Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Jingjing Jin, May Lee, Bin Bai, Yanwei Sun, Jing Qu, Rahmadsyah, Yuzer Alfiko, Chin Huat Lim, Antonius Suwanto, Maria Sugiharti, Limsoon Wong, Jian Ye (+2 others)
2016 DNA Research  
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
more » ... nal 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.
doi:10.1093/dnares/dsw036 pmid:27426468 pmcid:PMC5144676 fatcat:xcguwnikdfhcvoddn5qyeri334