National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV 25430, USA.
BMC Genomics. 2011 Apr 7;12:180. doi: 10.1186/1471-2164-12-180.
Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. An integrated physical and genetic map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) programs for improving rainbow trout aquaculture production.
The first generation integrated map of the rainbow trout genome is composed of 238 BAC contigs anchored to chromosomes of the genetic map. It covers more than 10% of the genome across segments from all 29 chromosomes. Anchoring of 203 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA) genetic map was achieved through mapping of 288 genetic markers derived from BAC end sequences (BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research) genetic map through markers that were not informative for linkage analysis in the NCCCWA mapping panel. The ratio of physical to genetic linkage distances varied substantially among chromosomes and BAC contigs with an average of 3,033 Kb/cM.
The integrated map described here provides a framework for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species and will facilitate comparative genome mapping with other salmonids and with model fish species. This resource will also facilitate efforts to assemble a whole-genome reference sequence for rainbow trout.
虹鳟（Oncorhynchus mykiss）是世界上养殖最广泛的冷水淡水鱼，也是许多研究领域的重要模式物种。由于人们对该物种作为研究模型的极大兴趣，以及对提高水产养殖生产效率性状的遗传改良的需求， justifies 了继续开发基因组学研究资源。许多与生产和生活史性状相关的数量性状位点（QTL）已在虹鳟中被鉴定出来。需要构建一个整合的物理图谱和遗传图谱，以促进 QTL 的精细定位，以及选择候选基因进行位置定位，以纳入标记辅助选择（MAS）计划，从而提高虹鳟水产养殖生产。
虹鳟基因组的第一代整合图谱由 238 个 BAC 连续体组成，这些连续体被锚定在遗传图谱的染色体上。它覆盖了来自 29 条染色体的所有片段的基因组的 10%以上。通过对 288 个遗传标记进行 BAC 末端序列（BES）作图、用先前作图的标记筛选 BAC 文库以及将 SNPs 与 BES 读数进行匹配，将 203 个连续体锚定到国家冷水和冷水水产养殖中心（NCCCWA）遗传图谱的染色体上。此外，通过在 NCCCWA 图谱面板中没有进行连锁分析的标记，将 35 个连续体锚定到 INRA（法国国家农业研究所）遗传图谱的连锁群上。物理与遗传连锁距离的比值在染色体和 BAC 连续体之间变化很大，平均为 3033 Kb/cM。
这里描述的整合图谱为虹鳟提供了一个强大的复合基因组图谱框架。该资源是该研究模型和经济重要物种基因组分析所必需的，并且将促进与其他鲑鱼和模式鱼类的比较基因组作图。该资源还将有助于组装虹鳟的全基因组参考序列。
