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[1]孟蒙,唐维,刘嘉,等.基于中华猕猴桃“红阳”转录组序列开发EST-SSR分子标记[J].应用与环境生物学报,2014,20(04):564-570.[doi:10.3724/SP.J.1145.2013.12034]
 MENG Meng,TANG Wei,LIU Jia,et al.Development of EST-SSR markers in Actinidia chinesis cv ‘Hongyang’ based on transcriptomic sequences[J].Chinese Journal of Applied & Environmental Biology,2014,20(04):564-570.[doi:10.3724/SP.J.1145.2013.12034]
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基于中华猕猴桃“红阳”转录组序列开发EST-SSR分子标记()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
20卷
期数:
2014年04期
页码:
564-570
栏目:
研究论文
出版日期:
2014-08-25

文章信息/Info

Title:
Development of EST-SSR markers in Actinidia chinesis cv ‘Hongyang’ based on transcriptomic sequences
作者:
孟蒙 唐维 刘嘉 黄胜雄 余进德 刘方方 林琳 张霞 刘永胜
1四川大学生命科学学院/水力学与山区河流开发保护国家重点实验室/生物资源与生态环境教育部重点实验室 成都 610064 2合肥工业大学生物与食品工程学院 合肥 230009
Author(s):
MENG Meng TANG Wei LIU Jia HUANG Shengxiong YU Jinde LIU Fangfang LIN Lin ZHANG Xia LIU Yongsheng
1Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China 2School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
关键词:
中华猕猴桃遗传分析转录组重复单元SSR种质资源
Keywords:
Actinidia chinesis genetic analysis transcriptome repeat motifs SSR germplasm resources
分类号:
S663.403
DOI:
10.3724/SP.J.1145.2013.12034
文献标志码:
A
摘要:
为开发猕猴桃EST-SSR标记,了解28个品种猕猴桃间的遗传多样性和遗传关系,对中华猕猴桃“红阳”的转录组序列进行分析,并根据分析结果设计SSR引物. 之后采用CTAB法提取28个品种猕猴桃的DNA作为SSR-PCR的扩增模板,并根据扩增结果进行聚类分析. 研究中共得到包含SSR的序列21 848条,其中重复单元为单碱基、双碱基、三碱基、四碱基、五碱基和六碱基的序列分别为1 642、15 965、3 141、248、368 和484条,随机选择其中46条序列设计SSR引物. 根据初步的PCR扩增,筛选出32对条带较少且明亮的引物分别对28个品种猕猴桃的DNA样本进行扩增,并对引物对应的SSR序列进行定位. 结果显示,32对引物对应的序列中有19条能够得到完整的所在基因、染色体以及染色体中具体位置的信息. 这些引物中有26对具有多态性,共统计到等位基因120个,每对引物得到1-11个等位基因,平均3.75个. 28个猕猴桃品种之间的遗传相似性系数在0.53-0.97之间,在遗传相似系数为0.72的水平上,可将它们分为5大类,分类结果与传统形态学的划分基本一致. 本研究揭示的各样本间的遗传关系可为未来猕猴桃的种质改良提供依据. 图4 表5 参33
Abstract:
A transcriptome analysis of kiwifruit (Actinidia chinese) cv ‘Hongyang’ was conducted to develop EST-SSR markers and analyze the genetic diversity and relationship among the 28 kiwifruit samples. Genomic DNA of 28 Actinidia samples were extracted with CTAB method and used as a template in SSR-PCR analysis and cluster analysis. In total, 21 848 SSR-containing sequences were obtained, of which 1 642, 15 965, 3 141, 248, 368 and 484 were mono-, di-, tri-, tetra-, penta- and hexa-nucleotide, respectively. Forty-six pairs of flanking SSR primers were developed based on the SSR sequences detected. Based on the results of the PCR analysis, 32 pairs of SSR primers were selected because they provided a relatively low number of clearly amplificated bands. We obtained the precise gene ID, chromosome No. and both start and end sites of 19 sequences. Out of the 32 SSRs, 26 were polymorphic and 120 alleles were observed. Each pair of primers amplified 1-11 alleles with an average of 3.75 alleles per SSR. Fifteen specific bands were detected in 11 samples. The dice similarity coefficient of 28 samples ranged from 0.53 to 0.97. Clustering analysis suggested that the 28 Actinidia samples could be divided into 5 groups with a dice similarity coefficient 0.72. The grouping result was in general agreement with the traditional morphology-based classification. The genetic relatedness identified in the analyzed Actinidia samples provides potential clues for the selection of germplasm of interest for crossbreeding and variety improvement.

参考文献/References:

1 Li JQ, Li XW, Soejarto DD. Actinidiaceae [M]//Wu ZY, Raven PH, Hong DY eds. Flora of China. Beijing: Science Press; St. Louis: Missouri Plant Garden Press, 2007. 334-362
2 Nishiyama I. Fruits of the Actinidia Genus [J]. Adv Food Nutr Res, 2007, 52: 293-324
3 Piombo G, Barouh N, Barea B, Boulanger R, Brat P, Pina M, Villeneuve P. Characterization of the seed oils from kiwi (Actinidia chinensis), passion fruit (Passiflora edulis) and guava (Psidiumguajava) [J]. Oleagineux Corps Gras Lipides, 2006, 13 (2): 195-199
4 Cravotto G, Bicchi C, Mantegna S, Binello A, Tomao V, Chemat F. Extraction of kiwi seed oil: Soxhlet versus four different non-conventional techniques [J]. Nat Prod Res, 2011, 25 (10): 974-981
5 Drummond L. The composition and nutritional value of kiwifruit [J]. Adv Food Nut Res , 2013, 68: 33-57
6 Huang SX, Ding J, Deng DJ, Tang W, Sun HH, Liu DY, Zhang L, Niu XL, Zhang X, Meng M, Yu JD, Liu J, Han Y, Shi W, Zhang DF, Cao SQ, Wei ZJ, Cui YL, Xia YH, Zeng HP, Bao K, Lin L, Min Y, Zhang H, Miao M, Tang XF, Zhu YZ, Sui Y, Li GW, Sun HJ, Yue JY, Sun JQ, Liu FF, Zhou LQ, Lei L, Zheng XQ, Liu M, Huang L, Song J, Xu CH, Li JW, Ye KY, Zhong SL, Lu BR, He GH, Xiao FM, Wang HL, Zheng HK, Fei ZJ, Liu YS. Draft genome of the kiwifruit Actinidia chinensis [J]. Nat Commun, 2013, 4: 3640
7 张妤艳, 马瑞娟, 俞明亮, 许建兰. 桃果形性状的SSR标记[J]. 江苏农业学报, 2013, 28 (6): 1424-1428 [Zhang YY, Ma RJ, Yu ML, Xu JL. Molecular marker linked to peach fruit shape by simple sequence repeat (SSR) [J]. Jiangsu J Agric Sci, 2013, 28 (6): 1424-1428]
8 Nishitani C, Terakami S, Sawamura Y, Takada N, Yamamoto T. Development of novel EST-SSR markers derived from Japanese pear (Pyrus pyrifolia) [J]. Breeding Sci, 2009, 59 (4): 391-400
9 吴文珊, 朱晓东, 陈友铃. 与薜荔性别相关的 SRAP 分子标记[J]. 应用与环境生物学报, 2008, 14 (5): 688-691 [Wu WS, Zhu XL, Chen YL. Identification of a sex-associated SRAP marker in Ficus pumila L. [J]. Chin J Appl Environ Biol, 2008, 14 (5): 688-691]
10 Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis [J]. Mol Breed, 1996, 2 (3): 225-238
11 Kashi Y, King D, Soller M. Simple sequence repeats as a source of quantitative genetic variation [J]. Trends Genet, 1997, 13 (2): 74-78
12 Barzegar R, Peyvast G, Ahadi AM, Rabiei B, Ebadi AA, Babagolzadeh A. Biochemical systematic, population structure and genetic variability studies among Iranian Cucurbita (Cucurbita pepo L.) accessions, using genomic SSRs and implications for their breeding potential [J]. Biochem Syst Ecol, 2013, 50: 187-198
13 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 Y, Qiang XL, Huang J, Zhang X, Tan AN, Zhao CQ, Chen J. Genetic diversity among barley varieties (lines) bred in China [J]. Chin J Appl Environ Biol, 2013, 19 (1): 79-83]
14 Ogundiwin EA, Peace CP, Gradziel TM, Parfitt DE, Bliss FA, Crisosto CH. A fruit quality gene map of Prunus [J]. BMC Genomics, 2009, 10 (1): 587
15 Chen XM, Luo YH, Xia XC, Xia LQ, Chen X, Ren ZL, He ZH, Jia JZ. Chromosomal location of powdery mildew resistance gene Pm16 in wheat using SSR marker analysis [J]. Plant Breed, 2005, 124 (3): 225-228
16 Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P. High transferability of bread wheat EST-derived SSRs to other cereals [J]. Theor Appl Genet, 2005, 111 (4): 677-687
17 Gasic K, Han YP, Kertbundit S, Shulaev V, Iezzoni AF, Stover EW, Bell RL, Wisniewski ME, Korban SS. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species [J]. Mol Breedi, 2009, 23 (3): 397-411
18 Huang WG, Cipriani G, Morgante M, Testolin R. Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species [J]. Theor Appl Genet, 1998, 97 (8): 1269-1278
19 Korkovelos AE, Mavromatis AG, Huang WG, Hagidimitriou M, Giakoundis A, Goulas CK. Effectiveness of SSR molecular markers in evaluating the phylogenetic relationships among eight Actinidia species [J]. Sci Hort, 2008, 116 (3): 305-310
20 Man YP, Wang YC, Zhang L, Li ZZ, Qin R, Jiang ZW, Sun XR, Liu CJ. Development of microsatellite markers in Actinidia arguta (Actinidiaceae) based on the NCBI data platform [J]. Am J Bot, 2011, 98 (11): e310 -e315
21 Weising K, Fung RWM, Keeling DJ, Atkinson RG, Gardner RC. Characterisation of microsatellites from Actinidia chinensis [J]. Mol Breeding, 1996, 2 (2): 117-131
22 Zhen YQ, Li Z, Huang HW. Molecular characterization of kiwifruit (Actinidia) cultivars and selections using SSR markers [J]. J Am Soc Hort Sci, 2004, 129 (3): 374-382
23 Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue [J]. Phytochem Bull, 1987, 19: 11-15
24 Mace ES, Buhariwalla HK, Crouch JH. A high-throughput DNA extraction protocol for tropical molecular breeding programs [J]. Plant Mol Biol Rep, 2003, 21 (4): 459-460
25 Salzman RA, Fujita T, Zhu-Salzman K, Hasegawa PM, Bressan RA. An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates [J]. Plant Mol Biol Rep, 1999, 17 (1): 11-17
26 Vieira EA, de Carvalho FIF, Bertan I, Kopp MM, Zimmer PD, Benin G, da Silva JAG, Hartwig I, Malone G, de Oliveira AC. Association between genetic distances in wheat (Triticum aestivum L.) as estimated by AFLP and morphological markers [J]. Gen Mol Biol, 2007, 30 (2): 392-399
27 Wu XJ, Huang AY, Xu ML, Wang C, Jia ZJ, Wang GC, Niu JF. Variation of expression levels of seven housekeeping genes at different life-history stages in Porphyra yezoensis [J]. PloS ONE, 2013, 8 (4): e60740
28 Cabras AD, Kremer M, Schulz S, Werner M, Hummel M, Komminoth P, H?fler G, H?fler H. Quality assessment in diagnostic molecular pathology: experience from a German-Austrian-Swiss multicenter trial [J]. Virchows Arch, 2000, 437 (1): 46-51
29 Jung S, Abbott A, Jesudurai C, Tomkins J, Main D. Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs [J]. Func Integr Genomics, 2005, 5 (3): 136-143
30 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
31 Han ZG, Wang CB, Song XL, Guo WZ, Gou JY, Li CH, Chen XY, Zhang TZ. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton [J]. Theor Appl Genet, 2006, 112 (3): 430-439
32 Kantety RV, La Rota M, Matthews DE, Sorrells ME. 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
33 Ferguson AR, Huang HW. Genetic resources of kiwifruit: domestication and breeding [J]. Hort Rev, 2007, 33: 1-121

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备注/Memo

备注/Memo:
四川省政府性基金项目(2013NZ0014)、安徽省政府性基金项目(2012AKKG0739)和国家重点基础研究发展计划项目(2011CB100401)资助 Supported by the Key Project from the Government of Sichuan Province (2013NZ0014), the Key Project from the Government of Anhui Province (2012AKKG0739), and the National Basic Research Program of China (973 Program) (2011CB100401)
更新日期/Last Update: 2014-08-26