Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
R&D Department, Wilmar International Plantation, Palembang, 30118, Indonesia.
Sci Rep. 2018 Jan 12;8(1):691. doi: 10.1038/s41598-017-18613-2.
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees. Mining this dataset detected 510,251 loci. After filtering out loci with low accuracy and more than 20% missing data, 11,394 SNPs were retained. Using these SNPs, in combination with 188 anchor SNPs and 123 microsatellites, we constructed a linkage map containing 10,023 markers covering 16 chromosomes. The map length is 2,938.2 cM with an average marker space of 0.29 cM. The large number of SNPs will supply ample choices of DNA markers in analysing the genetic diversity, population structure and evolution of oil palm. This high-density linkage map will contribute to mapping quantitative trait loci (QTL) for important traits, thus accelerating oil palm genetic improvement.
油棕（Elaeis guineensis Jacq.）是全球主要的产油作物和最重要的食用油资源。DNA 标记和遗传连锁图谱是进行标记辅助选择以加速遗传改良的重要资源。我们使用 Illumina NextSeq500 进行 RAD-seq 以发现全基因组 SNPs，并使用这些 SNPs 构建了一个来自 Deli Dura 和 AVROS Pisifera 杂交的油棕（Tenera）群体的连锁图谱。RAD-seq 在包含 155 棵树的育种群体中产生了 10.76 亿个单端读数。挖掘此数据集检测到 510,251 个基因座。过滤掉准确性低和超过 20%缺失数据的基因座后，保留了 11,394 个 SNP。使用这些 SNP，结合 188 个锚定 SNP 和 123 个微卫星，我们构建了一个包含 10,023 个标记的连锁图谱，覆盖了 16 条染色体。图谱长度为 2938.2 cM，平均标记间距为 0.29 cM。大量的 SNP 将为分析油棕的遗传多样性、种群结构和进化提供充足的 DNA 标记选择。该高密度连锁图谱将有助于对重要性状的数量性状基因座（QTL）进行定位，从而加速油棕的遗传改良。
