BanSatDB, a whole-genome-based database of putative and experimentally validated microsatellite markers of three Musa species
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摘要
The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%–32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB(http://webtom.cabgrid.res.in/bansatdb/) having the highest number(>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata(110,000), M. balbisiana(107,000), and M. itinerans(124,000)from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types(simple or compound),repeat nucleotides(1–6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability(DUS) tests of variety identification and for marker assisted selection(MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity.
The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%–32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB(http://webtom.cabgrid.res.in/bansatdb/) having the highest number(>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata(110,000), M. balbisiana(107,000), and M. itinerans(124,000)from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types(simple or compound),repeat nucleotides(1–6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability(DUS) tests of variety identification and for marker assisted selection(MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity.
The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%–32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB(http://webtom.cabgrid.res.in/bansatdb/) having the highest number(>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata(110,000), M. balbisiana(107,000), and M. itinerans(124,000)from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types(simple or compound),repeat nucleotides(1–6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability(DUS) tests of variety identification and for marker assisted selection(MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity.
引文
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[19]T.Rotchanapreeda,S.Wongniam,S.C.Swangpol,P.P.Chareonsap,N.Sukkaewmanee,J.Somana,Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas,Plant Syst.Evol.302(2016)739-761.
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[2]A.Lamare,S.R.Rao,Efficacy of RAPD,ISSR and DAMDmarkers in assessment of genetic variability and population structure of wild Musa acuminata colla,Physiol.Mol.Biol.Plants 21(2015)349-358,https://doi.org/10.1007/s12298-015-0295-1.
[3]P.Christelová,M.Valárik,E.H?ibová,I.Van den Houwe,S.Channelière,N.Roux,J.Dole?el,A platform for efficient genotyping in Musa using microsatellite markers,AoB Plants2011(2011),plr024.
[4]M.de Vries,C.A.Ferwerda,J.D.Flach,Choice of food crops in relation to actual and potential production in the tropics,Netherlands,J.Agric.Sci.15(1967)241-248.
[5]K.L.Durell,Intellectual Property Protection for Plant Derived Vaccine Technology:Here They Come are we Ready or Not?Lex Electronica,Vol.10,No.3,Hiver/Winter,http://www.lexelectronica.org/files/sites/103/10-3_durell.pdf 2006,Accessed date:16 November 2017.
[6]A.D'Hont,F.Denoeud,J.M.Aury,F.C.Baurens,F.Carreel,O.Garsmeur,B.Noel,S.Bocs,G.Droc,M.Rouard,C.Da Silva,K.Jabbari,C.Cardi,J.Poulain,M.Souquet,K.Labadie,C.Jourda,J.Lengellé,M.Rodier-Goud,A.Alberti,M.Bernard,M.Correa,S.Ayyampalayam,M.R.Mckain,J.Leebens-Mack,D.Burgess,M.Freeling,D.Mbéguié-A-Mbéguié,M.Chabannes,T.Wicker,O.Panaud,J.Barbosa,E.Hribova,P.Heslop-Harrison,R.Habas,R.Rivallan,P.Francois,C.Poiron,A.Kilian,D.Burthia,C.Jenny,F.Bakry,S.Brown,V.Guignon,G.Kema,M.Dita,C.Waalwijk,S.Joseph,A.Dievart,O.Jaillon,J.Leclercq,X.Argout,E.Lyons,A.Almeida,M.Jeridi,J.Dolezel,N.Roux,A.M.Risterucci,J.Weissenbach,M.Ruiz,J.C.Glaszmann,F.Quétier,N.Yahiaoui,P.Wincker,The banana(Musa acuminata)genome and the evolution of monocotyledonous plants,Nature 488(2012)213-217.
[7]M.W.Davey,R.Gudimella,J.A.Harikrishna,L.W.Sin,N.Khalid,J.Keulemans,A draft Musa balbisiana genome sequence for molecular genetics in polyploid,inter-and intra-specific Musa hybrids,BMC Genomics 14(2013)683.
[8]W.Wu,Y.Yang,W.He,M.Rouard,W.Li,M.Xu,Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus,Sci.Rep.6(2016),31586.
[9]B.J.Till,J.Jankowicz-Cieslak,L.Sági,O.A.Huynh,H.Utsushi,R.Swennen,R.Terauchi,C.Mba,Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling,Theor.Appl.Genet.121(2010)1381-1389.
[10]G.L.Jiang,Molecular markers and marker-assisted breeding in plants,in:S.B.Andersen(Ed.),Plant Breeding from Laboratories to Fields,InTech,2013,https://doi.org/10.5772/52583(Available from)https://www.intechopen.com/books/plant-breeding-from-laboratories-to-fields/molecularmarkers-and-marker-assisted-breeding-in-plants.
[11]A.D.Twyford,R.A.Ennos,Next-generation hybridization and introgression,Heredity 108(2012)179-189.
[12]J.E.Zalapa,H.Cuevas,H.Zhu,S.Steffan,D.Senalik,E.Zeldin,B.McCown,R.Harbut,P.Simon,Using nextgeneration sequencing approaches to isolate simple sequence repeat(SSR)loci in the plant sciences,Am.J.Bot.99(2012)193-208.
[13]H.Ellegren,Microsatellites:simple sequences with complex evolution,Nat.Rev.Genet.5(2004)435-445.
[14]G.Droc,D.Lariviere,V.Guignon,N.Yahiaoui,D.This,O.Garsmeur,A.Dereeper,C.Hamelin,X.Argout,J.F.Dufayard,J.Lengelle,F.C.Baurens,A.Cenci,B.Pitollat,A.D'Hont,M.Ruiz,M.Rouard,S.Bocs,The banana genome hub,Database 2013(2013),bat035.
[15]M.K.Biswas,Y.Liu,C.Li,O.Sheng,C.Mayer,G.Yi,Genomewide computational analysis of Musa microsatellites:classification,cross-taxon transferability,functional annotation,association with transposons&miRNAs,and genetic marker potential,PLoS One 10(2015),e0131312.
[16]C.Hamelin,G.Sempere,V.Jouffe,M.Ruiz,TropGeneDB,the multi-tropical crop information system updated and extended,Nucleic Acids Res.41(2013)D1172-D1175.
[17]M.Ruas,V.Guignon,G.Sempere,J.Sardos,Y.Hueber,H.Duvergey,A.Andrieu,R.Chase,C.Jenny,T.Hazekamp,B.Irish,K.Jelali,J.Adeka,T.Ayala-Silva,C.P.Chao,J.Daniells,B.Dowiya,B.Effa effa,L.Gueco,L.Herradura,L.Ibobondji,E.Kempenaers,J.Kilangi,S.Muhangi,P.Ngo Xuan,J.Paofa,C.Pavis,D.Thiemele,C.Tossou,J.Sandoval,A.Sutanto,G.Vangu Paka,G.Yi,I.Van den Houwe,N.Roux,M.Rouard,MGIS:managing banana(Musa spp.)genetic resources information and high-throughput genotyping data,Database2017(2017)(bax046).
[18]C.Witherup,D.Ragone,T.Wiesner-Hanks,B.Irish,B.Scheffler,S.Simpson,F.Zee,M.I.Zuberi,N.J.C.Zerega,Development of microsatellite loci in Artocarpus altilis(Moraceae)and cross-amplification in congeneric species,Appl.Plant Sci.1(2013),1200423.
[19]T.Rotchanapreeda,S.Wongniam,S.C.Swangpol,P.P.Chareonsap,N.Sukkaewmanee,J.Somana,Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas,Plant Syst.Evol.302(2016)739-761.
[20]T.Thiel,W.Michalek,R.Varshney,A.Graner,Exploiting ESTdatabases for the development and characterization of genederived SSR-markers in barley(Hordeum vulgare L.),Theor.Appl.Genet.106(2003)411-422.
[21]S.Rozen,H.Skaletsky,Primer3 on the WWW for general users and for biologist programmers,in:S.Misener,S.A.Krawetz(Eds.),Methods in Molecular Biology,Bioinformatics Methods and Protocols,Vol.132,Humana Press Inc,Totowa,New Jersey,USA 2000,pp.365-386.
[22]N.Simmonds,The Evolution of the Bananas,Longmans,London,UK,1962.
[23]R.Ortiz,R.Swennen,From crossbreeding to biotechnologyfacilitated improvement of banana and plantain,Biotechnol.Adv.32(2014)158-169.
[24]C.Shioiri,N.Takahata,Skew of mononucleotide frequencies,relative abundance of dinucleotides,and DNA strand asymmetry,J.Mol.Evol.53(2001)364-376.
[25]G.Haseneyer,T.Schmutzer,M.Seidel,R.Zhou,M.Mascher,C.C.Sch?n,S.Taudien,U.Scholz,N.Stein,K.F.Mayer,E.Bauer,From RNA-seq to large-scale genotyping-genomics resources for rye(Secale cereale L.),BMC Plant Biol.11(2011)131.
[26]E.Zietkiewicz,A.Rafalski,D.Labuda,Genome fingerprinting by simple sequence repeat(SSR)-anchored polymerase chain reaction amplification,Genomics 20(1994)176-183.
[27]M.J.Lawson,L.Zhang,V.Tech,Distinct patterns of SSRdistribution in the Arabidopsis thaliana and rice genomes,Genome Biol.7(2006)R14.
[28]P.F.Cavagnaro,D.A.Senalik,L.Yang,P.W.Simon,T.T.Harkins,C.D.Kodira,S.Huang,Y.Weng,Genome-wide characterization of simple sequence repeats in cucumber(Cucumis sativus L.),BMC Genomics 11(2010)569.
[29]I.R.G.Sequencing Project,The map-based sequence of the rice genome,Nature 436(2005)793-800.
[30]S.Li,T.Yin,Map and analysis of microsatellites in the genome of Populus:the first sequenced perennial plant,Sci.China Ser.C Life Sci.50(2007)690-699.
[31]J.Chen,N.Wang,L.C.Fang,Z.C.Liang,S.H.Li,B.H.Wu,Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries,BMC Plant Biol.15(2015)28.
[32]V.Arora Sarika,M.A.Iquebal,A.Rai,D.Kumar,PIPEMicroDB:microsatellite database and primer generation tool for pigeonpea genome,Database 2013(2013),bas054..
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