Volume 19 Issue 6
Dec.  2023
Turn off MathJax
Article Contents
Abstract
References
LU Hongyi, TIAN Haifeng, HU Qiaomu, LI Zhong. Parentage assignment of Monopterus albus using multiplex PCR of microsatallites[J]. South China Fisheries Science, 2023, 19(6): 97-106. DOI: 10.12131/20230081
Citation: LU Hongyi, TIAN Haifeng, HU Qiaomu, LI Zhong. Parentage assignment of Monopterus albus using multiplex PCR of microsatallites[J]. South China Fisheries Science, 2023, 19(6): 97-106. DOI: 10.12131/20230081
shu

Parentage assignment of Monopterus albus using multiplex PCR of microsatallites

  • 1.

    Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China

  • 2.

    College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China

More Information
  • Received Date: April 18, 2023
  • Revised Date: June 20, 2023
  • Accepted Date: July 26, 2023
  • Available Online: July 30, 2023
    Graphical Abstract
    • Abstract

  • In order to solve the problems in paternity test and genealogical management for improved variety breeding of Monopterus albus, we obtained 16 microsatellite markers with high polymorphism through whole genome searching of and following confirmation, and established two multiplex PCR sets by using 16 high polymorphic microsatellite markers and successfully applied to the parentage assignment for 11 full-sib M. albus families. The average allele number(Na) of 16 microsatellite was 5.562; the average of abserved heterozygosite(Ho) was 0.627; the average of expected heterozygosite(He) was 0.619; the average of polymorphic information content (PIC) was 0.564. Parentage analysis reveals that the combined exclusion probability of first parent given only the genotype of the offspring (CE-1P) was 0.999 999 99, the combined exclusion probability of a second candidate parent given the genotype of the offspring and one known parent (CE-2P) was 0.999 999 91, and combined exclusion probability of a parent pair given only the genotype of the offspring (CE-PP) was 0.999 964 76. The simulated identification rate of the 11 M. albus families was 99.96%, and the actual identification rate was 95%. Furthermore, the simulation analysis shows that the identification rate could reach over 95% in the case of 200 candidate parental individuals with known sexes and 150 candidate parental individuals with unknown sexes. The cluster analysis shows that 108 offspring could be clustered correctly except two, and the accuracy rate was 98.18%. The paternity method of M. albus established in this study provides important technical support for the future breeding program and management of germplasm resources of M. albus.

    • FullText(HTML)
    • References (47)
  • [1]
    陈锋. 黄鳝群体遗传结构的研究[D]. 武汉: 武汉大学, 2017: 1.
    [2]
    SHAFLAND P L, GESTRING K B, STANFORD M S. An assessment of the Asian swamp eel (Monopterus albus) in Florida[J]. Rev Fish Sci, 2010, 18(1): 25-39.
    [3]
    胡玉婷, 江河, 胡王, 等. 安徽长江流域黄鳝6个地理种群的遗传变异研究[J]. 四川动物, 2015, 34(1): 21-28.
    [4]
    农业部渔业渔政管理局. 2017 中国渔业统计年鉴[M]. 北京: 中国农业出版社, 2017: 32.
    [5]
    农业农村部渔业渔政管理局, 全国水产技术推广总站, 中国水产学会. 2018中国渔业统计年鉴[M]. 北京: 中国农业出版社, 2018: 32.
    [6]
    农业农村部渔业渔政管理局, 全国水产技术推广总站, 中国水产学会. 2019 中国渔业统计年鉴[M]. 北京: 中国农业出版社, 2019: 32.
    [7]
    农业农村部渔业渔政管理局, 全国水产技术推广总站, 中国水产学会. 2020 中国渔业统计年鉴[M]. 北京: 中国农业出版社, 2020: 32.
    [8]
    农业农村部渔业渔政管理局, 全国水产技术推广总站, 中国水产学会. 2021 中国渔业统计年鉴[M]. 北京: 中国农业出版社, 2021: 32.
    [9]
    何坤, 吴华东, 张士林, 等. 黄鳝nanos3基因克隆鉴定及其组织表达分析[J]. 南方农业学报, 2022, 53(8): 2321-2330.
    [10]
    文萍, 赵建, 李伟, 等. 基于微卫星多重PCR技术的黄喉拟水龟亲子鉴定[J]. 水生生物学报, 2015, 39(6): 1134-1141.
    [11]
    苗贵东, 杜民, 杨景峰, 等. 大菱鲆亲子鉴定的微卫星多重PCR技术建立及应用[J]. 中国海洋大学学报(自然科学版), 2011(Z1): 97-106.
    [12]
    谢敏敏, 王亚坤, 魏成清, 等. 基于微卫星标记的鼋亲子鉴定技术[J]. 水生生物学报, 2022, 46(12): 1932-1938.
    [13]
    DONG S R, KONG J, ZHANG T S, et al. Parentage determination of Chinese shrimp (Fenneropenaeus chinensis) based on microsatellite DNA markers[J]. Aquaculture, 2006, 258(1): 283-288.
    [14]
    辛苗苗, 张书环, 汪登强, 等. 多倍体中华鲟微卫星亲子鉴定体系的建立[J]. 淡水渔业, 2015, 45(4): 3-9.
    [15]
    YANG M, TIAN C X, LIANG X F, et al. Parentage determination of mandarin fish (Siniperca chuatsi) based on microsatellite DNA markers[J]. Biochem Syst Ecol, 2014, 54: 285-291. doi: 10.1016/j.bse.2014.03.003
    [16]
    ZHU K C, YU W B, HUANG J H, et al. Parentage determination in black tiger shrimp (Penaeus monodon) based on microsatellite DNA markers[J]. Aquac Int, 2017, 25(2): 827-836. doi: 10.1007/s10499-016-0082-1
    [17]
    刘臻, 罗小华, 鲁双庆, 等. 黄鳝微卫星标记筛选及其在不同性别表型群体中的遗传多态性[J]. 江苏农业学报, 2009, 25(2): 333-338.
    [18]
    LI L, LIU F, TU R J, et al. Characterization and multiplex genotyping of novel microsatellites from Asian swamp eel, Monopterus albus[J]. Conserv Genetics Resour, 2012, 4(2): 363-365. doi: 10.1007/s12686-011-9549-6
    [19]
    ZHANG F F, WANG Y L, MIN X, et al. Development and characterization of twenty-eight polymorphic microsatellite for rice field eel (Monopterus albus) using RAD tag sequencing[J]. Genet Mol Res, 2018, 17(1): gmr16039880.
    [20]
    TIAN H F, HU Q M, LI Z. A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data[J]. G3-Genes Genom Genet, 2021, 11(1): 1-9.
    [21]
    TIAN H F, HU Q M, LI Z. Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)[J]. Sci Prog 2021, 104(3): 368504211035597.
    [22]
    SAMBROOK J, FRITSCH E P, MANIATIS T. Molecular cloning: a laboratory manual[M]. Beijing: Science Press, 1996: 1.
    [23]
    BEIER S, THIEL T, MÜNCH T, et al. MISA-web: a web server for microsatellite prediction[J]. Bioinformatics, 2017, 33(16): 2583-2585. doi: 10.1093/bioinformatics/btx198
    [24]
    HOLLAND M M, PARSON W. GeneMarker® HID: a reliablesoftware tool for the analysis of forensic STR data[J]. J Forensic Sci, 2011, 56(1): 29-35. doi: 10.1111/j.1556-4029.2010.01565.x
    [25]
    KALINOWSKI S T, TAPER M, MARSHALL T C. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment[J]. Mol Ecol, 2007, 16(5): 1099-1106. doi: 10.1111/j.1365-294X.2007.03089.x
    [26]
    ROHLF F J. NTSYS-pc: microcomputer programs for numerical taxonomy and multivariate analysis[J]. Am Stat, 1987, 41(4): 330. doi: 10.2307/2684761
    [27]
    CHAMBERLAIN J S, GIBBS R A, RAINER J E, et al. Delection screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification[J]. Nucl Acid Res, 1988, 16(23): 11141-11156. doi: 10.1093/nar/16.23.11141
    [28]
    胡宗云, 杨培民, 闫有利. 3种淡水鱼病原菌多重PCR检测方法的建立与应用[J]. 水产科学, 2022, 41(4): 605-613.
    [29]
    CHI ZHANG. Semi-nested multiplex PCR enhanced method sensitivity of species detection in further-processed meats[J]. Food Control, 2013, 31(2): 326-330. doi: 10.1016/j.foodcont.2012.11.002
    [30]
    苏静, 陈佰鸿, 毛娟, 等. 酿酒葡萄4种病毒多重RT-PCR检测体系的建立[J]. 果树学报, 2017, 34(5): 632-638.
    [31]
    李东宇, 孔杰, 孟宪红, 等. 凡纳滨对虾 (Litopenaeus vannamei) 微卫星多重PCR体系的建立及其在家系亲权鉴定中的应用[J]. 渔业科学进展, 2016, 37(3): 58-67.
    [32]
    BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet. 1980, 32(3): 314-331.
    [33]
    邢露梅, 俞兆曦, 等. 基于微卫星多重PCR技术的兰州鲇亲子鉴定[J]. 水生生物学报, 2021, 45(3): 530-540.
    [34]
    何勇凤, 朱永久, 吴兴兵, 等. 基于微卫星标记的圆口铜鱼亲子鉴定技术[J]. 水生生物学报, 2019, 43(6): 1216-1223.
    [35]
    张毅, 孙东晓, 俞英, 等. 家养水牛30个微卫星标记的多重PCR体系建立及其多态性检测[J]. 遗传, 2008(1): 59-64.
    [36]
    WANG Y, WANG X X, WANG A M, et al. A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica Gmelin)[J]. Aquaculture, 2010, 308: S28-S33. doi: 10.1016/j.aquaculture.2010.05.037
    [37]
    方敏. 微卫星标记在鳙群体遗传、亲子鉴定及关联分析中的应用[D]. 南京: 南京农业大学, 2019: 49.
    [38]
    杨习文, 刘熠, 薛向平, 等. 基于微卫星标记的长江江苏段鲢 (Hypophthalmichthys molitrix) 增殖放流资源贡献率的评估[J]. 湖泊科学, 2020, 32(4): 1154-1164.
    [39]
    赵桐茂. 人类血型遗传学[M]. 北京: 科学出版社, 1987: 330-346.
    [40]
    张春雷, 佟广香, 匡友谊, 等. 哲罗鱼微卫星亲子鉴定的应用[J]. 动物学研究, 2010, 31(4): 395-400.
    [41]
    王新华, 俞小牧, 冯建新, 等. 黄河鲤全同胞家系的微卫星标记亲子鉴定[J]. 中国水产科学, 2016, 23(5): 1023-1031.
    [42]
    王鸿霞, 吴长功, 张留所, 等. 微卫星标记应用于凡纳滨对虾家系鉴别的研究[J]. 遗传, 2006(2): 179-183.
    [43]
    O'REILLY P T, HERBINGER C, WRIGHT J M. Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites[J]. Anim Genet, 1998, 29(5): 363-370. doi: 10.1046/j.1365-2052.1998.295359.x
    [44]
    韩叶, 郑伟, 康学会, 等. 基于微卫星标记的图们江大麻哈鱼亲子鉴定技术研究[J]. 南方水产科学, 2020, 16(4): 84-89.
    [45]
    周宇芳, 胡杭娇, 张龙韬, 等. 长江中下游黄鳝遗传多样性的微卫星分析[J]. 生物技术通报, 2011(11): 187-192.
    [46]
    ZHOU H X, HU Y T, JIANG H, et al. Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights[J]. PeerJ, 2020, 8: e8415. doi: 10.7717/peerj.8415
    [47]
    刘肖莲, 郝爽, 张连英, 等. 天津市3个黄鳝野生群体的遗传多样性分析[J]. 天津农业科学, 2021, 27(11): 40-43.
    • Related Articles

Catalog

    Get Citation
    PDF
    XML
    Article views (255) PDF downloads (35) Cited by()
    Related

    Supported by: Beijing Renhe Information Technology Co., Ltd.  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return