DNA分子标记技术的研究与应用
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摘要
DNA分子标记是继传统的形态学标记、细胞学标记、生化标记之后发展起来的以DNA为基础的遗传标记技术,因其独有的技术特点,迅速在各领域得到广泛的应用与发展。本研究总结概括了基于m RNA的表达序列标签(ESTs)、差异显示逆转录PCR (DDRT-PCR)、特征性差异分析(RDA)、基因表达系列分析(SAGE);基于目的基因的保守DNA衍生多态性(CDDP)、目标起始密码子多态性(SCoT)、保守区域扩增多态性(Co-RAP)和基于反转录转座子的反转录转座子位点间扩增多态性(IRAP)、反转录转座子-微卫星扩增多态性(REMAP)等几种新型DNA分子标记技术的原理、特点、优缺点,以及常见DNA分子标记技术的特点比较及其应用,以期在其基础上推动分子标记技术进一步融合、创新与发展。
DNA molecular marker is a DNA-based genetic marker technique which is developed after morphological marker, cytological marker and biochemical marker. It has been widely used and developed in various fields, due to its unique technical characteristic. In this research, the principle, characteristics, advantages and disadvantages of some new DNA molecular marker techniques were reviewed, such as the expressed sequence tags(ESTs), differential display reverse transcription PCR(DDRT-PCR), representative difference analysis(RDA),serial analysis of gene expression(SAGE) based on m RNA; the conserved DNA-derived polymorphism(CDDP), start codon targeted polymorphism(SCoT), conserved region amplification polymorphism(CoRAP) based on purpose gene; and the inter-retrotransposon amplified polymorphism(IRAP), retrotransposon-microsatellite amplified polymorphism(REMAP) based on retrotransposon. Meanwhile, the characteristics and application of several type of molecular markers were compared here aimed to promote the further integration, innovation and development of DNA molecular marker technique.
DNA molecular marker is a DNA-based genetic marker technique which is developed after morphological marker, cytological marker and biochemical marker. It has been widely used and developed in various fields, due to its unique technical characteristic. In this research, the principle, characteristics, advantages and disadvantages of some new DNA molecular marker techniques were reviewed, such as the expressed sequence tags(ESTs), differential display reverse transcription PCR(DDRT-PCR), representative difference analysis(RDA),serial analysis of gene expression(SAGE) based on m RNA; the conserved DNA-derived polymorphism(CDDP), start codon targeted polymorphism(SCoT), conserved region amplification polymorphism(CoRAP) based on purpose gene; and the inter-retrotransposon amplified polymorphism(IRAP), retrotransposon-microsatellite amplified polymorphism(REMAP) based on retrotransposon. Meanwhile, the characteristics and application of several type of molecular markers were compared here aimed to promote the further integration, innovation and development of DNA molecular marker technique.
引文
Adams M.D.,and Ve n ter J.C.,1991,Complementary DNA sequencing:expressed sequence tags and human genome project,Science,252(5013):1651-1656
Alain V.,Denis M.,Magali S.C.,and AndréE.,2002,A review on SNP and other types of molecular markers and their use in animal genetics,Genet.Sel.Evol.,34(3):275-305
Bachem C.W.,Rs V.D.H.,de Bruijn S.M.,Vreugdenhil D.,Zabeau M.,and Visser R G.,1996,Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP:analysis of gene expression during potato tuber development,Plant J.Cell Mol.Biol.,9(5):745
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Collard B.C.Y.,and Mackill D.J.,2009a,Conserved DNA-Derived Polymorphism(CDDP):A simple and novel method for generating DNA markers in plants,Plant Mol.Biol.Rep.,27(4):558-562
Collard B.C.Y.,and Mackill D.J.,2009b,Start codon targeted(SCoT)polymorphism:A simple,novel DNA marker technique for generating gene-targeted markers in plants,Plant Mol.Biol.Rep.,27(1):86-93
Dong J.,Ye Q.L.,Wang F.S.,and Li C.,2010,The mining of citrus EST-SNP and its application in cultivar discrimination,J.Integr.Agric.,9(2):179-190
Ferriol M.,PicóM.B.,and Nuez F.,2003,Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers,Genet.Resour.Crop Evol.,50(3):227-238
Hebert P.D.,Cywinska A.,Ball S.L.,and Dewaard J.R.,2003,Biolog ical identifications through DNA barcodes,270(1512):313-321
Hu Y.,Li Y.,Huang Y.Z.,and Liu P.W.,2016,Genetic diversity evaluation of sugarcane varieties using SSR and RAPDmarkers,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):2494-2503(胡杨,李赟,黄有总,刘平武,2016,利用SSR与RAPD分子标记评估甘蔗品种的遗传多样性,基因组学与应用生物学,35(9):2494-2503)
Jiang L.,and Zang D.,2017,Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers,Biotechnol.Biotechnol.Equip.,32(1):88-94
Kalendar R.,Grob T.,Regina M.,Suoniemi A.,and Schulman A.,1999,IRAP and REMAP:two new retrotransposon-based DNA fingerprinting techniques,Theor.Appl.Genet.,98(5):704-711
Konieczny A.,and Ausubel F.M.,1993,A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers,Plant J.Cell Mol.Biol.,4(2):403-410
Lander E.S.,1996,The new genomics:global views of biology,Science,274(5287):536-569
Leigh F.,Kalendar R.,Lea V.,Lee D.,Donini P.,and Schulman A.H.,2003,Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.,Mol.Genet.Genomics,269(4):464-474
Li G.,and Quiros C.F.,2001,Sequence-related amplified polymorphism(SRAP),a new marker system based on a simple PCR reaction:its application to mapping and gene tagging in Brassica,Theor.Appl.Genet.,103(2-3):455-461
Li Y.Y.,2013,Conserved DNA-derived polymorphism marker technique and its application,Shengwu Jishu(Biotechnology),23(4):78-83(李莹莹,2013,保守DNA衍生多态性CDDP分子标记技术及其应用,生物技术,23(4):78-83)
Liang P.,and Pardee A.B.,1992,Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction,Science,257(5072):967-971
Lisitsyn N.,Lisitsyn N.,and Wigler M.,1993,Cloning the differences between two complex genomes,Science,259(5097):946-951
Mahjbi A.,Baraket G.,Oueslati A.,and Salhi-Hannachi A.,2015,Start codon targeted(SCoT)markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species,Biochem.Syst.Ecol.,61:390-398
Noormohammadi Z.,Khalili N.I.,Baraki S.G,Sheidai M.,and Alishah O.,2016,Genetic screening of diploid and tetraploid cotton cultivars based on retrotransposon microsatellite amplified polymorphism markers(REMAP),An.Biol.,38:123-132
Velculescu V.E.,Zhang L.,Vogelstein B.,and Kinzler K.W.,1995,Serial analysis of gene expression,Science,270(5235):271-284
Vos P.,Hogers R.,Bleeker M.,Reijans M.,Van D.L.T.,Hornes M.,Frijters A.,Pot J.,Peleman J.,and Kuiper M.,1995,AFLP:a new technique for DNA fingerprinting,Nucleic Acids Res.,23(21):4407-4414
Vuylsteke M.,Peleman J.D.,and van Eijk M.J.,2007,AFLPtechnology for DNA fingerprinting,Nat.Protoc.,2(6):1387-1398
Wang L.Y.,Du Y.C.,Zhang B.,Shi Y.,Wang Q.J.,and Zhao F.K.,2008,Development of molecular markers IRAP and REMAP in eggplant,Yuanyi Xuebao(Acta Horticulturae Sinica),35(9):1363-1367(王利英,杜永臣,张斌,石瑶,王秋锦,赵福宽,2008,茄子IRAP和REMAP分子标记的开发,园艺学报,35(9):1363-1367)
Wang M.H.,Xi J.J.,Chen L.Y.,and Zhao L.W.,2017,Molecular marker technique based on molecular hybridization,Zhiwu Yisheng(Plant Doctor),30(9):48-51(王明湖,席杰君,陈玲瑜,赵丽稳,2017,分子杂交为核心的分子标记技术,植物医生,30(9):48-51)
Wang Q.,Zhang B.,and Lu Q.,2009,Conserved region amplification polymorphism(Co RAP),a novel marker technique for plant genotyping in salvia miltiorrhiza,Plant Mol.Biol.Rep.,27(2):139-143
Welsh J.,and Mcclelland M.,1990,Fingerprinting genomes using PCR with arbitrary primers,Nucleic Acids Res.,18(24):7213-7218
Williams J.G.,Kubelik A.R.,Livak K.J.,Rafalski J.A.,and Tingey S.V.,1990,DNA polymorphisms amplified by arbitrary primers are useful as genetic markers,Nucleic Acids Res.,18(22):6531-6535
Zhang J.J.,and Han B.,2011,Research advancement of EST in the Gramineae plants,Zhiwu Shenglixuebao(Plant Physiology Journal),47(3):229-234(张佳佳,韩冰,2011,禾本科植物EST的研究进展,植物生理学报,47(3):229-234)
Zhang Y.,2014,The production of molecular markers and the design of primers,Jiangsu Nongye Kexue(Jiangsu Agricultural Sciences),42(6):47-51(张羽,2014,分子标记技术的产生与引物设计,江苏农业科学,42(6):47-51)
Alain V.,Denis M.,Magali S.C.,and AndréE.,2002,A review on SNP and other types of molecular markers and their use in animal genetics,Genet.Sel.Evol.,34(3):275-305
Bachem C.W.,Rs V.D.H.,de Bruijn S.M.,Vreugdenhil D.,Zabeau M.,and Visser R G.,1996,Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP:analysis of gene expression during potato tuber development,Plant J.Cell Mol.Biol.,9(5):745
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Collard B.C.Y.,and Mackill D.J.,2009a,Conserved DNA-Derived Polymorphism(CDDP):A simple and novel method for generating DNA markers in plants,Plant Mol.Biol.Rep.,27(4):558-562
Collard B.C.Y.,and Mackill D.J.,2009b,Start codon targeted(SCoT)polymorphism:A simple,novel DNA marker technique for generating gene-targeted markers in plants,Plant Mol.Biol.Rep.,27(1):86-93
Dong J.,Ye Q.L.,Wang F.S.,and Li C.,2010,The mining of citrus EST-SNP and its application in cultivar discrimination,J.Integr.Agric.,9(2):179-190
Ferriol M.,PicóM.B.,and Nuez F.,2003,Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers,Genet.Resour.Crop Evol.,50(3):227-238
Hebert P.D.,Cywinska A.,Ball S.L.,and Dewaard J.R.,2003,Biolog ical identifications through DNA barcodes,270(1512):313-321
Hu Y.,Li Y.,Huang Y.Z.,and Liu P.W.,2016,Genetic diversity evaluation of sugarcane varieties using SSR and RAPDmarkers,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):2494-2503(胡杨,李赟,黄有总,刘平武,2016,利用SSR与RAPD分子标记评估甘蔗品种的遗传多样性,基因组学与应用生物学,35(9):2494-2503)
Jiang L.,and Zang D.,2017,Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers,Biotechnol.Biotechnol.Equip.,32(1):88-94
Kalendar R.,Grob T.,Regina M.,Suoniemi A.,and Schulman A.,1999,IRAP and REMAP:two new retrotransposon-based DNA fingerprinting techniques,Theor.Appl.Genet.,98(5):704-711
Konieczny A.,and Ausubel F.M.,1993,A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers,Plant J.Cell Mol.Biol.,4(2):403-410
Lander E.S.,1996,The new genomics:global views of biology,Science,274(5287):536-569
Leigh F.,Kalendar R.,Lea V.,Lee D.,Donini P.,and Schulman A.H.,2003,Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.,Mol.Genet.Genomics,269(4):464-474
Li G.,and Quiros C.F.,2001,Sequence-related amplified polymorphism(SRAP),a new marker system based on a simple PCR reaction:its application to mapping and gene tagging in Brassica,Theor.Appl.Genet.,103(2-3):455-461
Li Y.Y.,2013,Conserved DNA-derived polymorphism marker technique and its application,Shengwu Jishu(Biotechnology),23(4):78-83(李莹莹,2013,保守DNA衍生多态性CDDP分子标记技术及其应用,生物技术,23(4):78-83)
Liang P.,and Pardee A.B.,1992,Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction,Science,257(5072):967-971
Lisitsyn N.,Lisitsyn N.,and Wigler M.,1993,Cloning the differences between two complex genomes,Science,259(5097):946-951
Mahjbi A.,Baraket G.,Oueslati A.,and Salhi-Hannachi A.,2015,Start codon targeted(SCoT)markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species,Biochem.Syst.Ecol.,61:390-398
Noormohammadi Z.,Khalili N.I.,Baraki S.G,Sheidai M.,and Alishah O.,2016,Genetic screening of diploid and tetraploid cotton cultivars based on retrotransposon microsatellite amplified polymorphism markers(REMAP),An.Biol.,38:123-132
Velculescu V.E.,Zhang L.,Vogelstein B.,and Kinzler K.W.,1995,Serial analysis of gene expression,Science,270(5235):271-284
Vos P.,Hogers R.,Bleeker M.,Reijans M.,Van D.L.T.,Hornes M.,Frijters A.,Pot J.,Peleman J.,and Kuiper M.,1995,AFLP:a new technique for DNA fingerprinting,Nucleic Acids Res.,23(21):4407-4414
Vuylsteke M.,Peleman J.D.,and van Eijk M.J.,2007,AFLPtechnology for DNA fingerprinting,Nat.Protoc.,2(6):1387-1398
Wang L.Y.,Du Y.C.,Zhang B.,Shi Y.,Wang Q.J.,and Zhao F.K.,2008,Development of molecular markers IRAP and REMAP in eggplant,Yuanyi Xuebao(Acta Horticulturae Sinica),35(9):1363-1367(王利英,杜永臣,张斌,石瑶,王秋锦,赵福宽,2008,茄子IRAP和REMAP分子标记的开发,园艺学报,35(9):1363-1367)
Wang M.H.,Xi J.J.,Chen L.Y.,and Zhao L.W.,2017,Molecular marker technique based on molecular hybridization,Zhiwu Yisheng(Plant Doctor),30(9):48-51(王明湖,席杰君,陈玲瑜,赵丽稳,2017,分子杂交为核心的分子标记技术,植物医生,30(9):48-51)
Wang Q.,Zhang B.,and Lu Q.,2009,Conserved region amplification polymorphism(Co RAP),a novel marker technique for plant genotyping in salvia miltiorrhiza,Plant Mol.Biol.Rep.,27(2):139-143
Welsh J.,and Mcclelland M.,1990,Fingerprinting genomes using PCR with arbitrary primers,Nucleic Acids Res.,18(24):7213-7218
Williams J.G.,Kubelik A.R.,Livak K.J.,Rafalski J.A.,and Tingey S.V.,1990,DNA polymorphisms amplified by arbitrary primers are useful as genetic markers,Nucleic Acids Res.,18(22):6531-6535
Zhang J.J.,and Han B.,2011,Research advancement of EST in the Gramineae plants,Zhiwu Shenglixuebao(Plant Physiology Journal),47(3):229-234(张佳佳,韩冰,2011,禾本科植物EST的研究进展,植物生理学报,47(3):229-234)
Zhang Y.,2014,The production of molecular markers and the design of primers,Jiangsu Nongye Kexue(Jiangsu Agricultural Sciences),42(6):47-51(张羽,2014,分子标记技术的产生与引物设计,江苏农业科学,42(6):47-51)