Institut Génétique et Développement (UMR 6061) CNRS/Université de Rennes 1, Rennes, France.
BMC Genomics. 2012 Jun 6;13:222. doi: 10.1186/1471-2164-13-222.
The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited.
We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR(3500) and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish.
The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
尼罗罗非鱼（Oreochromis niloticus）是全球养殖量第二大的鱼类。它也是鱼类生理学研究的重要模式生物，尤其是因为它对各种环境有广泛的耐受性。由于它与东非快速物种形成的haplochromine 慈鲷有密切的关系，所以它是研究脊椎动物进化机制的良好模型。尼罗罗非鱼现有的基因组资源包括遗传图谱、BAC 末端序列和 ESTs，但比较基因组分析和数量性状基因座（QTL）图谱仍然有限。
我们构建了尼罗罗非鱼的高分辨率辐射杂种（RH）图谱，并对由 850 个基因、82 个 BAC 末端序列标记、154 个微卫星和 272 个单核苷酸多态性（SNP）组成的 1358 个标记进行了基因分型。其中，1296 个标记可在 81 个 RH 群中关联，而 62 个标记不连锁。RH 图谱的总大小为 34084 cR(3500)和 937310kb。它覆盖了整个基因组的 88%，估计标记间距离为 742 Kb。微卫星的图谱构建使图谱能够与遗传图谱整合。我们将 LG8 和 LG24 合并成一个连锁群，并证实 LG16-LG21 也合并在一起。通过对 55 个 BAC 的染色体原位杂交（FISH），证实了 RH 群与每条染色体和 LG 的定向和关联。50 个 RH 群被定位在 22 条染色体上，而 31 个仍然是小的孤立群。尼罗罗非鱼、刺鱼、青鳉和河豚之间的同线性关系已经确定。
RH 图谱和相关的 FISH 图谱为基因定位和 QTL 研究提供了宝贵的基因排序资源。所有具有相应 RH 群的遗传连锁群现在都有一个相应的染色体，可以在核型中识别。保守片段的定位表明，尼罗罗非鱼和其他模式鱼类之间发生了多次染色体间重排。这些图谱为组织即将到来的尼罗罗非鱼基因组序列提供了有价值的资源，并为东非慈鲷鱼类的进化研究奠定了基础。
