紫薇EST-SSR标记的开发和利用
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- 英文论文题名：Development and Utility of EST-SSR Markers in Lagerstroemia indica
- 论文作者：张恩亮 ; 王鹏 ; 李亚 ; 王淑安 ; 李林芳 ; 杨如同
- 英文论文作者：ZHANG En-liang ; WANG Peng ; LI Ya ; WANG Shu-an ; LI Lin-fang ; YANG Ru-tong ; Institute of Botany ; Jiangsu Province and Chinese Academy of Sciences
- 年：2016
- 作者机构：江苏省中国科学院植物研究所;
- 论文关键词：紫薇 ; EST-SSR ; 转录组测序 ; 分子标记
- 英文论文关键词：Largerstroemia indica ; EST-SSR ; Transcriptome sequencing ; Molecular markers
- 会议召开时间：2016-07-19
- 会议录名称：中国观赏园艺研究进展2016
- 语种：中文
- 分类号：S685.99
- 学会代码：EGYP
- 会议名称：2016年中国观赏园艺学术研讨会
- 会议地点：中国湖南长沙
- 主办单位：中国园艺学会观赏园艺专业委员会、国家花卉工程技术研究中心
- 学会名称：中国园艺学会
- 页数：6
- 文件大小：603k
- 原文格式：O
- 会议级别：全国
摘要
紫薇(Lagerstroemia indica)是我国著名的夏季观花木本植物,但是其EST-SSR的研究报道较少。本研究通过对RNA-seq测序获得45308条unigenes中的SSR特征进行分析后发现:9074条unigenes存在10905个SSR位点,1486条unigenes含有两个以上的SSR位点,550个位点是复合重复位点;从7620个SSRs位点中设计出4501对SSR引物;随机选择68对SSR引物进行检测,其中61对引物可以成功的扩增出清晰可用的条带,28对引物有多态性。
Lagerstroemia indica is a popular woody ornamental flowering plant in China.However,relatively little is known about its EST-SSR molecular markers.In this study,45308 unigenes from transcriptome sequencing were analyzed.A total of10905 EST-SSRs were recognized from 9074 unigenes.1486 sequences contained more than one SSR and 550 SSRs presented in compound formation.In this study,a total of 4501 primer pairs were designed from 7620 SSRs.To validate SSR markers,68 primer pairs were randomly selected to PCR amplification and 61 SSR markers were amplified successfully.Of these validated SSR markers,28 primer pairs were detected polymorphism.
Lagerstroemia indica is a popular woody ornamental flowering plant in China.However,relatively little is known about its EST-SSR molecular markers.In this study,45308 unigenes from transcriptome sequencing were analyzed.A total of10905 EST-SSRs were recognized from 9074 unigenes.1486 sequences contained more than one SSR and 550 SSRs presented in compound formation.In this study,a total of 4501 primer pairs were designed from 7620 SSRs.To validate SSR markers,68 primer pairs were randomly selected to PCR amplification and 61 SSR markers were amplified successfully.Of these validated SSR markers,28 primer pairs were detected polymorphism.
引文
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12.Grover,A.,&Sharma,P.C.(2014).Occurrence of simple sequence repeats in potato ests is not random;an in silicd study on distribution and length of simple sequence repeats[J].Potato Journal.
13.Grover,A.,Aishwarya,V.,&Sharma,P.C.(2007).Biased distribution of microsatellite motifs in the rice genome[J].Molecular Genetics&Genomics Mgg,277(5),469-80.
14.Gupta,P.K.,&Varshney,R.K.(2000).The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat[J].Euphytica,113(3),163-185.
15.Jain,A.,Ghangal,R.,Grover,A.,Raghuvanshi,S.,&Sharma,P.C.(2010).Development of est-based new ssr markers in seabuckthom[J].Physiology&Molecular Biology of Plants An International Journal of Functional Plant Biology,16(4),375-8.
16.Jung,S.,Abbott,A.,Jesudurai,C.,Tomkins,J.,&Main,D.(2005).Frequency,type,distribution and annotation of simple sequence repeats in rosaceae est[J].Functional&Integrative Genomics,5(3),136-43.
17.Kawase D.,Ueno S.,Tsumura Y.,Tomaru N.,Seo A.&Yumoto T.(2009).Development and characterization of EST-SSR markers for Sciadopitys verticillata(Sciadopityaceae)[J].Conservation Genetics,10(6),1997-1999.
18.Kumari,M.,Grover,A.,Yadav,P.V.,Arif,M.,&Ahmed,Z.(2013).Development of est-ssr markers through data mining and their use for genetic diversity study in indian accessions of jatropha curcas 1.:a potential energy crop.Genes&Genomics,35(5),661-670.
19.Kumpatla,S.P.,&Mukhopadhyay,S.(2005).Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species.,48(6),985-98.
20.Li,Y.,Zhang,Z.,Wang,P.,Wang,S.,Ma,L,&Li,L,et al.(2015).Comprehensive transcriptome analysis discovers novel candidate genes related to leaf color in a lagerstroemia indica,yellow leaf mutant[J].Genes&Genomics,37(10),851-863.
21.Liu,Y.,He,D.,Cai,M.,Tang,W.,Li,X.Y.,&Pan,H.T.,et al.(2013).Development of microsatellite markers for lagerstroemia indica(lythraceae)and related species[J].Applications in Plant Sciences,1(2),76-87.
22.Low,E.T.L,Alias,H.,Boon,S.H.,Shariff,E.M.,Tan,C.Y.A.,&Ooi,L C.,et al.(2008).Oil palm(elaeis guineensis,jacq.)tissue culture ests;identifying genes associated with callogenesis and embryogenesis[J].Bmc Plant Biology,8(3),:62.
23.Min W,Ping S,Ren XX,Zhang QX(2008)Recent advances in Lagerstroemia indica resources and breeding[J].Shandong For Sci Technol 175:66-68.(In Chinese)
24.Peng,Z.,Gallo,M.,Tillman,B.L.,Rowland,D.,&Wang,J.(2015).Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut(arachis hypogaea 1.)[J].Mgg Molecular&General Genetics,291(1),1-19.
25.Qiu,L,Yang,C.,Bo,T.,Yang,J.B.,&Liu,A.(2010).Exploiting est databases for the development and characterization of est-ssr markers in castor bean(ricinus communis,1.)[J].Bmc Plant Biology,10(4),1-10.
26.Varshney,R.K.,Graner,A.,&SorreEs,M.E.(2005).Genie microsatellite markers in plants;features and applications[J].Trends in Biotechnology,23(1),48-55.
27.Wang X.,Awadl P.,Pounders C.,Ntrigiano R.,Icabrera R.,EschefflerB.,Rpooler M.&Arinehart T.(2011).Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers[J].Journal of The American Society for Horticultural Science,136(2),116-128.
28.Wang,R.,Xu,S.,Jiang,Y.,Jiang,J.,Li,X.,&Liang,L,et al.(2013).De novo sequence assembly and characterization of lycoris aurea transcriptome using gs fix titanium platform of 454 pyrosequencing[J].Plos One,8(4),e60449.
29.Wu J.,Cai C.,Cheng F.,Cui H.&Zhou H.(2014).Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences[J].Molecular Breeding,34(4),1853-1866.
30.Yadav,H.K.,Ranjan,A.,Asif,M.H.,Mantri,S.,Sawant,S.V.,&Tuli,R.(2011).Est-derived ssr markers in jatropha curcas,1.;development,characterization,polymorphism,and transferability across the species/genera[J].Tree Genetics&Genomes,7(1),207-219.
31.Zhang Q.X.(1991).Studies on cultivars of crape-myrtle(Lagerstroemia indica)and their uses in urban greening[J].J Beijing For Univ 18:57-66(In Chinese).
2.Cabrera,R.I.(2004).Evaluating and promoting the cosmopolitan and multipurpose lagerstroemia[J].Acta Horticulturae,630,177-184.
3.Cai,M.,Pan,H.T.,Wang,X F.,He,D.,Wang,X Y.,&Wang,X.J.,et al.(2011).Development of novel microsatellites in lagerstroemi3.a indica and dna fingerprinting in chinese lagerstroemia cultivars[J].Scientia Horticulturae,131(1),385-394.
4.Cardie,L.,Ramsay,L.,Milbourne,D.,Macaulay,M.,Marshall,D.,&Waugh,R.(2000).Computational and experimental characterization of physically clustered simple sequence repeats in plants[J].Genetics,156(2),847-54.
5.Chen,C.,Ping,Z.,Choi,Y.A.,Shu,H.,&Jr,F.G.G.(2006).Mining and characterizing microsatellites from citrus ests[J].Theoretical&Applied Genetics,112(7),1248-1257.
6.Cheng Y.,Yang Y.,Wang Z.,Qi B.,Yin Y.&Li H.(2015).Development and Characterization of EST-SSR Markers in Taxodium'zhongshansa'[J].Plant Molecular Biology Reporter.33(6),1804-1814.
7.Doyle,J.(1990).Isolation of plant dna from fresh tissue.Focus,12,13-15.
8.Feng,S.P.,Li,W.G.,Huang,H.S.,Wang,J.Y.,&Wu,Y.T.(2009).Development,characterization and cross-species/genera transferability of est-ssr markers for rubber tree(hevea brasiliensis)[J].Molecular Breeding,23(1),85-97.
9.Fujimori,S.,Washio,T.,Higo,K.,Ohtomo,Y.,Murakami,K.,&Matsubara,K.,et al.(2003).A novel feature of microsatellites in plants:a distribution gradient along the direction of transcription[J].Febs Letters,554(1-2),17-22.
10.Gao,C.,Tang,Z.,Yin,J.,An,Z.,Fu,D.,&Li,J.(2011).Characterization and comparison of gene-based simple sequence repeats across brassica species[J].Molecular Genetics&Genomics Mgg,286(2),161-70.
11.Grover,A.,&Sharma,P.C.(2007).MicrosateUite motifs with moderate gc content are clustered around genes on arabidopsis thaliana chromosome 2[J].Silico Biology,7(2),201-13.
12.Grover,A.,&Sharma,P.C.(2014).Occurrence of simple sequence repeats in potato ests is not random;an in silicd study on distribution and length of simple sequence repeats[J].Potato Journal.
13.Grover,A.,Aishwarya,V.,&Sharma,P.C.(2007).Biased distribution of microsatellite motifs in the rice genome[J].Molecular Genetics&Genomics Mgg,277(5),469-80.
14.Gupta,P.K.,&Varshney,R.K.(2000).The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat[J].Euphytica,113(3),163-185.
15.Jain,A.,Ghangal,R.,Grover,A.,Raghuvanshi,S.,&Sharma,P.C.(2010).Development of est-based new ssr markers in seabuckthom[J].Physiology&Molecular Biology of Plants An International Journal of Functional Plant Biology,16(4),375-8.
16.Jung,S.,Abbott,A.,Jesudurai,C.,Tomkins,J.,&Main,D.(2005).Frequency,type,distribution and annotation of simple sequence repeats in rosaceae est[J].Functional&Integrative Genomics,5(3),136-43.
17.Kawase D.,Ueno S.,Tsumura Y.,Tomaru N.,Seo A.&Yumoto T.(2009).Development and characterization of EST-SSR markers for Sciadopitys verticillata(Sciadopityaceae)[J].Conservation Genetics,10(6),1997-1999.
18.Kumari,M.,Grover,A.,Yadav,P.V.,Arif,M.,&Ahmed,Z.(2013).Development of est-ssr markers through data mining and their use for genetic diversity study in indian accessions of jatropha curcas 1.:a potential energy crop.Genes&Genomics,35(5),661-670.
19.Kumpatla,S.P.,&Mukhopadhyay,S.(2005).Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species.,48(6),985-98.
20.Li,Y.,Zhang,Z.,Wang,P.,Wang,S.,Ma,L,&Li,L,et al.(2015).Comprehensive transcriptome analysis discovers novel candidate genes related to leaf color in a lagerstroemia indica,yellow leaf mutant[J].Genes&Genomics,37(10),851-863.
21.Liu,Y.,He,D.,Cai,M.,Tang,W.,Li,X.Y.,&Pan,H.T.,et al.(2013).Development of microsatellite markers for lagerstroemia indica(lythraceae)and related species[J].Applications in Plant Sciences,1(2),76-87.
22.Low,E.T.L,Alias,H.,Boon,S.H.,Shariff,E.M.,Tan,C.Y.A.,&Ooi,L C.,et al.(2008).Oil palm(elaeis guineensis,jacq.)tissue culture ests;identifying genes associated with callogenesis and embryogenesis[J].Bmc Plant Biology,8(3),:62.
23.Min W,Ping S,Ren XX,Zhang QX(2008)Recent advances in Lagerstroemia indica resources and breeding[J].Shandong For Sci Technol 175:66-68.(In Chinese)
24.Peng,Z.,Gallo,M.,Tillman,B.L.,Rowland,D.,&Wang,J.(2015).Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut(arachis hypogaea 1.)[J].Mgg Molecular&General Genetics,291(1),1-19.
25.Qiu,L,Yang,C.,Bo,T.,Yang,J.B.,&Liu,A.(2010).Exploiting est databases for the development and characterization of est-ssr markers in castor bean(ricinus communis,1.)[J].Bmc Plant Biology,10(4),1-10.
26.Varshney,R.K.,Graner,A.,&SorreEs,M.E.(2005).Genie microsatellite markers in plants;features and applications[J].Trends in Biotechnology,23(1),48-55.
27.Wang X.,Awadl P.,Pounders C.,Ntrigiano R.,Icabrera R.,EschefflerB.,Rpooler M.&Arinehart T.(2011).Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers[J].Journal of The American Society for Horticultural Science,136(2),116-128.
28.Wang,R.,Xu,S.,Jiang,Y.,Jiang,J.,Li,X.,&Liang,L,et al.(2013).De novo sequence assembly and characterization of lycoris aurea transcriptome using gs fix titanium platform of 454 pyrosequencing[J].Plos One,8(4),e60449.
29.Wu J.,Cai C.,Cheng F.,Cui H.&Zhou H.(2014).Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences[J].Molecular Breeding,34(4),1853-1866.
30.Yadav,H.K.,Ranjan,A.,Asif,M.H.,Mantri,S.,Sawant,S.V.,&Tuli,R.(2011).Est-derived ssr markers in jatropha curcas,1.;development,characterization,polymorphism,and transferability across the species/genera[J].Tree Genetics&Genomes,7(1),207-219.
31.Zhang Q.X.(1991).Studies on cultivars of crape-myrtle(Lagerstroemia indica)and their uses in urban greening[J].J Beijing For Univ 18:57-66(In Chinese).