Jiangsu Marine Fishery Research Institute, Nantong 226007, China.
National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
Genes (Basel). 2022 Oct 31;13(11):1992. doi: 10.3390/genes13111992.
Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations ( < 0.05) or extremely significant correlations ( < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy-Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.
黑鲷是一种重要的海水养殖鱼类，其产量在中国各种海水养殖鱼类中排名第五。本研究采用 Illumina 高通量测序技术对黑鲷的总 RNA 进行测序，共筛选出 61 个候选 SNP（单核苷酸多态性），并通过 GATK4（基因组分析工具包）软件和 MALDI-TOF MS（基质辅助激光解吸/电离飞行时间质谱）进行基因分型。实验结果表明，共成功分型 60 个 SNP，成功率为 98.36%。主成分分析和生长性状相关分析结果表明，体重为第一主成分，累积贡献率为 74%。不同生长性状之间存在显著相关（<0.05）或极显著相关（<0.01）。遗传参数分析和关联分析结果表明，scaffold12-12716321、scaffold13-4787950、scaffold2-13687576 和 scaffold290-11890 这四个 SNP 满足多态信息含量要求，符合 Hardy-Weinberg 平衡。它们的基因型与生长性状的表型存在显著差异。本研究开发的这四个 SNP 分子标记将为进一步探索与黑鲷生长性状相关的分子标记奠定基础，为其生长机制的进一步研究提供科学参考。同时，这些分子标记可应用于黑鲷的生产实践，实现分子水平的选择性育种，加快育种进程。
