|本期目录/Table of Contents|

[1]陈欣,余懋群,龙海,等.大麦EST-SSR分子标记开发及特征分析[J].应用与环境生物学报,2018,24(01):102-106.[doi: 10.19675/j.cnki.1006-687x.2017.03037]
 CHEN Xin,YU Maoqun,LONG Hai**,et al.Data mining and analysis for simple sequence repeats in expressed sequence tags from barley[J].Chinese Journal of Applied & Environmental Biology,2018,24(01):102-106.[doi: 10.19675/j.cnki.1006-687x.2017.03037]
点击复制

大麦EST-SSR分子标记开发及特征分析()
分享到:

《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
24卷
期数:
2018年01期
页码:
102-106
栏目:
研究论文
出版日期:
2018-02-09

文章信息/Info

Title:
Data mining and analysis for simple sequence repeats in expressed sequence tags from barley
作者:
陈欣余懋群龙海邓光兵潘志芬徐德林张洁
1成都军区总医院 成都 610083 2中国科学院成都生物研究所 成都 610041 3遵义医学院 遵义 563099 4四川省农业科学院生物技术核技术研究所 成都 610061
Author(s):
CHEN Xin YU Maoqun LONG Hai** DENG Guangbing PAN Zhifen XU DelinZHANG Jie
1 Chengdu Military General Hospital, Chengdu 610083, China 2 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China 3 Zunyi Medical University, Zunyi 563099, China 4 Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
关键词:
大麦表达序列标签简单序列重复分子标记生物信息
Keywords:
barley expressed sequence tag simple sequence repeat molecular mark bioinformation
分类号:
S512.303
DOI:
10.19675/j.cnki.1006-687x.2017.03037
摘要:
大麦是一种古老的栽培作物,也是分子遗传学研究中常用的模式植物,为满足大麦基因作图、遗传多样性、种质资源鉴定和分子辅助育种等研究的需求,拟在NCBI公共数据库基础上,开发基于表达序列标签(EST)的简单序列重复(SSR)分子标记. 从NCBI数据库中获得了525 781条大麦EST序列,将这些序列进行聚类和去冗余后共获得61 902个Unigene,随后通过MISA软件搜索Unigene中的SSR位点,并设计引物9 659对,最后通过电子PCR(E–PCR)和普通PCR对引物进行验证. 结果显示:(1)61 902个Unigene中含有SSR位点24 648个,其中复合SSR位点5 843个,约占3.42%,单纯SSR位点23 805个,约占96.58%;(2)经E-PCR验证后发现9 659对SSR引物中有1 060对(11%)能够成功扩增出产物;(3)随机选取的11对引物经普通PCR验证发现,这些引物都能在2份野生大麦品种、2份栽培大麦品种及1份小麦、硬粒小麦、荆州黑麦和节节麦中成功扩增. 本研究表明日益丰富的EST公共数据库是大麦SSR分子标记的重要来源;利用EST公共数据库、SSR搜索软件,结合E–PCR验证是开发SSR分子标记省时高效的手段. (图1 表2 参38)
Abstract:
1 Chengdu Military General Hospital, Chengdu 610083, China 2 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China 3 Zunyi Medical University, Zunyi 563099, China 4 Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China

参考文献/References:

1 陈明贤, 张国平. 大麦的利用现状及前景探讨[J]. 大麦与谷类科学, 2010 (3): 11-14 [Chen MX, Zhang GP. The situation and prospect of barley utilization [J]. Barley Cereal Sci, 2010 (3): 11-14]
2 Dickin E, Steele K, Edwards-Jones G, Wright D. Agronomic diversity of naked barley (Hordeum vulgare L.): a potential resource for breeding new food barley for Europe [J]. Euphytica, 2012, 184 (1): 85-99
3 Lu H, Redus MA, Coburn JR, Rutger JN, McCOUCH SR, Tai TH. Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis [J]. Crop Sci, 2005, 45 (1): 66-76
4 Chakravarthi BK, Naravaneni R. SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa L) [J]. Afr J Biotechnol, 2006, 5 (9): 684-688
5 Chen H, Song Y, Li LT, Khan MA, Li XG, Korban SS, Wu J, Zhang SL. Construction of a high-density simple sequence repeat consensus genetic map for pear (Pyrus spp.) [J]. Plant Mol Biol Rep, 2014, 33 (2): 1-10
6 罗文永, 胡骏, 李晓方. 微卫星序列及其应用[J]. 遗传, 2003, 25 (5): 615-619 [Luo WY, Hu J, Li XF. The evolution and application of microsatellites [J]. Hereditas, 2003, 25 (5): 615-619].
7 刘燕, 强小林, 黄静, 张笑, 谭爱女, 赵纯钦, 陈静. 中国大麦育成品种(系)的遗传多样性[J]. 应用与环境生物学报, 2013, 19 (1): 79-83 [Liu Q, Qiang XL, Huang J, Zhang X, Tan AL, Zhao CQ, Chen J. Genetic diversity among barley varieties (lines) bred in China [J]. Chin J Appl Environ Biol, 2013, 19 (1): 79-83]
8 Qin D, Dong J, Xu F, Guo G, Ge S, Xu Q, Xu Y, Li M. Characterization and fine mapping of a novel barley stage green-revertible albino gene (HvSGRA) by bulked segregant analysis based on SSR assay and specific length amplified fragment sequencing [J]. BMC Genomics, 2015, 16 (1): 838
9 Varshney RK, Marcel TC, Ramsay L, Russell J, R?der MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A. A high density barley microsatellite consensus map with 775 SSR loci [J]. Theor Appl Genet, 2007, 114 (6): 1091-1103
10 Rosset FJ, Fernando PJ, Caroline T, Euclydes M, Luciano C, Andréa DC. Assessment of genetic diversity in Brazilian barley using SSR markers [J]. Genet Mol Biol, 2016, 39 (1): 86-96
11 Yan S, Sun D, Sun G. Genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes [J]. PLoS ONE, 2015, 10 (3): e0121106
12 Choudhary S, Sethy NK, Shokeen B, Bhatia S. Development of chickpea EST-SSR markers and analysis of allelic variation across related species [J]. Theor Appl Genet, 2009, 118 (3): 591-608
13 Ellis JR, Burke JM. EST-SSRs as a resource for population genetic analyses [J]. Heredity, 2007, 99 (2): 125-32
14 Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys [J]. Plant Sci, 2007, 173 (6):638-649
15 Yadav HK, Ranjan A, Asif MH, Mantri S, Sawant SV, Tuli R. EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera [J]. Tree Genet Genom, 2011, 7 (1): 207-219
16 孙蛟龙, 方扬, 靳艳玲, 马欣荣, 陶向, 赵海. 浮萍转录组数据SSR位点的生物信息学分析[J]. 应用与环境生物学报, 2015, 21 (3): 401-405 [Sun JL, Fang Y, Jin YL, Ma XR, Tao X, Zhao H. Bioinformatic analysis on SSR information in duckweed transcriptome. Chin J Appl Environ Biol [J]. 2015, 21 (3): 401-405]
17 Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz) [J]. PLoS ONE, 2017, 12 (5): e0177456
18 Meng M, Tang W, Liu J, Huang S, Yu J, Liu F, Lin L, Zhang X, Liu Y. Development of EST-SSR markers in Actinidia chinesis cv ‘Hongyang’ based on transcriptomic sequences [J]. Chin J Appl Environ Biol, 2014, 20 (4): 564-570
19 Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) [J]. Theor Appl Genet, 2003, 106 (3): 411-422
20 Schuler GD. Sequence mapping by electronic PCR [J]. Gen Res, 1997, 7 (5): 541-550
21 张文静, 厉永鹏, 李集临, 张延明. 大麦基因组和分子育种研究进展[J]. 中国生物工程杂志, 2012, 32 (5): 107-112 [Zhang WJ, Li YP, Li JL, Zhang YM. Advances in Barley Genome and Molecular Breeding [J]. Chin. Biotechnol, 2012, 32 (5): 107-112]
22 Emebiri LCEC. EST-SSR markers derived from an elite barley cultivar (Hordeum vulgare Morex) : polymorphism and genetic marker potential [J]. Genome, 2009, 52 (8): 665
23 Emebiri LC. An EST-SSR marker tightly linked to the barley male sterility gene (msg6) located on chromosome 6H [J]. J Hered, 2010, 101 (6): 769
24 Aitken KS, Mcneil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J. Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane [J]. BMC Plant Biol, 2014, 14 (1): 190
25 Kong Q, Xiang C, Yu Z. Development of EST‐SSRs in Cucumis sativus from sequence database [J]. BMC Plant Biol, 2006, 6 (4): 1234-1236
26 Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton [J]. Theor Appl Genet, 2006, 112 (3): 430-439
27 Feng S, Li W, Huang H, Wang J, Wu Y. Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) [J]. Mol Breeding, 2009, 23 (1): 85-97
28 Kantety R, La Rota M, Matthews D, Sorrells M. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat [J]. Plant Mol Biol, 2002, 48 (5-6): 501-510
29 金基强, 崔海瑞, 陈文岳, 卢美贞, 姚艳玲, 忻雅, 龚晓春. 茶树EST-SSR的信息分析与标记建立[J]. 茶叶科学, 2006, 26 (1): 17-23 [Jin JQ, Cui HR, Chen WY, Lu MZ, Yao YL, Qi Y, Gong XC. Data mining for SSRs in ESTs and development of EST-SSR marker in tea plant (Camellia sinensis) [J]. J Tea Sci, 2006, 26 (1): 17-23]
30 Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA [J]. Gen Res, 2000, 10 (1): 72-80
31 Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Mccouch SR, Park WD, Ayres N, Cartinhour S. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) [J]. Theor Appl Gen, 2000, 100 (5): 713-722
32 Chin E, Shu H, Smith J, Senior M. Maize simple repetitive DNA sequences: abundance and allele variation [J]. Genome, 1996, 39 (5): 866-873
33 Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants [J]. Genetics, 2000, 156 (2): 847-854
34 李小白, 张明龙, 崔海瑞. 油菜EST资源的SSR信息分析[J]. 中国油料作物学报, 2007, 29 (1): 20-25 [Li XB, Zhang ML, Cui HR. Analysis of SSR information in EST resource of oilseed rape [J]. Chin J Oil Crop Sci, 2007, 29 (1): 20-25]
35 葛佳, 谢华, 崔崇士, 洪剑明, 马荣才. 大白菜表达序列标签SSR标记分析[J]. 农业生物技术学报, 2005, 13 (4): 423-428 [Ge J, Xie H, Cui CS, Hong JM, Ma RC. Analysis of Expressed Sequence Tags (ESTs) Derived SSR markers in Chinese cabbage (Brassica campestris L.ssp. pekinensis) [J]. J Agric Biotechnol, 2005, 13 (4): 423-428]
36 Fraser L, Harvey C, Crowhurst R, De Silva H. EST-derived microsatellites from Actinidia species and their potential for mapping [J]. Theor Appl Genet, 2004, 108 (6): 1010-1016
37 Areshchenkova T, Ganal M. Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources [J]. Theor Appl Gen, 2002, 104 (2-3): 229-235
38 Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) [J]. Theor Appl Genet, 2004, 109 (4): 800-805

相似文献/References:

[1]刘燕,强小林,黄静,等.中国大麦育成品种(系)的遗传多样性[J].应用与环境生物学报,2013,19(01):79.[doi:10.3724/SP.J.1145.2013.00079]
 LIU Yan,QIANG Xiaolin,HUANG Jing,et al.Genetic Diversity Among Barley Varieties (Lines) Bred in China[J].Chinese Journal of Applied & Environmental Biology,2013,19(01):79.[doi:10.3724/SP.J.1145.2013.00079]

更新日期/Last Update: 2018-02-09