Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

WU Min; DU Hong-yan; WUYUN Tana; LIU Pan-feng; JING Teng

Volume 28 Issue 3

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Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

1.
Non-timber Forestry R&D Center, Chinese Academy of Forestry, Zhengzhou 450003, He'nan, China
2.
Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, He'nan, China
3.
Paulownia R&D Center of China of State Forestry Aolministratior, Zhengzhou 450003, He'nan, China

Received Date: 2014-04-30

Abstract

Based on genome sequencing of Eucommia ulmoides, the perfect SSR (17 nucleotide repeats) and compound SSR sequences were searched from Eucommia genome (26,947/854,758,160 bp) by using MISA. 488,592 SSR loci were found from 25,694 Scaffolds, accounting for 95.3% of the total Scaffolds. The results indicated that every 1 749 bp contained one SSR microsatellite on the average. The SSRs which had mononucleotide repeats were the most of all, accounting for 54.34%, and the dinucleotide repeats accounted for 20.47%. The percentage of compound SSR, trinucleotide repeats, tetranucleotide repeats, pentanucleotide repeats, hexanucleotide repeats, and heptanucleotides repeats were 20.29%, 23.89%, 0.77%, 0.13%, 0.10% and 0.01%, respectively. Meanwhile, the A/T repeats were predominant type among these SSRs. A total of 290 pairs of primer was designed and synthesized. The primers were verified by using 8 Eucommia clones, among which 162 pairs of primers were able to amplify products and 16 pairs of them were polymorphic and stable. 84 alleles were detected in these Eucommia clones, (5.25 alleles per SSR locus in average). The results are applicable for analyzing genetic diversity constructing genetic map, and identifying early sex status by using SSR molecular markers on Eucommia ulmoides.
- Eucommia ulmoides,
- genome,
- SSR,
- marker development,
- polymorphism

References

[1]	Mrazek J, Guo X, Shah A.Simple sequence repeats in prokaryotic genomes [J].PNAS, 2007, 104(20):8472-8477.
[2]	Tóth G, Gáspári Z, Jurka J.Microsatellites in different eukaryotic genomes[J].survey and analysis.Genome Research, 2000, 10(7):967-981.
[3]	Li C Y, Korol A B, Fahima T, et al. Microsatellites with in genes: structure, function, and evolution[J]. Mol Biol Evol, 2004, 21(6):991-1007.
[4]	敖日格乐, 贾晓, 葛台明, 等.SSR分子标记的开发策略概述[J].湖北民族学院学报, 2009, 27(4):462-467.
[5]	Hazan J, Dubay C, Pankowiak M C, et al.A genetic linkage map of human chromosome 20 composed entirely of microsatellite markers[J].Genomics, 1992, 12(2):183-189.
[6]	Copeland N G, Jenkins N A, Gilbert D J, et al. A genetic linkage map of the mouse.: Current applications and future prospects[J].Science, 1993(262):57-66.
[7]	刘列钊, 林呐.油菜简单重复序列SSR研究进展[J].生命科学, 2004, 16(3):173-176.
[8]	张芝玉, 王伏雄, 钱南芬.等.杜仲花粉形态的研究[J].植物分类学报, 1988, 26(5): 367-370.
[9]	杜红岩, 胡文臻, 俞锐.杜仲产业绿皮书:中国杜仲橡胶资源与产业发展报告[M], 社会科学文献出版社(2013):001-009.
[10]	张檀, 张康健, 杨吉安, 等.杜仲脂酶同工酶地理递变及生长预测的研究[J].西北林学院学报, 1993, 8(4):20-23.
[11]	王瑷琦, 黄璐琦, 邵爱娟, 等.孑遗植物杜仲的遗传多样性RAPD分析和保护策略研究[J].中国中药杂志, 2006, 31(19):1583-1586.
[12]	邓建云, 李建强, 黄宏文.一株具有特异AFLP指纹图谱的杜仲古树[J]..武汉植物学研究, 2006, 24(6):509-513
[13]	Kalia R, Rai M, Kalia S, et al.Microsatellite markers.: an overview of there cent progress in plants[J].Euphytica, 2011, 177(3):309-334.
[14]	Wu Mingqian, Chen Shuanglin, Wang Meixia, et al.An analysis of the genetic diversity and genetic structure of Eucommia ulmoides using inter-simple sequence repeat (ISSR) markers[J].African Journal of Biotechnology, 2011, 10(84):19505-19513.
[15]	杜红岩, 乌云塔娜, 刘攀峰.基于杜仲转录组序列的SSR分子标记的开发[J].林业科学, 2013, 49(5):176-181.
[16]	Katti M V, Ranjekar P K, Gupta V S.Differential distribution of simple sequence repeats in eukaryotic genome sequences[J].Mol Bio Evol, 2001, 18(7):1161-1167.
[17]	Karaoglu H, Lee C M Y, Meyer W.Survey of simple sequence repeats in completed fungal genomes[J].Molecular Biology and Evolution, 2005, 22 (3):639-649.
[18]	Biet E, Sun J S, Dutreix M.Conserved sequence preference in DNA binding among recombination proteins.: an effect of ssDNA secondary structure[J].Nucleic Acids Research, 1999, 27(2):596-600.
[19]	Ellegren H.Microsatellites.: simple sequences with complex evolution[J].Nature Reviews Genetics, 2004, 5(6):435-445. Hamada H.A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes[M].Proc Natl A cad Sci USA, 1982, 79(21):6465-6469.
[20]	Wei Wenliang, Qi Xiaoqiong, Wang Linhai, et al.Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J].BMC Genomics, 2011, 12(1):451
[21]	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.
[22]	郑燕, 张耿, 吴为人, 禾木科植物微卫星序列的特征分析和比较[J].基因组学与应用生物学, 2011, 30(5):513-520.
[23]	马秋月, 戴晓港, 陈赢男, 等. 枣基因组的微卫星特征[J]. 林业科学, 2013, 49(12):81-87.
[24]	史洁, 尹佟明, 管宏伟, 等. 油茶基因组微卫星特征分析[J]. 南京林业大学党报, 2012, 36(2):47-51.
[25]	Saha M C. Mian M A R, Eujayl I, et al. Tall fescie EST-SSR markers with transfer ability across several grass species[J]. Theor Appl Genet, 2004, 109(4): 783-791.
[26]	Dreisigacker S, Zhang P, Warburton M L, et al. SSR and pedigree andalyses of genetic diversity among CIMMYT wheat lines targeted to different mega environments[J]. Crop Science, 2004, 44(2):381-388.
[27]	黄海燕, 杜红岩, 乌云塔娜, 朱高浦.基于SSR分子标记的杜仲遗传多样性体系建立[J].林业科学研究, 2013, 26(6):795-799.
[28]	Cho Y G, Ishii T, Temnykh S, et al. Diversity of microsatellites derived from genomic libearies and GenBank sequences in rice(Oryza sativa L.)[J]. Theor Appl Genet, 2000, 100(5):713-722.

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

1. Non-timber Forestry R&D Center, Chinese Academy of Forestry, Zhengzhou 450003, He'nan, China

2. Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, He'nan, China

3. Paulownia R&D Center of China of State Forestry Aolministratior, Zhengzhou 450003, He'nan, China

Received Date: 2014-04-30

Abstract: Based on genome sequencing of Eucommia ulmoides, the perfect SSR (17 nucleotide repeats) and compound SSR sequences were searched from Eucommia genome (26,947/854,758,160 bp) by using MISA. 488,592 SSR loci were found from 25,694 Scaffolds, accounting for 95.3% of the total Scaffolds. The results indicated that every 1 749 bp contained one SSR microsatellite on the average. The SSRs which had mononucleotide repeats were the most of all, accounting for 54.34%, and the dinucleotide repeats accounted for 20.47%. The percentage of compound SSR, trinucleotide repeats, tetranucleotide repeats, pentanucleotide repeats, hexanucleotide repeats, and heptanucleotides repeats were 20.29%, 23.89%, 0.77%, 0.13%, 0.10% and 0.01%, respectively. Meanwhile, the A/T repeats were predominant type among these SSRs. A total of 290 pairs of primer was designed and synthesized. The primers were verified by using 8 Eucommia clones, among which 162 pairs of primers were able to amplify products and 16 pairs of them were polymorphic and stable. 84 alleles were detected in these Eucommia clones, (5.25 alleles per SSR locus in average). The results are applicable for analyzing genetic diversity constructing genetic map, and identifying early sex status by using SSR molecular markers on Eucommia ulmoides.

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Reference (28)

[1]	Mrazek J, Guo X, Shah A.Simple sequence repeats in prokaryotic genomes [J].PNAS, 2007, 104(20):8472-8477.
[2]	Tóth G, Gáspári Z, Jurka J.Microsatellites in different eukaryotic genomes[J].survey and analysis.Genome Research, 2000, 10(7):967-981.
[3]	Li C Y, Korol A B, Fahima T, et al. Microsatellites with in genes: structure, function, and evolution[J]. Mol Biol Evol, 2004, 21(6):991-1007.
[4]	敖日格乐, 贾晓, 葛台明, 等.SSR分子标记的开发策略概述[J].湖北民族学院学报, 2009, 27(4):462-467.
[5]	Hazan J, Dubay C, Pankowiak M C, et al.A genetic linkage map of human chromosome 20 composed entirely of microsatellite markers[J].Genomics, 1992, 12(2):183-189.
[6]	Copeland N G, Jenkins N A, Gilbert D J, et al. A genetic linkage map of the mouse.: Current applications and future prospects[J].Science, 1993(262):57-66.
[7]	刘列钊, 林呐.油菜简单重复序列SSR研究进展[J].生命科学, 2004, 16(3):173-176.
[8]	张芝玉, 王伏雄, 钱南芬.等.杜仲花粉形态的研究[J].植物分类学报, 1988, 26(5): 367-370.
[9]	杜红岩, 胡文臻, 俞锐.杜仲产业绿皮书:中国杜仲橡胶资源与产业发展报告[M], 社会科学文献出版社(2013):001-009.
[10]	张檀, 张康健, 杨吉安, 等.杜仲脂酶同工酶地理递变及生长预测的研究[J].西北林学院学报, 1993, 8(4):20-23.
[11]	王瑷琦, 黄璐琦, 邵爱娟, 等.孑遗植物杜仲的遗传多样性RAPD分析和保护策略研究[J].中国中药杂志, 2006, 31(19):1583-1586.
[12]	邓建云, 李建强, 黄宏文.一株具有特异AFLP指纹图谱的杜仲古树[J]..武汉植物学研究, 2006, 24(6):509-513
[13]	Kalia R, Rai M, Kalia S, et al.Microsatellite markers.: an overview of there cent progress in plants[J].Euphytica, 2011, 177(3):309-334.
[14]	Wu Mingqian, Chen Shuanglin, Wang Meixia, et al.An analysis of the genetic diversity and genetic structure of Eucommia ulmoides using inter-simple sequence repeat (ISSR) markers[J].African Journal of Biotechnology, 2011, 10(84):19505-19513.
[15]	杜红岩, 乌云塔娜, 刘攀峰.基于杜仲转录组序列的SSR分子标记的开发[J].林业科学, 2013, 49(5):176-181.
[16]	Katti M V, Ranjekar P K, Gupta V S.Differential distribution of simple sequence repeats in eukaryotic genome sequences[J].Mol Bio Evol, 2001, 18(7):1161-1167.
[17]	Karaoglu H, Lee C M Y, Meyer W.Survey of simple sequence repeats in completed fungal genomes[J].Molecular Biology and Evolution, 2005, 22 (3):639-649.
[18]	Biet E, Sun J S, Dutreix M.Conserved sequence preference in DNA binding among recombination proteins.: an effect of ssDNA secondary structure[J].Nucleic Acids Research, 1999, 27(2):596-600.
[19]	Ellegren H.Microsatellites.: simple sequences with complex evolution[J].Nature Reviews Genetics, 2004, 5(6):435-445. Hamada H.A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes[M].Proc Natl A cad Sci USA, 1982, 79(21):6465-6469.
[20]	Wei Wenliang, Qi Xiaoqiong, Wang Linhai, et al.Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J].BMC Genomics, 2011, 12(1):451
[21]	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.
[22]	郑燕, 张耿, 吴为人, 禾木科植物微卫星序列的特征分析和比较[J].基因组学与应用生物学, 2011, 30(5):513-520.
[23]	马秋月, 戴晓港, 陈赢男, 等. 枣基因组的微卫星特征[J]. 林业科学, 2013, 49(12):81-87.
[24]	史洁, 尹佟明, 管宏伟, 等. 油茶基因组微卫星特征分析[J]. 南京林业大学党报, 2012, 36(2):47-51.
[25]	Saha M C. Mian M A R, Eujayl I, et al. Tall fescie EST-SSR markers with transfer ability across several grass species[J]. Theor Appl Genet, 2004, 109(4): 783-791.
[26]	Dreisigacker S, Zhang P, Warburton M L, et al. SSR and pedigree andalyses of genetic diversity among CIMMYT wheat lines targeted to different mega environments[J]. Crop Science, 2004, 44(2):381-388.
[27]	黄海燕, 杜红岩, 乌云塔娜, 朱高浦.基于SSR分子标记的杜仲遗传多样性体系建立[J].林业科学研究, 2013, 26(6):795-799.
[28]	Cho Y G, Ishii T, Temnykh S, et al. Diversity of microsatellites derived from genomic libearies and GenBank sequences in rice(Oryza sativa L.)[J]. Theor Appl Genet, 2000, 100(5):713-722.

Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

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通讯作者: 陈斌, bchen63@163.com

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Characterization of Genomic Microsatellites and Development of SSR Markers of Eucommia ulmoides

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