Volume 2 Issue 5
Oct.  2006
Turn off MathJax
Article Contents
Abstract
References
Related Articles
LI Lihao, YU Dahui. Methods for isolating microsatellite DNA loci from genomic DNA and the applications in aquatic animals[J]. South China Fisheries Science, 2006, 2(5): 74-80.
Citation: LI Lihao, YU Dahui. Methods for isolating microsatellite DNA loci from genomic DNA and the applications in aquatic animals[J]. South China Fisheries Science, 2006, 2(5): 74-80.
shu

Methods for isolating microsatellite DNA loci from genomic DNA and the applications in aquatic animals

  • 1.

    South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China

  • 2.

    Shanghai Fisheries University, Shanghai 200090, China

More Information
  • Received Date: April 08, 2006
  • Revised Date: April 28, 2005
    Graphical Abstract
    • Abstract

  • Microsatellite DNAs, or single sequence repeats (SSRs), are small array of one to six tandemly repeated bases that spread throughout the genome. Microsatellite DNAs are highly polymorphic, abundant, co-dominantly inheritant, simple in practice and readily transferable. Thus they have been widely used in many fields and have become one of the most popular molecular markers. Yet microsatellite DNAs need to be isolated de novo from species that are being examined for the first time. There are a number of ways to obtain microsatellite markers from genomic DNA. The aim of the present paper is to review the state-of-the-art methods of microsatellite DNA isolation for reference.

    • FullText(HTML)
    • References (42)
  • [1]
    何平. 真核生物中的微卫星及其应用[J]. 遗传, 1998, 20(4): 42-47. https://d.wanfangdata.com.cn/periodical/Ch9QZXJpb2RpY2FsQ0hJTmV3UzIwMjQxMTA1MTcxMzA0EhVDQVMyMDEzMDMwNDAwMDAwODYwODUaCDVkbjI1aTRk
    [2]
    O'REILLY P, WRIGHT J M. The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture[J]. Fish Biol, 1995, 47(Sup A): 29-35. doi: 10.1111/j.1095-8649.1995.tb06042.x
    [3]
    TAUTZ D. Hypervariability of simple sequence as a general source for polymorphic DNA markers[J]. Nucleic Acid Res, 1989, 17(16): 6463-6471. doi: 10.1093/nar/17.16.6463
    [4]
    GOLDSTEIN D B, ROEMER G W, SMITH D A, et al. The use of microsatellite variation to infer population structure and demographic history in a natural model system[J]. Genet, 1999, 151(2): 791-801. doi: 10.1093/genetics/151.2.797
    [5]
    刘志毅, 相建海. 微卫星DNA分子标记在海洋动物遗传分析中的应用[J]. 海洋科学, 2001, 25(6): 11-13. doi: 10.3969/j.issn.1000-3096.2001.06.004
    [6]
    杜长斌, 楼允东, 沈俊宝, 等. 微卫星分子标记技术在鱼类遗传连锁图谱构建中的应用[J]. 上海水产大学学报, 2000, 9(3): 254-258. doi: 10.3969/j.issn.1004-7271.2000.03.013
    [7]
    O'Malley K G, SAKAMOTO T, DANZMANN R G, et al. Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes[J]. Heredity, 2003, 94(4): 273-284. doi: 10.1093/jhered/esg067
    [8]
    EDWARDS Y J, ELGAR G, CLARK M S, et al. The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analysis[J]. Mol Biol, 1998, 278(4): 843-854. doi: 10.1006/jmbi.1998.1752
    [9]
    徐鹏, 周令华, 田丽萍, 等. 从中国对虾ESTs中筛选微卫星标记的研究[J]. 水产学报, 2003, 27(3): 213-218. doi: 10.3321/j.issn:1000-0615.2003.03.004
    [10]
    李红蕾, 宋林生, 王玲玲, 等. 栉孔扇贝EST中微卫星标记的筛选[J]. 高技术通讯, 2003, 13(12): 72-75. doi: 10.3321/j.issn:1002-0470.2003.12.015
    [11]
    鲁双庆, 刘少军, 刘红玉, 等. 黄鳝微卫星引物筛选及其在保护遗传学上的应用[J]. 水产学报, 2005, 29(5): 612-618. doi: 10.3321/j.issn:1000-0615.2005.05.005
    [12]
    林凯东, 罗琛. 鲤的微卫星引物对草鱼基因组分析适用性的初步研究[J]. 激光生物学报, 2003, 12(2): 121-127. doi: 10.3969/j.issn.1007-7146.2003.02.009
    [13]
    孙效文, 贾智英, 魏东旺, 等. 磁珠富集法与小片段克隆法筛选微卫星的比较研究[J]. 中国水产科学, 2005, 12(2): 127-132. doi: 10.3321/j.issn:1005-8737.2005.02.003
    [14]
    陈微, 张全启, 于海洋, 等. 牙鲆微卫星标记的筛选及群体多态性分析[J]. 中国水产科学, 2005, 12(2): 682-687. doi: 10.3321/j.issn:1005-8737.2005.06.003
    [15]
    PANIEGO N, ECHAIDE M, MUNOZ M, et al. Microsatellite isolation and characterization in sunflower[J]. Genome, 2002, 45(1): 34-43. doi: 10.1139/g01-120
    [16]
    RASSMANN K, SCHLTTERER C, TAUTZ D. Isolation of simple sequence loci for use in polymerase chain reaction-based DNA fingerprinting[J]. Electrophoresis, 1991, 12(2/3): 113-118. doi: 10.1002/elps.1150120205
    [17]
    ZHIVOTOVSKY L A, FELDMAN M W. Microsatellite variability and genetic distances[J]. Proc Natl Acad Sci USA, 1995, 92(17): 11549-11552. doi: 10.1073/pnas.92.25.11549
    [18]
    COOPER G, AMOS W, BELLAMY R, et al. An empirical exploration of the (δμ)2 genetic distance for 213 human microsatellite markers[J]. Am J Hum Genet, 1999, 65(4): 1125-1133. doi: 10.1086/302574
    [19]
    LIU B H. Statistical Genomics: Linkage, Mapping and QTL Analysis[M]. [S. l. ]: CRC Press, Boca Raton, FA, 1998: 611.
    [20]
    WILLIAMS J G, KUBELIK A R, LIVAK K J, et al. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers[J]. Nucleic Acids Res, 1990, 18(22): 6531-6535. doi: 10.1093/nar/18.22.6531
    [21]
    RICHARDSON T, CATO S, RAMSER J, et al. Hybridization of microsatellites to RAPD: a new source of polymorphic markers[J]. Nucleic Acids Res, 1995, 23(18): 3798-3799. doi: 10.1093/nar/23.18.3798
    [22]
    LUNT D H, HUTCHINSON W F, CARVALHO G R. An efficient method for PCR-based identification of microsatellite arrays (PIMA)[J]. Mol Ecol, 1999, 8(5): 893-894. doi: 10.1007/978-1-62703-389-3_3
    [23]
    ENDER A, SCHWENK K, STDLER T, et al. RAPD identification of microsatellites in Daphnia[J]. Mol Ecol, 1996, 5(4): 463-472. doi: 10.1111/j.1365-294X.1996.tb00339.x
    [24]
    DÕAMATO M E, LUNT D H, CARVALHO G R. Microsatellite markers for the hake Macruronus magellanicus amplify other gadoid fish[J]. Mol Ecol, 1999, 8(6): 1086-1087. doi: 10.1046/j.1365-294X.1999.00655_7.x
    [25]
    CIFARELLI R A, GALLITELLI M, CELLINI F. Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones[J]. Nucleic Acids Res, 1995, 23(18): 3802-3803. doi: 10.1093/nar/23.18.3802
    [26]
    OSTRANDER E A, JONG P M, RINE J, et al. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences[J]. Proc Natl Acad Sci USA, 1992, 89(8): 3419-3423. doi: 10.1073/pnas.89.8.3419
    [27]
    PAETKAU D. Microsatellites obtained using strand extension: an enrichment protocol[J]. Biotech, 1999, 26(4): 690-697. doi: 10.2144/99264st05
    [28]
    KARAGYOZOV L, KALCHEVA I D, CHAPMAN V M. Construction of small-insert genomic DNA libraries highly enriched for simple sequence repeats[J]. Nucleic Acids Res, 1993, 21(16): 3911-3912. doi: 10.1093/nar/21.16.3911
    [29]
    HAMILTON M B, PINCUS E L, DI-FIORE A, et al. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites[J]. Biotech, 1999, 27(3): 500-507. doi: 10.2144/99273st03
    [30]
    KIJAS J M, FOWLER J C, GARBETT C A, et al. Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles[J]. Biotech, 1994, 16(4): 656-662. https://pubmed.ncbi.nlm.nih.gov/8024786/
    [31]
    KANDPAL R P, KANDPAL G, WEISSMAN S M. Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region specific markers[J]. Proc Natl Acad Sci USA, 1994, 91(1): 88-92. doi: 10.1073/pnas.91.1.88
    [32]
    ARMOUR J A, NEUMANN R, GOBERT S, et al. Isolation of human simple repeat loci by hybridization selection[J]. Hum Mol Genet, 1994, 3(4): 599-605. doi: 10.1093/hmg/3.4.599
    [33]
    LI Q, PARK C, KIJIMA A. Isolation and characterization of microsatellite loci in the Pacific abalone (Haliotis Discus hannai) [J]. J Shellf Res, 2002, 21(2): 811-815. https://www.researchgate.net/publication/279598661_Isolation_and_characterization_of_microsatellite_loci_in_the_Pacific_abalone_Haliotis_discus_hannai
    [34]
    LI Q, PARK C, KIJIMA A. A llelic transmission of microsatellites and application to kinship analysis in newly hatched Pacific abalone larvae [J]. Fish Sci, 2003, 69(5): 881-887. doi: 10.1046/j.1444-2906.2003.00703.x
    [35]
    BRONW J L, HARDWICK J, WRIGHT A F. A simple method for rapid isolation of microsatellites from yeast artificial chromosomes[J]. Mol Cellular Probes, 1995, 9(1): 53-58. doi: 10.1016/s0890-8508(95)91022-0
    [36]
    GAO G Q, HE G H, LI Y R. Microsatellite enrichment from AFLP fragments by magnetic beads[J]. Acta Botanica Sinica, 2003, 45(11): 1266-1269. https://www.researchgate.net/publication/255610745_Microsatellite_Enrichment_from_AFLP_Fragments_by_Magnetic_Beads
    [37]
    韩柱强, 高国庆, 韦鹏霄, 等. 利用标记分析栽培花生多态性及亲缘关系[J]. 花生学报, 2003, 32(增刊): 295-300.
    [38]
    ZANE L, BARGELLON L, PATARNELLO T. Strategies for microsatellite isolation: a review[J]. Mol Ecol, 2002, 11(1): 1-16. doi: 10.1046/j.0962-1083.2001.01418.x
    [39]
    高国庆, HE G H, 李杨瑞. 花生微卫星DNA分离方法的研究[J]. 中国油料作物学报, 2003, 25(3): 30-33. https://cpfd.cnki.com.cn/Article/CPFDTOTAL-GXKX200311001003.htm
    [40]
    孙效文, 鲁翠云, 梁利群. 磁珠富集法分离草鱼微卫星分子标记[J]. 水产学报, 2005, 29(4): 482-486. https://kns.cnki.net/kcms2/article/abstract?v=NK8hpUzgeRXVf1Yc3ad6xRzkvhKTFd924OMHtuq2lbeStgjqd-XeqyuqUhtJ-658bPUfX6V6-W0MqGbnhAqM-OvSD_E7090tmJvNIaOW-QQER9i6NmASG9Z57oVpjzmYaAtbhrGUfdhz_wCxMh2Wq1_hKOHHFMIYvoEFzNPKXrfZkRaTAI4aIOLKh68ZFO7X&uniplatform=NZKPT&language=CHS
    [41]
    巍东旺, 楼允东, 孙效文, 等. 鲤鱼微卫星分子标记的筛选[J]. 动物学研究, 2001, 22(3): 238-241. doi: 10.3321/j.issn:0254-5853.2001.03.013
    [42]
    徐鹏, 周岭华, 相建海, 等. 中国对虾微卫星DNA的筛选[J]. 海洋与湖沼, 2001, 32(3): 255-259. doi: 10.3321/j.issn:0029-814X.2001.03.004
    • Related Articles

  • Related Articles

    [1]LI Bingbu, WANG Guixing, ZHANG Xiaoyan, LIU Yufeng, HE Zhongwei, CAO Wei, REN Jiangong, REN Yuqin, ZHANG Yitong, SAN Lize, WANG Yufen, HOU Jilun. Association analysis of SNPs polymorphisms in mstn gene of Paralichthys olivaceus with growth traits[J]. South China Fisheries Science, 2024, 20(2): 119-128. DOI: 10.12131/20230165
    [2]HUANG Guoqiang, CAO Suhui, LIU Xujia, PENG Yinhui, LIU Yonghong, HUANG Lianghua, ZHONG Shengping. A preliminary study on enrichment of stable isotope from diets by mud crab (Scylla paramamosain)[J]. South China Fisheries Science, 2021, 17(3): 19-26. DOI: 10.12131/20200227
    [3]ZHU Bing, FAN Jiajia, BAI Junjie, JIANG Peng. Gold grass carp microsatellite polymorphism and its comparative analysis with four grass carp populations from China[J]. South China Fisheries Science, 2017, 13(2): 51-58. DOI: 10.3969/j.issn.2095-0780.2017.02.007
    [4]WANG Chunxiao, GAO Fengying, LU Maixin, LIU Zhigang, ZHU Huaping, YE Xing. Sequence polymorphism of 5′-flanking regions of GHSR genes and genetic diversity of two populations of Nile tilapia (Oreochromis niloticus)[J]. South China Fisheries Science, 2015, 11(1): 18-25. DOI: 10.3969/j.issn.2095-0780.2015.01.003
    [5]OU Yanyan, LIU Zhigang, LIU Jinshang. Study on body-color polymorphism of Chlamys nobilis in Liusha Bay[J]. South China Fisheries Science, 2012, 8(5): 15-24. DOI: 10.3969/j.issn.2095-0780.2012.05.003
    [6]ZHU Lijing, SUN Zhongxiang, CHEN Shuyin, JI Hongjiu, XU Xiaofeng, SHEN Songdong. Microsatellite enrichment by magnetic beads in Coelomactra antiquate[J]. South China Fisheries Science, 2011, 7(4): 10-15. DOI: 10.3969/j.issn.2095-0780.2011.04.002
    [7]LI Jun, YU Ziniu. Single nucleotide polymorphisms and their application in genetic studies on marine organisms[J]. South China Fisheries Science, 2010, 6(3): 74-80. DOI: 10.3969/j.issn.1673-2227.2010.03.014
    [8]ZHOU Fa-lin, JIANG Shi-gui, JIANG Yong-jie, HUANG Jian-hua, MA Zhi-ming. Polymorphism of mtDNA 16S rRNA gene and control region sequence in Penaeus monodon of Sanya, Hainan[J]. South China Fisheries Science, 2006, 2(6): 13-18.
    [9]GONG Jinbo, SU Tianfeng, XIA Junhong, GONG Shiyuan, JIANG Shigui. Polymorphism study of the mitochondrial DNA D-loop control region sequences from black porgy Acanthopagrus schlegeli, in the costal waters of China[J]. South China Fisheries Science, 2006, 2(4): 24-30.
    [10]YU Dahui, WANG Xiaoyu, GUO Yihui, HUANG Guiju, WANG Aimin. Segregation of RAPD markers in F1 generation of Pinctada fucata family[J]. South China Fisheries Science, 2005, 1(6): 1-7.

Catalog

    Get Citation
    PDF
    XML
    Article views (5102) PDF downloads (3236) Cited by()
    Related

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

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return