Dor Lior, Shirak Andrey, Gorshkov Sergei, Band Mark R, Korol Abraham, Ronin Yefim, Curzon Arie, Hulata Gideon, Seroussi Eyal, Ron Micha
Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel.
Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel.
G3 (Bethesda). 2014 Jun 5;4(8):1455-64. doi: 10.1534/g3.114.011387.
The white grouper (Epinephelus aeneus) is a promising candidate for domestication and aquaculture due to its fast growth, excellent taste, and high market price. A linkage map is an essential framework for mapping quantitative trait loci for economic traits and the study of genome evolution. DNA of a single individual was deep-sequenced, and microsatellite markers were identified in 177 of the largest scaffolds of the sequence assembly. The success rate of developing polymorphic homologous markers was 94.9% compared with 63.1% of heterologous markers from other grouper species. Of the 12 adult mature fish present in the broodstock tank, two males and two females were identified as parents of the assigned offspring by parenthood analysis using 34 heterologous markers. A single full-sib family of 48 individuals was established for the construction of first-generation linkage maps based on genotyping data of 222 microsatellites. The markers were assigned to 24 linkage groups in accordance to the 24 chromosomal pairs. The female and male maps consisting of 203 and 202 markers spanned 1053 and 886 cM, with an average intermarker distance of 5.8 and 5.0 cM, respectively. Mapping of markers to linkage groups ends was enriched by using markers originating from scaffolds harboring telomeric repeat-containing RNA. Comparative mapping showed high synteny relationships among the white grouper, kelp grouper (E. bruneus), orange-spotted grouper (E. coioides), and Nile tilapia (Oreochromis niloticus). Thus, it would be useful to integrate the markers that were developed for different groupers, depending on sharing of sequence data, into a comprehensive consensus map.
由于生长速度快、肉质鲜美且市场价格高，白线石斑鱼（Epinephelus aeneus）是驯化和水产养殖的理想候选品种。连锁图谱是定位经济性状数量性状基因座和研究基因组进化的重要框架。对单个个体的DNA进行了深度测序，并在序列组装的177个最大支架中鉴定出微卫星标记。开发多态性同源标记的成功率为94.9%，而来自其他石斑鱼物种的异源标记的成功率为63.1%。在亲鱼池中现有的12条成年成熟鱼中，通过使用34个异源标记进行亲权分析，确定了两条雄性和两条雌性为指定后代的亲本。基于222个微卫星的基因分型数据，建立了一个由48个个体组成的单全同胞家系，用于构建第一代连锁图谱。根据24对染色体，将这些标记分配到24个连锁群中。雌性和雄性图谱分别由203个和202个标记组成，跨度分别为1053和886厘摩，标记间平均距离分别为5.8和5.0厘摩。通过使用来自含有端粒重复序列的RNA的支架上的标记，丰富了标记在连锁群末端的定位。比较图谱显示，白线石斑鱼、黑边石斑鱼（E. bruneus）、斜带石斑鱼（E. coioides）和尼罗罗非鱼（Oreochromis niloticus）之间具有高度的共线性关系。因此，根据序列数据的共享情况，将为不同石斑鱼开发的标记整合到一个综合的共识图谱中将会很有用。
