Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA.
Scottish Oceans Institute, University of St. Andrews, East Sands, St. Andrews, Fife, KY16 8LB, UK.
BMC Genomics. 2018 Feb 23;19(1):163. doi: 10.1186/s12864-018-4541-0.
Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome.
The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map.
The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.
南方比目鱼 Paralichthys lethostigma 历史上在美国南部的大西洋和墨西哥湾沿岸支撑着一个重要的渔业。过去几年，墨西哥湾西部的幼鱼数量较低，这引发了人们对产卵种群可能过度捕捞的担忧。目前，该资源的管理包括释放养殖的幼鱼来补充海湾和河口；此外，人们越来越关注该物种商业水产养殖的潜力。目前，南方比目鱼没有基因组资源。在这里，我们使用两个养殖的家系和双消化、限制位点相关 DNA（ddRAD）测序，创建了一个由数千个单核苷酸多态性（SNP）组成的简化基因组文库，这些 SNP 分布在整个基因组中。
确定每个含 SNP 基因座的相对位置，以创建一个覆盖南方比目鱼 24 个连锁群基因组的高密度遗传图谱。利用共识图谱，确定了南方比目鱼与其他 7 个基因组图谱已公布的鱼类之间的共线性区域。最后，利用共线性块将欧洲比目鱼转录本中鉴定的基因定位于日本比目鱼生长和抗病性相关 QTL 以及与生态毒理学和渗透压调节反应相关的基因，定位到南方比目鱼的连锁图谱上。
连锁图谱提供的信息将丰富恢复工作，为解释该物种内的空间遗传变异提供基础，最终进一步了解南方比目鱼对当地环境条件未来变化的适应潜力和恢复力。此外，该图谱将有助于利用遗传标记来增强恢复和商业水产养殖。
