Ong Ai-Ling, Teh Chee-Keng, Mayes Sean, Massawe Festo, Appleton David Ross, Kulaveerasingam Harikrishna
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Serdang 43400, Selangor Darul Ehsan, Malaysia.
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK.
Plants (Basel). 2020 Nov 3;9(11):1476. doi: 10.3390/plants9111476.
Oil palm ( Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species-date palm ( L.) and coconut palm ( L.)-confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of , which consists of 107 species belonging to
油棕（Jacq.）是经济上重要的棕榈物种中交易最多的作物。在此，我们报告了一个长度为1.2 Gb的扩展版本基因组，物理基因组覆盖率从之前的43%提高到了79%。这一提升是通过将另外1968个原本未定位的可公开获得的支架整合到物理基因组中实现的。通过整合三个超密集连锁图谱并利用它们来定位基因组支架，16条假分子得到了扩展。如我们所示，改进后的基因组提高了全基因组关联研究（GWAS）的定位分辨率，并允许进一步鉴定候选基因/蛋白质编码区域（CDS）以及可能与之相关的任何非编码RNA以便进行进一步研究。然后，我们在一项比较基因组学研究中使用新的物理图谱与另外两种在农业和经济上重要的棕榈物种——枣椰树（L.）和椰子树（L.）进行比较，证实了这些棕榈物种之间高度保守的共线性。我们还使用改进后的油棕基因组组装版本作为棕榈基因组参考来扩展枣椰树的物理图谱。油棕改进后的基因组将使分子育种方法能够加速作物改良，特别是在由107个物种组成的最大亚科中。
