Zoologisches Institut, Evolutionsbiologie, Universität Basel, Vesalgasse 1, 4051 Basel, Switzerland.
BMC Genomics. 2010 Sep 22;11:508. doi: 10.1186/1471-2164-11-508.
Daphnia magna is a well-established model species in ecotoxicology, ecology and evolution. Several new genomics tools are presently under development for this species; among them, a linkage map is a first requirement for estimating the genetic background of phenotypic traits in quantitative trait loci (QTL) studies and is also very useful in assembling the genome. It also enables comparative studies between D. magna and D. pulex, for which a linkage map already exists.
Here we describe the first genetic linkage map of D. magna. We generated 214 F2 (intercross) clonal lines as the foundation of the linkage analysis. The linkage map itself is based on 109 microsatellite markers, which produced ten major linkage groups ranging in size from 31.1 cM to 288.5 cM. The total size of this linkage map extends to 1211.6 Kosambi cM, and the average interval for the markers within linkage groups is 15.1 cM. The F2 clones can be used to map QTLs for traits that differ between the parental clones. We successfully mapped the location of two loci with infertility alleles, one inherited from the paternal clone (Iinb1) and the other from the maternal clone (Xinb3).
The D. magna linkage map presented here provides extensive coverage of the genome and a given density of markers that enable us to detect QTLs of moderate to strong effects. It is similar in size to the linkage map of D. pulex.
大型溞是生态毒理学、生态学和进化领域中一种成熟的模式物种。目前正在为该物种开发几种新的基因组学工具；其中，连锁图谱是估计数量性状基因座（QTL）研究中表型性状遗传背景的首要要求，对于组装基因组也非常有用。它还使大型溞和 D. pulex 之间的比较研究成为可能，后者已经存在连锁图谱。
本文描述了大型溞的第一张遗传连锁图谱。我们生成了 214 个 F2（杂交）克隆系作为连锁分析的基础。连锁图谱本身基于 109 个微卫星标记，产生了十个主要的连锁群，大小从 31.1 cM 到 288.5 cM。该连锁图谱的总大小扩展到 1211.6 Kosambi cM，连锁群内标记的平均间隔为 15.1 cM。这些 F2 克隆可用于绘制来自亲本品系的不同特征的 QTL 图谱。我们成功地定位了两个具有不育等位基因的位点，一个来自父系克隆（Iinb1），另一个来自母系克隆（Xinb3）。
本文提供的大型溞连锁图谱覆盖了基因组的大部分区域，并且标记密度较高，能够检测到中等至强效应的 QTL。它的大小与 D. pulex 的连锁图谱相似。
