Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.
Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China.
BMC Genomics. 2019 Jul 22;20(1):598. doi: 10.1186/s12864-019-5981-x.
High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.
In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation.
The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.
高分辨率遗传连锁图谱对于水产养殖物种的 QTL 作图、基因组序列组装和标记辅助选择至关重要。脊尾白虾 Exopalaemon carinicauda 是中国东部和朝鲜西部沿海自然分布的最具经济价值的虾类之一。然而，在该物种中，用于经济性状遗传改良的基因组学和遗传学信息相当有限。
本研究利用下一代测序技术对脊尾白虾进行了基因组普查，并构建了其高分辨率遗传连锁图谱。估计基因组大小为 9.33Gb，杂合率为 0.26%，重复序列比例为 76.62%。通过基因组注释鉴定了 65772 个蛋白质编码基因。共获得 10384 个 SNP 用于高通量基因分型，并将其分配到脊尾白虾的正反交回交家系的 45 个连锁群（LG）中，平均标记间距分别为 0.73cM 和 0.55cM。基于高分辨率连锁图谱，共检测到与五个生长性状相关的 23 个 QTL。所有 QTL 可解释总生长性状变异的 8.8-15.7%。
通过基因组普查分析更准确地估计了 E. carinicauda 的基因组大小，揭示了其基本的基因组结构。首张脊尾白虾高分辨率回交遗传连锁图谱和与生长性状相关的 QTL 将为 E. carinicauda 及其他对虾属虾类的 QTL 精细定位、基因组组装和遗传改良提供重要信息。
