SNP技术在葡萄研究中的应用进展
|
摘要
自单核苷酸多态性(Single Nucleotide Polymorphism,SNP)技术问世以来,在葡萄杂交育种和分子设计育种、品种鉴定、数量性状位点(quantitative trait locus,QTL)鉴定等领域已得到广泛应用。本文综述了前、后基因组时代SNP技术在葡萄研究中的应用与发展。在后基因组时代,SNP技术的发展更加迅猛,特别是近3年来利用SNP技术在葡萄果实性状、抗病性及品种鉴定等领域的应用明显增多,说明其应用前景广阔。并预测该技术在葡萄设计育种领域将会引起更多的关注。
Since the advent of SNP(Single Nucleotide Polymorphism) technique, it has been widely used in grape cross breeding, molecular design breeding, variety identi?cation, QTL(quantitative trait locus) identi?cation and other ?elds. In this paper, the application and development of SNP technology in grape research in pre-genome and post-genome era were reviewed. In the post-genome era, SNP technology has developed rapidly. In the past three years, more and more studies were applied on grapes, particularly, in the ?eld of fruit character, disease resistance and variety identi?cation has increased clearly, and its application prospect will be broader. It is predicted that this technique will attract more attention in the ?eld of grape design breeding.
Since the advent of SNP(Single Nucleotide Polymorphism) technique, it has been widely used in grape cross breeding, molecular design breeding, variety identi?cation, QTL(quantitative trait locus) identi?cation and other ?elds. In this paper, the application and development of SNP technology in grape research in pre-genome and post-genome era were reviewed. In the post-genome era, SNP technology has developed rapidly. In the past three years, more and more studies were applied on grapes, particularly, in the ?eld of fruit character, disease resistance and variety identi?cation has increased clearly, and its application prospect will be broader. It is predicted that this technique will attract more attention in the ?eld of grape design breeding.
引文
[1]郜金荣.分子生物学[M].化学工业出版社,2011.
[2]石莹,李穆,何平,等.SNP技术及其在作物研究上的应用[J].汉斯农业科学杂志,2014,4(3):60-65.
[3]CHEVREUX B,PFISTERER T,DRESCHER B,et al.Using the miraEST Assembler for Reliable and Automated mRNATranscript Assembly Vezzulliand SNP Detection in Sequenced ESTs[J].Genome Research,2004,14(6):1147-1159.
[4]TROGGIO M,MALACARNE G,COPPOLA G,et al.A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine(Vitis vinifera L.)Anchoring Pinot Noir Bacterial Artificial Chromosome[J].Contigs Genetics,2007,176(4):2637-2650.
[5]VEZZULLI S,TROGGIO M,COPPOLA G,et al.A reference integrated map for cultivated grapevine(Vitis vinifera L.)from three crosses,based on 283 SSR and 501 SNP-based markers[J].Theoretical Applied and Genetics,2008,117(4):499-511.
[6]JAILLON O,AURY J M,NOEL B,et al.The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J].Nature,2007,449(7161):463-467.
[7]LIJAVETZKY D,CABEZAS JA,IBá?EZ A,et al.High throughput SNP discovery and genotyping in grapevine(Vitis vinifera L.)by combining a re-sequencing approach and SNPlex technology[J].BMC Genomics,2007,8:424.
[8]VEZZULLI S,MICHELETTI D,RIAZ S,et al.A SNPtransferability survey within the genus Vitis[J].BMC Plant Biology,2008(8):128.
[9]PINDO M,VEZZULLI S,COPPOLA G,et al.SNP highthroughput screening in grapevine using the SNPlex?genotyping system[J].Bmc Plant Biology,2008,8(1):12.
[10]MYLES S,CHIA JM,HURWITZ B,et al.Rapid Genomic Characterization of the Genus Vitis[J].PLoS One,2010,5(1):e8219.
[11]MILLER A J,MATASCI N,SCHWANINGER H,et al.Vitis Phylogenomics:Hybridization Intensities from a SNP Array Outperform Genotype Calls[J].PLoS One,2013,8(11):e78680.
[12]DE LORENZIS G,CHIPASHVILI R,FAILLA O,et al.Study of genetic variability in Vitis vinifera L.germplasm by highthroughput Vitis18kSNP array:the case of Georgian genetic resources[J].BMC Plant Biology,2015,15:154.
[13]CHEN J,WANG N,FANG L C,et al.Construction of a highdensity genetic map and QTLs mapping for sugars and acids in grape berries[J].BMC Plant Biololy,2015,15:28.
[14]HOUEL C,CHATBANYONG R,DOLIGEZ A,et al.Identification of stable QTLs for vegetative and reproductive traits in the microvine(Vitis vinifera L.)using the 18 K Infinium chip[J].BMC Plant Biology,2015,15(1):1-19.
[15]ZYPRIAN E,OCH?NER I,SCHWANDER F,et al.Quantitative trait loci affecting pathogen resistance and ripening of grapevines[J].Molecular Genetic and Genomics,2016,291(4):1573-1594.
[16]TELLO J,TORRES-PéREZ R,GRIMPLET J,et al.Association analysis of grapevine bunch traits using a comprehensive approach[J].Theoretical and Applied Genetics,2016,129(2):227-242.
[17]PEREIRA L,MARTINS-LOPES P.Vitis vinifera L.SingleNucleotide Polymorphism Detection with High-Resolution Melting Analysis Based on the UDP-Glucose Flavonoid3-O-Glucosyltransferase Gene[J].Journal of Agricultural Food and Chemistry,2015,63(41):9165-9174.
[18]CATALANO V,MORENO-SANZ P,LORENZI S,et al.Experimental Review of DNA-Based Methods for Wine Traceability and Development of a Single-Nucleotide Polymorphism(SNP)Genotyping Assay for Quantitative Varietal Authentication[J].Journal of Agricultural Food and Chemistry,2016,64(37):6969-6984.
[19]GUO D L,ZHAO H L,LI Q,et al.Genome-wide association study of berry related traits in grape[Vitis vinifera L.]based on genotyping-by-sequencing markers[J].Horticulture Research,2019,6:11.
[20]LIANG Z,DUAN S,SHENG J,et al.Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses[J].Nature Communications,2019,10(1):1190.
[21]LAUCOU V,LAUNAY A,BACILIERI R,et al.Extended diversity analysis of cultivated grapevine Vitis vinifera with 10Kgenome-wide SNPs[J].PLoS One,2018,13(2):e0192540.
[22]SAPKOTA S,CHEN L L,YANG S,et al.Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis derived'Norton'[J].Theoretical and Applied Genetic,2019,132(1):137-147.
[23]SMITH H M,SMITH B P,MORALES N B,et al.SNP markers tightly linked to root knot nematode resistance in grapevine(Vitis cinerea)identified by a genotyping-bysequencing approach followed by Sequenom MassARRAY validation[J].PLoS One,2018,13(2):e0193121.
[24]MA Z Y,WEN J,ICKERT-BOND SM,et al.Phylogenomics,biogeography,and adaptive radiation of grapes[J].Molecular Phylogenetics and Evolution,2018,129:258-267.
[25]DE LORENZIS G,MERCATI F,BERGAMINI C,et al.SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination[J].BMC Plant Biology,2019,19(1):7.
[26]GOMES S,CASTRO C,BARRIAS S,et al.Alternative SNP detection platforms,HRM and biosensors,for varietal identification in Vitis vinifera L.using F3H and LDOX genes[J].Scientifics Reports,2018,8(1):5850.
[27]KLEIN L L,MILLER A J,CIOTIR C,et al.High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDAVitis germplasm collections[J].American Journal of Botany,2018,105(2):215-226.
[28]DELAME M,PRADO E,BLANC S,et al.Introgression reshapes recombination distribution in grapevine interspecific hybrids[J/OL].(2018-12-08)[2019-01-20].https://link.springer.com/article/10.1007/s00122-018-3260-x.
[29]MERCENARO L,NIEDDU G,PORCEDDU A,et al.Sequence Polymorphisms and Structural Variations among Four Grapevine(Vitis vinifera L.)Cultivars Representing Sardinian Agriculture[J].Frontiers in Plant Science,2017(8):1279.
[30]MARRANO A,BIROLO G,PRAZZOLI,et al.MLSNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines(V.vinifera L.)[J].PLoS One,2017,12(1):e0170655.
[31]TABIDZE V,PIPIA I,GOGNIASHVILI M,et al.Whole genome comparative analysis of four Georgian grape cultivars[J].Molecular Genetics and Genomics,2017,292(6):1377-1389.
[32]ZHOU Y,MASSONNET M,SANJAK J S,et al.Evolutionary genomics of grape(Vitis vinifera ssp.vinifera)domestication[J].Proceedings of the National Academy of Sciences USA,2017,114(44):11715-11720.
[33]GOTO-YAMAMOTO N.Japan Wine,its characteristics and research[J].Bioscience Biotechnology and Biochemistry,2018(22):1-6.
[2]石莹,李穆,何平,等.SNP技术及其在作物研究上的应用[J].汉斯农业科学杂志,2014,4(3):60-65.
[3]CHEVREUX B,PFISTERER T,DRESCHER B,et al.Using the miraEST Assembler for Reliable and Automated mRNATranscript Assembly Vezzulliand SNP Detection in Sequenced ESTs[J].Genome Research,2004,14(6):1147-1159.
[4]TROGGIO M,MALACARNE G,COPPOLA G,et al.A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine(Vitis vinifera L.)Anchoring Pinot Noir Bacterial Artificial Chromosome[J].Contigs Genetics,2007,176(4):2637-2650.
[5]VEZZULLI S,TROGGIO M,COPPOLA G,et al.A reference integrated map for cultivated grapevine(Vitis vinifera L.)from three crosses,based on 283 SSR and 501 SNP-based markers[J].Theoretical Applied and Genetics,2008,117(4):499-511.
[6]JAILLON O,AURY J M,NOEL B,et al.The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J].Nature,2007,449(7161):463-467.
[7]LIJAVETZKY D,CABEZAS JA,IBá?EZ A,et al.High throughput SNP discovery and genotyping in grapevine(Vitis vinifera L.)by combining a re-sequencing approach and SNPlex technology[J].BMC Genomics,2007,8:424.
[8]VEZZULLI S,MICHELETTI D,RIAZ S,et al.A SNPtransferability survey within the genus Vitis[J].BMC Plant Biology,2008(8):128.
[9]PINDO M,VEZZULLI S,COPPOLA G,et al.SNP highthroughput screening in grapevine using the SNPlex?genotyping system[J].Bmc Plant Biology,2008,8(1):12.
[10]MYLES S,CHIA JM,HURWITZ B,et al.Rapid Genomic Characterization of the Genus Vitis[J].PLoS One,2010,5(1):e8219.
[11]MILLER A J,MATASCI N,SCHWANINGER H,et al.Vitis Phylogenomics:Hybridization Intensities from a SNP Array Outperform Genotype Calls[J].PLoS One,2013,8(11):e78680.
[12]DE LORENZIS G,CHIPASHVILI R,FAILLA O,et al.Study of genetic variability in Vitis vinifera L.germplasm by highthroughput Vitis18kSNP array:the case of Georgian genetic resources[J].BMC Plant Biology,2015,15:154.
[13]CHEN J,WANG N,FANG L C,et al.Construction of a highdensity genetic map and QTLs mapping for sugars and acids in grape berries[J].BMC Plant Biololy,2015,15:28.
[14]HOUEL C,CHATBANYONG R,DOLIGEZ A,et al.Identification of stable QTLs for vegetative and reproductive traits in the microvine(Vitis vinifera L.)using the 18 K Infinium chip[J].BMC Plant Biology,2015,15(1):1-19.
[15]ZYPRIAN E,OCH?NER I,SCHWANDER F,et al.Quantitative trait loci affecting pathogen resistance and ripening of grapevines[J].Molecular Genetic and Genomics,2016,291(4):1573-1594.
[16]TELLO J,TORRES-PéREZ R,GRIMPLET J,et al.Association analysis of grapevine bunch traits using a comprehensive approach[J].Theoretical and Applied Genetics,2016,129(2):227-242.
[17]PEREIRA L,MARTINS-LOPES P.Vitis vinifera L.SingleNucleotide Polymorphism Detection with High-Resolution Melting Analysis Based on the UDP-Glucose Flavonoid3-O-Glucosyltransferase Gene[J].Journal of Agricultural Food and Chemistry,2015,63(41):9165-9174.
[18]CATALANO V,MORENO-SANZ P,LORENZI S,et al.Experimental Review of DNA-Based Methods for Wine Traceability and Development of a Single-Nucleotide Polymorphism(SNP)Genotyping Assay for Quantitative Varietal Authentication[J].Journal of Agricultural Food and Chemistry,2016,64(37):6969-6984.
[19]GUO D L,ZHAO H L,LI Q,et al.Genome-wide association study of berry related traits in grape[Vitis vinifera L.]based on genotyping-by-sequencing markers[J].Horticulture Research,2019,6:11.
[20]LIANG Z,DUAN S,SHENG J,et al.Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses[J].Nature Communications,2019,10(1):1190.
[21]LAUCOU V,LAUNAY A,BACILIERI R,et al.Extended diversity analysis of cultivated grapevine Vitis vinifera with 10Kgenome-wide SNPs[J].PLoS One,2018,13(2):e0192540.
[22]SAPKOTA S,CHEN L L,YANG S,et al.Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis derived'Norton'[J].Theoretical and Applied Genetic,2019,132(1):137-147.
[23]SMITH H M,SMITH B P,MORALES N B,et al.SNP markers tightly linked to root knot nematode resistance in grapevine(Vitis cinerea)identified by a genotyping-bysequencing approach followed by Sequenom MassARRAY validation[J].PLoS One,2018,13(2):e0193121.
[24]MA Z Y,WEN J,ICKERT-BOND SM,et al.Phylogenomics,biogeography,and adaptive radiation of grapes[J].Molecular Phylogenetics and Evolution,2018,129:258-267.
[25]DE LORENZIS G,MERCATI F,BERGAMINI C,et al.SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination[J].BMC Plant Biology,2019,19(1):7.
[26]GOMES S,CASTRO C,BARRIAS S,et al.Alternative SNP detection platforms,HRM and biosensors,for varietal identification in Vitis vinifera L.using F3H and LDOX genes[J].Scientifics Reports,2018,8(1):5850.
[27]KLEIN L L,MILLER A J,CIOTIR C,et al.High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDAVitis germplasm collections[J].American Journal of Botany,2018,105(2):215-226.
[28]DELAME M,PRADO E,BLANC S,et al.Introgression reshapes recombination distribution in grapevine interspecific hybrids[J/OL].(2018-12-08)[2019-01-20].https://link.springer.com/article/10.1007/s00122-018-3260-x.
[29]MERCENARO L,NIEDDU G,PORCEDDU A,et al.Sequence Polymorphisms and Structural Variations among Four Grapevine(Vitis vinifera L.)Cultivars Representing Sardinian Agriculture[J].Frontiers in Plant Science,2017(8):1279.
[30]MARRANO A,BIROLO G,PRAZZOLI,et al.MLSNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines(V.vinifera L.)[J].PLoS One,2017,12(1):e0170655.
[31]TABIDZE V,PIPIA I,GOGNIASHVILI M,et al.Whole genome comparative analysis of four Georgian grape cultivars[J].Molecular Genetics and Genomics,2017,292(6):1377-1389.
[32]ZHOU Y,MASSONNET M,SANJAK J S,et al.Evolutionary genomics of grape(Vitis vinifera ssp.vinifera)domestication[J].Proceedings of the National Academy of Sciences USA,2017,114(44):11715-11720.
[33]GOTO-YAMAMOTO N.Japan Wine,its characteristics and research[J].Bioscience Biotechnology and Biochemistry,2018(22):1-6.