桃EST-SSR引物的开发及通用性分析
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摘要
本研究基于NCBI-EST数据库开发了4 526对桃EST-SSR引物,探究桃EST-SSR引物在蔷薇科30个物种的通用性,并对上述30个物种进行了聚类分析。结果表明,以单核苷酸、二核苷酸和三核苷酸重复最多,分别占35.80%、36.43%和25.56%;抽选了100对EST-SSR引物在12个桃品种中共扩增出237个条带,其中有79对引物具有多态性;期望杂合度平均为0.38;观察杂合度平均为0.12;引物鉴别力平均为0.41;66.67%的桃EST-SSR引物在30个蔷薇科物种中扩增出多态性条带,说明桃EST-SSR引物在蔷薇科植物中具有较高的通用性。
In this study, 4 526 pairs of EST-SSR primers from Prunus persica were developed based on NCBI-EST database to investigate the transferability of peach EST-SSR primers in 30 species of Rosaceae. Also,the cluster analysis of the above 30 species was carried out. The results showed that single nucleotide, dinucleotide and trinucleotide repeats accounted for 35.80%, 36.43% and 25.56% respectively. A total of 237 bands were amplified from 100 pairs of EST-SSR primers in 12 peach cultivars, of which 79 pairs were polymorphic. The average expected heterozygosity was 0.38, the average observed heterozygosity was 0.12, and the average primer discrimination was 0.41. 66.67% of peach EST-SSR primers amplified polymorphic bands in 30 Rosaceae species,indicating that peach EST-SSR primers have high transferability in Rosaceae plants.
In this study, 4 526 pairs of EST-SSR primers from Prunus persica were developed based on NCBI-EST database to investigate the transferability of peach EST-SSR primers in 30 species of Rosaceae. Also,the cluster analysis of the above 30 species was carried out. The results showed that single nucleotide, dinucleotide and trinucleotide repeats accounted for 35.80%, 36.43% and 25.56% respectively. A total of 237 bands were amplified from 100 pairs of EST-SSR primers in 12 peach cultivars, of which 79 pairs were polymorphic. The average expected heterozygosity was 0.38, the average observed heterozygosity was 0.12, and the average primer discrimination was 0.41. 66.67% of peach EST-SSR primers amplified polymorphic bands in 30 Rosaceae species,indicating that peach EST-SSR primers have high transferability in Rosaceae plants.
引文
Arús P.,Verde I.,Sosinski B.,Zhebentyayeva T.,and Abbott A.G.,2012,The peach genome,Tree Genetics&Genomes,8(3):531-547
Cipriani G.,Lot G.,Huang W.G.,Marrazzo M.T.,Peterlunger E.,and Testolin R.,1999,AC/GT and AG/CT microsatellite repeats in peach(Prunus persica(L.)Batsch):isolation,characterisation and cross-species amplification in Prunus,Theor.Appl.Genet.,99(1-2):65-72
Di Rienzo A.,Peterson A.C.,Garza J.C.,Valdes A.M.,Slatkin M.,and Freimer N.B.,1994,Mutational processes of simple-sequence repeat loci in human populations,Proc.Natl.Acad.Sci.USA,91(8):3166-3170
Dirlewanger E.,Cosson P.,Tavaud M.,Aranzana J.,Poizat C.,Zanetto A.,Arús P.,and Laigret F.,2002,Development of microsatellite markers in peach(Prunus persica(L.)Batsch)and their use in genetic diversity analysis in peach and sweet cherry(Prunus avium L.),Theor.Appl.Genet.,105(3):127-138
Gan L.,2006,Genetic diversity of in vitro culture of Pyrus detected by molecular markers,Thesis for M.S.,Sichuan Agricultural University,Supervisor:Tang H.R.,pp.16-17(甘玲,2006,梨离体保存材料遗传差异的分子检测,硕士学位论文,四川农业大学,导师:汤浩茹,pp.16-17)
Gao D.,Du F.,and Zhu Y.Y.,2009,Low-background and high-resolution contracted silver-stained method in poly acrylamide gels electrophoresis,Yichuan(Genetics),31(6):668-673(高东,杜飞,朱有勇,2009,低背景,高分辨率PAGE简易银染法,遗传,31(6):668-673)
Gupta K.P.,Rustgi S.,Sharma S.,Singh R.,Kumar N.,and Balyan S.H.,2003,Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat,Mol.Genet.Genomics,270(4):315-323
Kantety R.V.,La Rota M.,Matthews D.E.,and Sorrells1 M.E.,2002,Data mining for simple sequence repeats in expressed sequence tags from barley,maize,rice,sorghum and wheat,Plant Mol.Biol.,48(5-6):501-510
Ogundiwin E.A.,MartíC.,Forment J.,Pons C.,Granell A.,Gradziel T.M.,Peace C.P.,and Crisosto C.H.,2008,Development of chill peach genomic tools and identification of cold-responsive genes in peach fruit,Plant Mol.Biol.,68(6):379-397
Shangguan L.F.,Li X.Y.,Ning N.,Wang Y.Z.,Zhang Z.,and Fang J.G.,2011,Development of EST-SSR markers in apricot,Yuanyi Xuebao(Acta Horticulturae Sinica),38(1):43-54(上官凌飞,李晓颖,宁宁,王玉柱,章镇,房经贵,2011,杏EST-SSR标记的开发,园艺学报,38(1):43-54)
Vendramin E.,Dettori M.T.,Giovinazzi J.,Micall S.,Quarta R.,and Verde I.,2007,A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species,Mol.Ecol.Notes,7(2):307-310
Verde I.O.,Abbott A.G.,Scalabrin S.,Jung S.,Shu S.,Marroni F.,Zhebentyayeva T.,Dettori M.T.,Grimwood J.,Cattonaro F.,Zuccolo A.,Rossini L.,Jenkins J.,Vendramin E.O.,Meisel L.A.,Decroocq V.,Sosinski B.,Prochnik S.,Mitros T.,Policriti A.,Cipriani G.,Dondini L.,Ficklin S.,Goodstein D.M.,Xuan P.,Del Fabbro C.,Aramini V.,Copetti D.,Gonzalez S.,Horner D.S.,Falchi R.,Lucas S.,Mica E.,Maldonado J.,Lazzari B.,Bielenberg D.,Pirona R.,Miculan M.,Barakat A.,Testolin R.,Stella A.,Tartarini S.,Tonutti P.,Arús P.,Orellana A.,Wells C.,Main D.,Vizzotto G.,Silva H.,Salamini F.,Schmutz J.,Morgante M.,and Rokhsar D.S.,2013,The high-quality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity,domestication and genome evolution,Nat.Genet.,45(5):487-494
Wang Y.,Georgi L.L.,Zhebentyayeva T.N.,Reighard G.L.,Scorza R.,and Abbott A.G.,2002,High-throughput targeted SSR marker development in peach(Prunus persica),Genome,45(2):319-328
Cipriani G.,Lot G.,Huang W.G.,Marrazzo M.T.,Peterlunger E.,and Testolin R.,1999,AC/GT and AG/CT microsatellite repeats in peach(Prunus persica(L.)Batsch):isolation,characterisation and cross-species amplification in Prunus,Theor.Appl.Genet.,99(1-2):65-72
Di Rienzo A.,Peterson A.C.,Garza J.C.,Valdes A.M.,Slatkin M.,and Freimer N.B.,1994,Mutational processes of simple-sequence repeat loci in human populations,Proc.Natl.Acad.Sci.USA,91(8):3166-3170
Dirlewanger E.,Cosson P.,Tavaud M.,Aranzana J.,Poizat C.,Zanetto A.,Arús P.,and Laigret F.,2002,Development of microsatellite markers in peach(Prunus persica(L.)Batsch)and their use in genetic diversity analysis in peach and sweet cherry(Prunus avium L.),Theor.Appl.Genet.,105(3):127-138
Gan L.,2006,Genetic diversity of in vitro culture of Pyrus detected by molecular markers,Thesis for M.S.,Sichuan Agricultural University,Supervisor:Tang H.R.,pp.16-17(甘玲,2006,梨离体保存材料遗传差异的分子检测,硕士学位论文,四川农业大学,导师:汤浩茹,pp.16-17)
Gao D.,Du F.,and Zhu Y.Y.,2009,Low-background and high-resolution contracted silver-stained method in poly acrylamide gels electrophoresis,Yichuan(Genetics),31(6):668-673(高东,杜飞,朱有勇,2009,低背景,高分辨率PAGE简易银染法,遗传,31(6):668-673)
Gupta K.P.,Rustgi S.,Sharma S.,Singh R.,Kumar N.,and Balyan S.H.,2003,Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat,Mol.Genet.Genomics,270(4):315-323
Kantety R.V.,La Rota M.,Matthews D.E.,and Sorrells1 M.E.,2002,Data mining for simple sequence repeats in expressed sequence tags from barley,maize,rice,sorghum and wheat,Plant Mol.Biol.,48(5-6):501-510
Ogundiwin E.A.,MartíC.,Forment J.,Pons C.,Granell A.,Gradziel T.M.,Peace C.P.,and Crisosto C.H.,2008,Development of chill peach genomic tools and identification of cold-responsive genes in peach fruit,Plant Mol.Biol.,68(6):379-397
Shangguan L.F.,Li X.Y.,Ning N.,Wang Y.Z.,Zhang Z.,and Fang J.G.,2011,Development of EST-SSR markers in apricot,Yuanyi Xuebao(Acta Horticulturae Sinica),38(1):43-54(上官凌飞,李晓颖,宁宁,王玉柱,章镇,房经贵,2011,杏EST-SSR标记的开发,园艺学报,38(1):43-54)
Vendramin E.,Dettori M.T.,Giovinazzi J.,Micall S.,Quarta R.,and Verde I.,2007,A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species,Mol.Ecol.Notes,7(2):307-310
Verde I.O.,Abbott A.G.,Scalabrin S.,Jung S.,Shu S.,Marroni F.,Zhebentyayeva T.,Dettori M.T.,Grimwood J.,Cattonaro F.,Zuccolo A.,Rossini L.,Jenkins J.,Vendramin E.O.,Meisel L.A.,Decroocq V.,Sosinski B.,Prochnik S.,Mitros T.,Policriti A.,Cipriani G.,Dondini L.,Ficklin S.,Goodstein D.M.,Xuan P.,Del Fabbro C.,Aramini V.,Copetti D.,Gonzalez S.,Horner D.S.,Falchi R.,Lucas S.,Mica E.,Maldonado J.,Lazzari B.,Bielenberg D.,Pirona R.,Miculan M.,Barakat A.,Testolin R.,Stella A.,Tartarini S.,Tonutti P.,Arús P.,Orellana A.,Wells C.,Main D.,Vizzotto G.,Silva H.,Salamini F.,Schmutz J.,Morgante M.,and Rokhsar D.S.,2013,The high-quality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity,domestication and genome evolution,Nat.Genet.,45(5):487-494
Wang Y.,Georgi L.L.,Zhebentyayeva T.N.,Reighard G.L.,Scorza R.,and Abbott A.G.,2002,High-throughput targeted SSR marker development in peach(Prunus persica),Genome,45(2):319-328