R & D Department, Wilmar International Plantation, Palembang, Indonesia.
authors.forename: Chin Huat
authors.initials: CH
authors.lastname: Lim
authors.affiliation: Biotech Lab, Wilmar International, Jakarta, Indonesia.
authors.forename: Antonius
authors.initials: A
authors.lastname: Suwanto
authors.affiliation: Biotech Lab, Wilmar International, Jakarta, Indonesia.
authors.forename: Maria
authors.initials: M
authors.lastname: Sugiharti
authors.affiliation: School of Computing, National University of Singapore, Singapore.
authors.forename: Limsoon
authors.initials: L
authors.lastname: Wong
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.|State key laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ye
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.|Laboratory of Plant Molecular Biology, The Rockefeller University, New York, USA.
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore jianye@im.ac.cn chua@mail.rockefeller.edu genhua@tll.org.sg.|Department of Biological Sciences, National University of Singapore, Singapore.|School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore.
authors.forename: Gen Hua
authors.initials: GH
authors.lastname: Yue
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D011110:Polymorphism, Genetic
keywords: SNP; breeding; genome; palm; sequencing