State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
Fisheries Research Institute of Fujian, Xiamen, China.
Mar Biotechnol (NY). 2020 Feb;22(1):130-144. doi: 10.1007/s10126-019-09938-2. Epub 2020 Jan 3.
Takifugu bimaculatus is a euryhaline species, distributed ranging from the southern Yellow Sea to the South China Sea. Their tolerance to a wide range of salinity and temperature, coupled with a desirable firm texture, makes T. bimaculatus a strong candidate for Takifugu aquaculture in subtropics areas. Due to the increasing demand in markets and emerging of the Takifugu aquaculture industry, close attention has been paid to improvement on the T. bimaculatus production. In aquaculture, the great effort has been put into marker-assisted selective breeding, and efficient improvement was realized. However, few genetic resources on T. bimaculatus are provided so far. Aiming at understanding the genetic basis underlying important economic growth traits, facilitating genetic improvement and enriching the genetic resource in T. bimaculatus, we constructed the first genetic linkage map for T. bimaculatus via double digestion restriction-site association DNA sequencing and conducted quantitative traits locus (QTL) mapping for growth-related traits. The map comprised 1976 single nucleotide polymorphism markers distributed on 22 linkage groups (LG), with a total genetic distance of 2039.74 cM. Based on the linkage map, a chromosome-level assembly was constructed whereby we carried out comparative genomics analysis, verifying the high accuracy on contigs ordering of the linkage map. On the other hand, 18 QTLs associated with growth traits were detected on LG6, LG7, LG8, LG10, LG20, and LG21 with phenotypical variance ranging from 15.1 to 56.4%. Candidate genes participating in cartilage development, fat accumulation, and other growth-related regulation activities were identified from these QTLs, including col11a1, foxa2, and thrap3. The linkage map provided a solid foundation for chromosomes assembly and refinement. QTLs reported here unraveled the genomic architecture of some growth traits, which will advance the investigation of aquaculture breeding efforts in T. bimaculatus.
红鳍东方鲀是一种广盐性物种，分布于从南黄海到南海。它们对盐度和温度范围有很强的耐受性，加上理想的坚实质地，使红鳍东方鲀成为亚热带地区养殖的理想选择。由于市场需求的增加和养殖红鳍东方鲀产业的兴起，人们密切关注红鳍东方鲀的生产改进。在水产养殖中，已经投入了大量的精力进行标记辅助选择育种，并实现了有效的改进。然而，迄今为止，关于红鳍东方鲀的遗传资源仍然很少。为了了解重要经济增长性状的遗传基础，促进遗传改良和丰富红鳍东方鲀的遗传资源，我们通过双酶切限制位点关联 DNA 测序构建了红鳍东方鲀的第一张遗传连锁图谱，并对生长相关性状进行了数量性状位点（QTL）作图。图谱包含 1976 个单核苷酸多态性标记，分布在 22 个连锁群（LG）上，总遗传距离为 2039.74cM。基于该连锁图谱，构建了一个染色体水平的组装图谱，进行了比较基因组学分析，验证了图谱上的 contigs 排序的高精度。另一方面，在 LG6、LG7、LG8、LG10、LG20 和 LG21 上检测到与生长性状相关的 18 个 QTL，表型方差范围为 15.1%至 56.4%。从这些 QTL 中鉴定出参与软骨发育、脂肪积累和其他生长相关调控活动的候选基因，包括 col11a1、foxa2 和 thrap3。该连锁图谱为染色体组装和细化提供了坚实的基础。这里报道的 QTL 揭示了一些生长性状的基因组结构，这将推进红鳍东方鲀水产养殖的研究。
