热带海洋学报

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黄鳍棘鲷SNP标记开发与验证

赵虹博 郑国彬 刘贤德 黄良敏 杨乐   

  1. 集美大学水产学院,农业农村部东海海水养殖重点实验室,福建 厦门,361021

  • 收稿日期:2022-05-13 修回日期:2022-07-09 出版日期:2022-07-14 发布日期:2022-07-14
  • 通讯作者: 刘贤德
  • 基金资助:
    国家重点研发计划(2018YFD0901404)和厦门湾黄鳍鲷放流效果评价(S20166)

SNP discovery and verify of Acanthopagrus latus

ZHENG Guobin,ZHAO Hongbo,HUANG Liangmin,ZHANG Jing,LIU Xiande   

  1. Fishery College of Jimei University, Key Laboratory of Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen 361021, Fujian, China

  • Received:2022-05-13 Revised:2022-07-09 Online:2022-07-14 Published:2022-07-14
  • Contact: Xian-de Liu
  • Supported by:
    National Key R&D Program of China (2018YFD0901404) and Evaluation of the Release Effect of Acanthopagrus latus in Xiamen Bay (S20166)

摘要: 本实验以我国东南沿海重要的经济鱼类黄鳍棘鲷 (Acanthopagrus latus) 为研究对象,通过对50尾野生黄鳍棘鲷基因组重测序开发SNP(single nucleotide polymorphism)标记,并利用MassARRAY?质谱分析系统对部分SNP标记进行验证。研究结果如下:1)50尾野生黄鳍棘鲷重测序共产生约233.48Gb(gigabyte) Raw data,过滤接头和低质量数据后,共获得233.43Gb Clean data,每个样品平均数据量为4.67Gb,平均GC(guanine cytosine)含量为42.85%,Q(quality)20在96.56%以上,Q30在91.1%以上,Clean data与参考基因组的比对率为98.06 % ?99.47 %;2)通过GATK(genome analysis toolkit)分析,从50个个体中共挖掘出13843766个SNP,经过滤后获得6501个高质量SNP;3)从高质量的SNP标记中,随机挑选30个SNP使用MassARRAY(matrix assisted laser desorption/ionization time of flight mass spectrometry, MALDI-TOF-MS)技术进行分型,其检出率(可以分型的位点)为98%,MassARRAY分型结果与基因组重测序分型结果一致率为64.83%,这说明两种技术在SNP分型方面存在差异。综上所述,本研究初步建立了黄鳍棘鲷SNP标记挖掘、过滤与验证的方法,开发的SNP位点可用于后续黄鳍棘鲷增殖放流效果评估及基因组选择育种研究。

关键词: 黄鳍棘鲷, 重测序, SNP, MassARRAY

Abstract: In this experiment, ‘Acanthopagrus latus’, which is an important economic fish in the southeast coast of China, was used as the experimental material. The SNPs were discovered by DNA re-sequencing in fifty A. latus, and partial SNPs were genotyped using MassARRAY? DNA mass spectrometry. The results as followed: 1) The re-sequencing of 50 wild A. latus generated a total of about 233.48 Gb raw data. After filtering adapters and low-quality data, 233.43 Gb clean data were obtained. The average data size of each sample was 4.67 Gb, and the average GC content was 42.85%, Q20 is above 96.56%, Q30 is above 91.1%, and the comparison rate between clean data and the reference genome is 98.06%?99.47%; 2) A total of 13,843,766 SNPs were discovered from 50 individuals by GATK, and 6,501 high-quality SNPs were obtained after filtering; 3) Thirty SNPs from the high-quality SNP were selected randomly and genotyped using MassARRAY technology. The detection rate (loci that can be genotyped) of was reached 98%. The consistency between genome re-sequencing and MassARRAY results was 64.83%, which indicated that the two techniques were different in detecting SNPs. In summary, a method for mining, filtering and validating SNP markers of A. latus bream has been established in this study, and the developed SNP loci can be used in evaluation of proliferation and stocking effect and genome selection breeding of A. latus in the future.

Key words: Acanthopagrus latus, Re-sequencing, SNP, MassARRAY