NEIKER-Basque Institute for Agricultural Research and Development - Basque Research and Technology Alliance (BRTA). Campus Agroalimentario de Arkaute s/n, 01192, Arkaute, Spain.
Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia.
Sci Rep. 2020 Jun 19;10(1):9998. doi: 10.1038/s41598-020-67118-y.
A high-density genetic linkage map from a controlled cross of two oil palm (Elaeis guineensis) genotypes was constructed based on Single Primer Enrichment Technology (SPET) markers. A 5K panel of hybridization probes were used for this purpose which was derived from previously developed SNP primers in oil palm. Initially, 13,384 SNPs were detected which were reduced to 13,073 SNPs after filtering for only bi-allelic SNP. Around 75% of the markers were found to be monomorphic in the progeny, reducing the markers left for linkage mapping to 3,501. Using Lep-MAP3 software, a linkage map was constructed which contained initially 2,388 markers and had a total length of 1,370 cM. In many cases several adjacent SNP were located on the same locus, due to missing recombination events between them, leading to a total of 1,054 loci on the 16 LG. Nevertheless, the marker density of 1.74 markers per cM (0.57 cM/marker) should allow the detection of QTLs in the future. This study shows that cost efficient SPET markers are suitable for linkage map construction in oil palm and probably, also in other species.
基于单引物富集技术 (SPET) 标记,构建了来自两个油棕 (Elaeis guineensis) 基因型控制杂交的高密度遗传连锁图谱。为此,使用了源自先前在油棕中开发的 SNP 引物的 5K 杂交探针面板。最初检测到 13384 个 SNP,经过仅对双等位 SNP 的过滤,将其减少到 13073 个 SNP。大约 75%的标记在后代中表现为单态性,这将用于连锁映射的标记减少到 3501 个。使用 Lep-MAP3 软件,构建了一个连锁图谱,其中最初包含 2388 个标记,总长度为 1370cm。在许多情况下,由于它们之间缺少重组事件,几个相邻的 SNP 位于同一个基因座上,导致在 16 个 LG 上共有 1054 个基因座。然而,1.74 个标记/厘米的标记密度(0.57 厘米/标记)应该允许在未来检测到 QTL。本研究表明,具有成本效益的 SPET 标记适用于油棕的连锁图谱构建,也可能适用于其他物种。