Development of SSR Markers of Musella lasiocarpa by Data Mining in Musa EST Sequences

LI Wen-juan; MA Hong; LI Zheng-hong; WAN You-ming; LIU Xiu-xian; ZHOU Cui-li

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Development of SSR Markers of Musella lasiocarpa by Data Mining in Musa EST Sequences

1.
Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, Yunnan, China

Received Date: 2011-11-02

Abstract

21 129 non-redundant clusters, containing 3 818 contigs and 17 311 singletons, were identified from a total of 31 308 publicly available Musa EST sequences. 4 944 (23.40%) of them contained 5 416(25.63%) SSR motifs, and the di-(21.80%), tri-(52.55%) and tetra-nucleotide (14.55%) are the main motifs of all SSRs obtained. AG/CT repeats were dominant in di-nucleotide motif, AAG/CTT and AGG/CCT repeats were dominant in tri-nucleotide motif, AAAG/CTTT and AAAT/ATTT repeats were dominant in tetra-nucleotide motif. 238 EST sequences were randomly selected on molecular markers development, for PCR amplification and polymorphism analysis in Musella lasiocarpa. Of which, 116 pairs of SSR primers successfully amplified PCR product and 78 pairs gave clear bands. 49 of them were found to be polymorphic. A set of 15 polymorphic SSR markers from above 49 SSR markers selected were analyzed using 24 individuals from 4 wild M. lasiocarpa populations. The average allele number of 3.067 per locus was detected with a range from 2 to 7. The observed heterozygosities per marker were ranged from 0.042 to 0.750 (mean 0.250) and expected heterozygosities were 0.232 to 0.823 (mean 0.522).
- Musella,
- EST-SSR,
- polymorphic primer,
- molecular markers

References

[1]	Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review [J]. Molecular Ecology, 2002,11(1):1-16
[2]	Squirrell J, Hollingsworth P M, Woodhead M, et al. How much effort is required to isolate nuclear microsatellites from plants? [J]. Molecular Ecology, 2003,12:1339-1348
[3]	Cordeiro G M, Casu R, McIntyre C L, et al. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum [J]. Plant Science, 2001,160(6):1115-1123
[4]	Kuleung C, Baenziger P S, Dweikat I. Transferability of SSR markers among wheat, rye and triticale [J]. Theoretical and Applied Genetics, 2004,108(6):1147-1150
[5]	郑丽珊,石玉真,王静毅,等.棉花EST-SSRs在香蕉中的通用性[J]. 中国农学通报, 2008,24(1):33-37
[6]	Falke K C, Susic Z, Hackauf B, et al. Establishment of introgression libraries in hybrid rye(Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics [J]. Theoretical and Applied Genetics, 2008,117:641-652
[7]	Tahan O, Geng Y P, Zeng L Y, et al. Assessment of genetic diversity and population structure of Chinese wild almond, Amygdalus nana, using EST- and genomic SSRs [J]. Biochemical Systematics and Ecology, 2009,37(3):146-153
[8]	徐小彪,姜春芽,廖娇,等.中华猕猴桃矮型性状EST-SSR连锁标记的筛选[J]. 园艺学报, 2010,37(4):553-558
[9]	Thiel T, Michalek W, Varshney R K, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) [J]. Theoretical and Applied Genetics, 2003,106(3): 411-422
[10]	吴征镒.云南植物志(第二卷)[M].北京:科学出版社,1979
[11]	Ma H, Pan Q J, Wang L, et al. Musella lasiocarpa var. rubribracteata (Musaceae), a New Variety from Sichuan, China [J]. Novon, 2011,21:349-353
[12]	潘庆杰,李正红,王雁, 等.地涌金莲野生与栽培种群遗传多样性的RAPD分析[J].林业科学研究, 2007,20(5):668-672
[13]	Yang C Y, Huang Y, Long C L. Isolation and characterization of 17 polymorphic microsatellite loci for Musella lasiocarpa (Musaceae) [J]. Hortscience, 2009,44(7):2041-2042
[14]	Doyle J J, Doyle J L. Isolation of plant DNA from fresh tissue [J]. Focus, 1990,12:13-15
[15]	Huang X, Madan A. CAP3:A DNA sequence assembly program[J]. Genome Research, 1999,9:868-877
[16]	Rozen S, Skaletsky H J. PRIMER 3 on the www for general users and for biologist programmers // Krawetz S, Misener S. Methods in Molecular Biology. Totowa, New Jersey, Humana Press, 2000:365-386
[17]	Kantety R V, Rota M L, Matthews D E, et al. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat [J]. Plant Molecular Biology, 2002,48:501- 510
[18]	Nicot N, Chiquet V, Gandon B, et al. Study of simple sequence repeat (SSR) markers from wheat expressed sequences tags (ESTs) [J]. Theoretical and Applied Genetics, 2004,109:800-805
[19]	Cardle L, Ramsay L, Milbourne D, et al. Computational and experimental characterization of physically clustered simple sequence repeats in plants [J]. Genetics, 2000,156:847-854
[20]	王静毅,陈业渊,刘伟良,等.香蕉EST-SSRs标记的开发与应用[J]. 遗传, 2008,30(7):933-940
[21]	Varshney R K, Thiel T, Stein N, et al. Insilico analysis on frequency and distribution of microsatellites in ESTs of some cereal species [J]. Cellular and Molecular Biology Letters, 2002,7(2A):537-546
[22]	Chapman M A, Hvala J, Strever J, et al. Development, poly-morphism and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.) [J]. Theoretical and Applied Genetics, 2009,120:85-91
[23]	Huang H, Lu J, Ren Z B, et al. Mining and validating grape (Vitis L.) EST-SSR markers for genotyping and mapping [J]. Molecular Breeding, 2010, DOI:10.1007/s11032-010-9477-2
[24]	Rota L R, Kantety R V, Yu J K. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat and barley [J]. BMC Genomics, 2005,6:23
[25]	Feng S P, Li W G, Huang H S, et al. Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) [J]. Molecular Breeding, 2009,23:85-97
[26]	Ellis J R and Burke J M. EST-SSRs as a resource for population genetics analysis [J]. Heredity, 2007,99(2):125-132
[27]	Areshchenkova T, Ganal M W. Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources [J]. Theoretical and Applied Genetics, 2002,104:229-235
[28]	Ramsay L, Macaulay M, Ivanissivich S, et al. A simple sequence repeat-based linkage map of barley [J]. Genetics, 2000,156:1997-2005

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Development of SSR Markers of Musella lasiocarpa by Data Mining in Musa EST Sequences

1. Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, Yunnan, China

Received Date: 2011-11-02

Available Online: 2012-04-13

Abstract: 21 129 non-redundant clusters, containing 3 818 contigs and 17 311 singletons, were identified from a total of 31 308 publicly available Musa EST sequences. 4 944 (23.40%) of them contained 5 416(25.63%) SSR motifs, and the di-(21.80%), tri-(52.55%) and tetra-nucleotide (14.55%) are the main motifs of all SSRs obtained. AG/CT repeats were dominant in di-nucleotide motif, AAG/CTT and AGG/CCT repeats were dominant in tri-nucleotide motif, AAAG/CTTT and AAAT/ATTT repeats were dominant in tetra-nucleotide motif. 238 EST sequences were randomly selected on molecular markers development, for PCR amplification and polymorphism analysis in Musella lasiocarpa. Of which, 116 pairs of SSR primers successfully amplified PCR product and 78 pairs gave clear bands. 49 of them were found to be polymorphic. A set of 15 polymorphic SSR markers from above 49 SSR markers selected were analyzed using 24 individuals from 4 wild M. lasiocarpa populations. The average allele number of 3.067 per locus was detected with a range from 2 to 7. The observed heterozygosities per marker were ranged from 0.042 to 0.750 (mean 0.250) and expected heterozygosities were 0.232 to 0.823 (mean 0.522).

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Reference (28)

[1]	Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review [J]. Molecular Ecology, 2002,11(1):1-16
[2]	Squirrell J, Hollingsworth P M, Woodhead M, et al. How much effort is required to isolate nuclear microsatellites from plants? [J]. Molecular Ecology, 2003,12:1339-1348
[3]	Cordeiro G M, Casu R, McIntyre C L, et al. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum [J]. Plant Science, 2001,160(6):1115-1123
[4]	Kuleung C, Baenziger P S, Dweikat I. Transferability of SSR markers among wheat, rye and triticale [J]. Theoretical and Applied Genetics, 2004,108(6):1147-1150
[5]	郑丽珊,石玉真,王静毅,等.棉花EST-SSRs在香蕉中的通用性[J]. 中国农学通报, 2008,24(1):33-37
[6]	Falke K C, Susic Z, Hackauf B, et al. Establishment of introgression libraries in hybrid rye(Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics [J]. Theoretical and Applied Genetics, 2008,117:641-652
[7]	Tahan O, Geng Y P, Zeng L Y, et al. Assessment of genetic diversity and population structure of Chinese wild almond, Amygdalus nana, using EST- and genomic SSRs [J]. Biochemical Systematics and Ecology, 2009,37(3):146-153
[8]	徐小彪,姜春芽,廖娇,等.中华猕猴桃矮型性状EST-SSR连锁标记的筛选[J]. 园艺学报, 2010,37(4):553-558
[9]	Thiel T, Michalek W, Varshney R K, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) [J]. Theoretical and Applied Genetics, 2003,106(3): 411-422
[10]	吴征镒.云南植物志(第二卷)[M].北京:科学出版社,1979
[11]	Ma H, Pan Q J, Wang L, et al. Musella lasiocarpa var. rubribracteata (Musaceae), a New Variety from Sichuan, China [J]. Novon, 2011,21:349-353
[12]	潘庆杰,李正红,王雁, 等.地涌金莲野生与栽培种群遗传多样性的RAPD分析[J].林业科学研究, 2007,20(5):668-672
[13]	Yang C Y, Huang Y, Long C L. Isolation and characterization of 17 polymorphic microsatellite loci for Musella lasiocarpa (Musaceae) [J]. Hortscience, 2009,44(7):2041-2042
[14]	Doyle J J, Doyle J L. Isolation of plant DNA from fresh tissue [J]. Focus, 1990,12:13-15
[15]	Huang X, Madan A. CAP3:A DNA sequence assembly program[J]. Genome Research, 1999,9:868-877
[16]	Rozen S, Skaletsky H J. PRIMER 3 on the www for general users and for biologist programmers // Krawetz S, Misener S. Methods in Molecular Biology. Totowa, New Jersey, Humana Press, 2000:365-386
[17]	Kantety R V, Rota M L, Matthews D E, et al. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat [J]. Plant Molecular Biology, 2002,48:501- 510
[18]	Nicot N, Chiquet V, Gandon B, et al. Study of simple sequence repeat (SSR) markers from wheat expressed sequences tags (ESTs) [J]. Theoretical and Applied Genetics, 2004,109:800-805
[19]	Cardle L, Ramsay L, Milbourne D, et al. Computational and experimental characterization of physically clustered simple sequence repeats in plants [J]. Genetics, 2000,156:847-854
[20]	王静毅,陈业渊,刘伟良,等.香蕉EST-SSRs标记的开发与应用[J]. 遗传, 2008,30(7):933-940
[21]	Varshney R K, Thiel T, Stein N, et al. Insilico analysis on frequency and distribution of microsatellites in ESTs of some cereal species [J]. Cellular and Molecular Biology Letters, 2002,7(2A):537-546
[22]	Chapman M A, Hvala J, Strever J, et al. Development, poly-morphism and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.) [J]. Theoretical and Applied Genetics, 2009,120:85-91
[23]	Huang H, Lu J, Ren Z B, et al. Mining and validating grape (Vitis L.) EST-SSR markers for genotyping and mapping [J]. Molecular Breeding, 2010, DOI:10.1007/s11032-010-9477-2
[24]	Rota L R, Kantety R V, Yu J K. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat and barley [J]. BMC Genomics, 2005,6:23
[25]	Feng S P, Li W G, Huang H S, et al. Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) [J]. Molecular Breeding, 2009,23:85-97
[26]	Ellis J R and Burke J M. EST-SSRs as a resource for population genetics analysis [J]. Heredity, 2007,99(2):125-132
[27]	Areshchenkova T, Ganal M W. Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources [J]. Theoretical and Applied Genetics, 2002,104:229-235
[28]	Ramsay L, Macaulay M, Ivanissivich S, et al. A simple sequence repeat-based linkage map of barley [J]. Genetics, 2000,156:1997-2005

Development of SSR Markers of Musella lasiocarpa by Data Mining in Musa EST Sequences

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通讯作者: 陈斌, bchen63@163.com

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Development of SSR Markers of Musella lasiocarpa by Data Mining in Musa EST Sequences

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