High-throughput and high-density (HD) genetic marker genotyping systems are critical to optimize the efficiency of oil palm breeding and improvement programmes. This study reports the development of the 78 K Infinium® HD customized SNP array, which was used to genotype a thousand palms of a commercial Deli dura x AVROS pisifera family. A total 64,108 (∼82.0%) polymorphic SNP markers were identified of which, 57, 465 (89.6%) were mapped onto the genetic map that has the largest number of markers published so far in oil palm and holds 14,781 SNPs on 2,363 orphan scaffolds (whose chromosomal locations were unknown), which will improve the existing oil palm reference genome (EG5.1). The SNPs were highly informative based on the parent-to-progeny allelic inheritance analysis. The data demonstrated that 4.3% of the progeny resulted from unintentional self-fertilization of the dura female parent. These unintended ‘selfs’ are highly inbred, which will affect their yield. This study also for the first time, describes the homozygosity in the Deli dura and AVROS pisifera, two important parental lines widely used in commercial seed production. As expected, both the parental palms were highly homozygous, having 138 Mb homozygous regions in common, with 70.3% identical alleles. Such a detailed genetic analysis of the individual palm has been made possible with this customized HD SNP array, which will be a valuable tool for routine application in oil palm improvement programmes. The strategy used to design and apply the array will also be of interest for wider scientific research.

高通量和高密度 (HD) 遗传标记基因分型系统对于优化油棕育种和改良计划的效率至关重要。本研究报告了 78 K Infinium ® HD 定制 SNP 阵列的开发，该阵列用于对商业 Deli dura x AVROS pisifera的一千个手掌进行基因分型家庭。共鉴定出 64,108 个（~82.0%）多态性 SNP 标记，其中 57 个、465 个（89.6%）被映射到遗传图谱上，该遗传图谱迄今为止在油棕中发表的标记数量最多，并且在 2,363 个孤儿支架上拥有 14,781 个 SNP （其染色体位置未知），这将改进现有的油棕参考基因组（EG5.1）。基于亲代到子代等位基因遗传分析，SNPs 具有很高的信息量。数据表明，4.3% 的后代是由硬脑膜母本的无意自花受精造成的。这些意外的“自我”是高度近交的，这将影响它们的产量。这项研究也是第一次，描述了 Deli dura和 AVROS pisifera中的纯合性，广泛用于商业种子生产的两个重要亲本系。正如预期的那样，两个亲本手掌都是高度纯合的，共有 138 Mb 纯合区域，具有 70.3% 相同的等位基因。这种定制的 HD SNP 阵列使得对单个棕榈树进行如此详细的遗传分析成为可能，这将成为油棕改良计划中常规应用的宝贵工具。用于设计和应用阵列的策略也将引起更广泛科学研究的兴趣。