Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
Fish Shellfish Immunol. 2018 Feb;73:158-166. doi: 10.1016/j.fsi.2017.12.005. Epub 2017 Dec 5.
The high concentration of ammonia from deteriorated aquaculture environments and the intensive culture system could increase the susceptibility to pathogens and even cause high mortality in Litopenaeus vannamei. In addition, we have revealed that the ammonia-tolerant shrimp also have high disease resistance in L. vannamei. In the present study, in order to identify SNP markers associated with tolerance to ammonia toxicity, we developed and characterized SNPs from our previous transcriptome sequencing data of ammonia-stressed and control groups, and a marker-trait association analysis was performed for marker-assisted selection (MAS) to increase production in L. vannamei. A total of 318,919 SNPs were identified from the transcriptome sequences, and 25,772 SNPs were found from the 1826 ammonia-responsive genes with functional annotation. We selected 49 SNPs from 26 ammonia-responsive genes that had strong homologies to known genes in the shrimp and probably involved in immune function as candidate markers for genotyping, among which 39 SNPs were polymorphic for further marker-trait association analysis with the ammonia-tolerant (AT) and ammonia-sensitive (AS) groups. Finally, 12 out of the 49 SNP markers were identified to be associated with ammonia tolerance, containing 10 loci with significantly different allele frequencies and 10 loci with significantly different genotyping frequencies between the AT and AS groups. Among the associated markers, the G allele of TSP-1 (the first locus from the thrombospondin gene), the A allele of TSP-3, and the C allele of XBP1-5 (the fifth locus from X-box binding protein 1) only presented in the AT groups, but they were absent from the AS groups, which would be the preference of the MAS for the ammonia-tolerant shrimp. In addition, when the 12 associated SNP markers were used for analysis, the genetic diversity of the AT groups were significantly higher than that of the AS groups, but when the 39 loci were used there was no difference. This is the first report for the markers associated with ammonia tolerance in this species, indirectly with disease resistance, which provided important potential for genetic selection to increase survival rate and production in shrimp farming.
高浓度的氨来自恶化的水产养殖环境和集约化养殖系统，这可能会增加对病原体的易感性，甚至导致凡纳滨对虾的高死亡率。此外，我们已经揭示了耐氨虾在凡纳滨对虾中也具有高抗病性。在本研究中，为了鉴定与氨毒性耐受相关的 SNP 标记，我们从之前的氨胁迫和对照组的转录组测序数据中开发和表征了 SNP，并进行了标记-性状关联分析，以进行标记辅助选择 (MAS) 来提高凡纳滨对虾的产量。从转录组序列中鉴定出 318919 个 SNP，从具有功能注释的 1826 个氨应答基因中发现 25772 个 SNP。我们从 26 个氨应答基因中选择了 49 个与虾中已知基因具有强同源性且可能参与免疫功能的 SNP 作为候选标记进行基因分型，其中 39 个 SNP 为多态性，可进一步与耐氨 (AT) 和氨敏感 (AS) 群体进行标记-性状关联分析。最后，从 49 个 SNP 标记中鉴定出 12 个与氨耐受相关的标记，其中 10 个标记的等位基因频率有显著差异，10 个标记的基因型频率在 AT 和 AS 群体之间有显著差异。在相关标记中，TSP-1（血栓素基因的第一个位点）的 G 等位基因、TSP-3 的 A 等位基因和 XBP1-5（X 盒结合蛋白 1 的第五个位点）的 C 等位基因仅存在于 AT 群体中，但不存在于 AS 群体中，这将是 MAS 对耐氨虾的偏好。此外，当使用 12 个相关 SNP 标记进行分析时，AT 群体的遗传多样性显著高于 AS 群体，但当使用 39 个标记时，没有差异。这是首次报道与该物种氨耐受相关的标记，间接与抗病性相关，这为提高虾养殖存活率和产量的遗传选择提供了重要的潜力。
