Rexroad Caird E, Palti Yniv, Gahr Scott A, Vallejo Roger L
USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia, USA.
BMC Genet. 2008 Nov 19;9:74. doi: 10.1186/1471-2156-9-74.
Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species.
A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci.
The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.
表征性状和标记遗传模式的遗传图谱已在众多物种中构建出来，并用于研究生物医药、农业、生态学及进化生物学领域的问题。过去十年，由于虹鳟在水产养殖和游钓渔业中的受关注程度，以及作为与癌症发生、毒理学、比较免疫学、疾病生态学、生理学和营养相关研究的模式生物，虹鳟遗传图谱的发展取得了显著进展。我们利用微卫星标记构建了虹鳟的第二代遗传图谱，以促进影响水产养殖生产效率性状的数量性状基因座的鉴定，并从模式鱼类的基因组序列中提取比较信息。
通过对国家冷水水产养殖中心（NCCCWA）参考家系作图群体的10个亲本和150个后代进行基因分型，构建了一个遗传图谱，该图谱排列了1124个微卫星位点，平均性别距离为2927.10厘摩（Kosambi），分辨率为2.6厘摩。代表由近期全基因组复制事件产生的位点对的微卫星标记，在虹鳟基因组中鉴定出180个重复区域。通过表达序列标签或细菌人工染色体与基因相关的微卫星，与四齿鲀、斑马鱼、河豚和青鳉产生了比较定位，从而对199个位点进行了同源性定位。
第二代NCCCWA遗传图谱提高了微卫星标记密度，并量化了远交群体中两性之间重组率的差异。它有可能与细胞遗传学图谱和其他物理图谱整合，识别出近期基因组复制事件产生的虹鳟基因组的旁系同源区域，并将比较图谱与斑马鱼、青鳉、四齿鲀和河豚基因组进行锚定。这一资源将有助于通过精细定位和候选基因的位置克隆来鉴定影响目标性状的基因。
