Scientia Agricultura Sinica ›› 2011, Vol. 44 ›› Issue (19): 4037-4049.doi: 10.3864/j.issn.0578-1752.2011.19.014

• HORTICULTURE • Previous Articles     Next Articles

Characteristics of SSRs Derived from ESTs and Development of EST-SSR Markers in Litchi (Litchi chinensis Sonn.)

 SUN  Qing-Ming, MA  Wen-Chao, MA  Shuai-Peng, ZHAO  Jun-Sheng, BAI  Li-Jun, CHEN  Jie-Zhen, CAI  Chang-He, XIANG  Xu, 欧Liang-Xi   

  1. 1.广东省农业科学院果树研究所
    2.农业部南亚热带果树生物学与遗传资源利用重点实验室
    3.华南师范大学生命科学学院
    4.华南农业大学园艺学院
  • Received:2011-05-17 Online:2011-10-01 Published:2011-06-22

PDF

1076

Cited

18

Abstract:  【Objective】 The objective of this study was to characterize litchi SSRs derived from ESTs and to develop EST-SSR markers for possible use of the markers in the studies of litchi genetic diversities, linkage mapping and phylogenetic relationships.【Method】 SSRIT (simple sequence repeat identification tool) was used to search SSRs in 1 331 unigenes obtained from a cDNA library of pericarp cell enlargement period of litchi. EST-SSR primers were subsequently designed using Primer5.0. The validity and revealing power of the primers were tested by PCR amplification of 16 litchi germplasm accessions showing apparent morphological variations and by PAGE analysis of the PCR products. 【Result】 A search of 1 331 Unigene sequences of litchi identified a total of 220 SSRs that occurred in 189 Unigenes. The average SSR density was one SSR per 4.42 kb of EST sequences, and the average SSR length was 18.43 bp. The dinucleotide and trinucleotide repeats, which were 37.27% and 31.82%, respectively, were the most abundant SSRs detected and accounted for 69.09% of the total. Among the 72 observed repeat motifs, GA/CT was the most abundant (16.82%), followed by AG/TC(14.55%), A/T(11.82%)，AT/TA(5.00%) and GAA/CTT (3.64%). The number of repeats in a SSR was quite different with different repeat motifs. Among the 150 EST-SSR primer pairs designed, 122 (81.33%) yielded ideal PCR products, and 100 of them showed polymorphic bands. 【Conclusion】 There were abundant SSR loci in ESTs of litchi, and the efficiency of developing SSR markers from litchi ESTs was high. The study has generated 100 EST-SSR markers which are potentially useful in the analysis of genetic variations of litchi. More SSR markers could be developed from EST-SSRs identified in this study.

Key words:

[1]陈厚彬. 中国荔枝现状和发展分析.世界热带农业信息, 2008(6): 3-6.

Chen H B. Status and development analysis of China's litchi. World Tropical Agriculture Information, 2008(6): 3-6. (in Chinese)

[2]曾  淇, 昝逢刚, 李明芳, 郑学勤. 分子标记技术在荔枝研究中的应用. 热带作物学报, 2009, 30(4): 544-550.

Zeng Q, Zan F G, Li M F, Zheng X Q. Advances on application of molecular markers in litchi researches. Chinese Journal of Tropical Crops, 2009, 30(4): 544-550. (in Chinese)

[3]Hua Y Z, Tian Z Z, Lu M Y, Wang Z G. EST-SSR sequences revealed the relationship of D-genome in diploid and tetraploid species in Gossypium. Plant Science, 2009, 176: 397- 405.

[4]李明芳, 郑学勤. 荔枝SSR标记的研究. 遗传, 2004, 26(6): 911-916.

Li M F, Zheng X Q. Development of SSR markers in litchi (Litchi chinensis). Hereditas, 2004, 26(6): 911-916. (in Chinese)

[5]Viruel M A, Hormaza J I. Development, characterization and variability analysis of microsatellites in lyche (Litchi chinensis Sonn, Sapindaceae). Theoretical and Applied Genetics, 2004, 108(5): 896-902.

[6]傅嘉欣, 王  英, 周  佳, 赵海燕, 黄穗生, 胡又厘, 胡桂兵, 刘成明. 利用SSR技术进行荔枝龙眼种质资源的遗传多样性分析. 荔枝学术研讨会专刊, 广州, 广东. 2010: 49-58.

Fu J X, Wang Y, Zhou J, Zhao H Y, Huang S S, Hu Y L, Hu G B, Liu C M. Genetic diversity of germplasm resources of litchi and longan by SSR analysis. Proceedings of 2010 China National Workshop on Litchi, Guangzhou, Guangdong, 2010: 49-58. (in Chinese)

[7]Eujayl I, SorrellsM E, Baum M, Wolters P, Powell W. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theoretical and Applied Genetics, 2002, 104: 399-407.

[8]潘海涛, 汪俊君, 王盈盈, 齐照良, 李斯深. 小麦 EST-SSR 标记的开发和遗传作图. 中国农业科学, 2010, 43(3): 452-461.

Pan H T, Wang J J, Wang Y Y, Qi Z L, Li S S. Development and mapping of EST-SSR markers in wheat. Scientia Agricultura Sinica, 2010, 43(3): 452-461. (in Chinese)

[9]Yu J K, La R M, Kantety R V, Sorrells M E. EST-derived SSR markers for comparative mapping in wheat and rice. Molecular Genetics and Genomics, 2004, 271: 742-751.

[10]Han Z G, Wang C B, Song X L, Guo W Z, Gou J Y, Li C H, Chen X Y, Zhang T Z. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theoretical and Applied Genetics, 2006, 112: 430-439.

[11]江 东, 钟广炎, 洪棋斌. 柑橘EST-SSR 分子标记分析. 遗传学报, 2006, 33(4): 345-353.

Jiang D, Zhong G Y, Hong Q B. Analysis of microsatellites in citrus unigenes. Acta Genetica Sinica, 2006, 33(4): 345-353. (in Chinese)

[12]王静毅, 陈业渊, 刘伟良, 武耀廷. 香蕉EST-SSRs 标记的开发与应用. 遗传, 2008, 30(7): 933-940.

Wang J Y, Chen Y Y, Liu W L, Wu Y T. Development and application of EST-derived SSR markers for bananas (Musa nana Lour.). Hereditas, 2008, 30(7): 933-940. (in Chinese)

[13]王西成, 姜淑苓, 上官凌飞, 曹玉芬, 乔玉山, 章  镇, 房经贵. 梨EST-SSR标记的开发及其在梨品种遗传多样性分析中的应用评价. 中国农业科学, 2010, 43(24): 5079-5087.

Wang X C, Jiang S L, Shangguan L F, Cao Y F, Qiao Y S, Zhang Z, Fang J G. Development of EST-derived SSR markers for pear and evaluation of their application in pear genetic diversity analysis. Scientia Agricultura Sinica, 2010, 43(24): 5079-5087. (in Chinese)

[14]朱 艳, 郝艳宾, 王克建, 吴春林, 王维霞, 齐建勋, 周  军. 核桃EST-SSR信息分析与标记的初步建立. 果树学报, 2009, 26(3): 394-398.

Zhu Y, Hao Y B, Wang K J, Wu C L, Wang W X, Qi J X, Zhou J. Analysis of SSRs information and development of SSR markers from walnut ESTs. Journal of Fruit Science, 2009，26(3): 394-398. (in Chinese)

[15]Puchooa D. A simple, rapid and efficient method for the extraction of genomic DNA from lychee (Litchi chinensis Sonn.). African Journal of Biotechnology, 2004, 3 (4): 253-255.

[16]向  旭, 欧良喜, 陈厚彬, 孙清明, 陈洁珍, 蔡长河, 白丽军, 赵俊生. 中国96个荔枝种质资源的EST-SSR遗传多样性分析. 基因组学与应用生物学, 2010, 29(6): 1082-1092.

Xiang X, Ou L X, Chen H B, Sun Q M, Chen J Z, Cai C H, Bai L J, Zhao J S. EST-SSR analysis of genetic diversity in 96 litchi (Litchi chinensis Sonn.) germplasm resources in China. Genomics and Applied Biology, 2010, 29(6): 1082-1092. (in Chinese)

[17]McCouch S R, Chen X, Panaud O, Temnykh S, Xu Y, Cho Y G, Huang N, Ishii T, Blair M. Microsatellite marker development, mapping and application in rice genetics and breeding. Plant Molecular Biology, 1997, 35: 89-99.

[18]Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2000, 156: 847-854.

[19]Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics, 2002, 30: 194-200.

[20]李孟军, 肖  寒, 卢金东, 王兴军. 花生微卫星标记的研究进展. 植物学通报, 2008, 3 :373-380.

Li M J, Xiao H, Lu J D, Wang X J. Reviews on microsatellite markers in peanut. Chinese Bulletin of Botany, 2008, 3: 373-380. (in Chinese)

[21]Kantety R V, La Rota M, Matthews D E, Sorrells M E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Molecular Biology, 2002, 48: 501-510.

[22]Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S. Transferable EST-SSRs markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics Genomics, 2003, 270: 315-323.

[23]柳展基, 孙  萍, 步  迅. 花生EST资源的SSR信息分析. 花生学报, 2008, 37(4): 6-11.

Liu Z J, Sun P, Bu X. Analysis of SSR information in EST resource of peanut. Journal of Peanut Science, 2008, 37(4): 6-11. (in Chinese)

[24]Tang J, Baldwin S J, Jacobs J M, Linden C G, Voorrips R E, Leunissen J A, van Eck H, Vosman B. Large-scale identification of polymorphic microsatellites using an in silico approach. BioMed Central Bioinformatics, 2008, 9:374-387.

[25]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. BioMed Central Genomics, 2005, 6 (1): 23.

[26]Chin E C, Senior M L, Shu H, Smith J S. Maize simple repetitive DNA sequences: Abundance and allele variation. Genome, 1996, 39(5): 866-873.

[27]Sook J, Abbott A, Jesudurai C. Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae EST. Functional and Integrative Genomics, 2005, 5: 136-143.

[28]王长彪, 郭旺珍, 蔡彩平, 张天真. 雷蒙德氏棉EST-SSRs分布特征及开发与利用. 科学通报, 2006, 51: 316-320.

Wang C B, Guo W Z, Cai C P, Zhang T Z. Characteristics of SSRs derived from ESTs and development of EST-SSR markers in Raymond's cotton. Chinese Science Bulletin, 2006, 51: 316-320. (in Chinese)

[29]张艳欣, 林忠旭, 李  武, 涂礼莉, 聂以春, 张献龙. 海岛棉EST-SSR引物的开发与应用研究. 科学通报, 2007, 52(15): 1779-1787.

Zhang Y X, Lin Z X, Li W, Tu L L, Nie Y C, Zhang X L. Development and applification of EST-SSR markers in island cotton.  Chinese Science Bulletin, 2007, 52(15): 1779-1787. (in Chinese)

[30]Weber J L. Informativeness of human (dC-dA)n•(dG-dT)n polymorphisms. Genomics, 1990, 7: 524-530.

[31]Smulders M J M, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B. Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theoretical and Applied Genetics, 1997, 94:264-272.

[32]He C, Poysa V, Yu K. Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical and Applied Genetics, 2003, 106:363-373.

[33]Ellegren H. Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 2004, 5:435-445.

[34]Struss D, Plieske J. The use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied Genetics, 1998, 97: 308-315.

[35]Danin P Y, Reis N, Tzuri G, Katzir N. Development and Characterization of microsatellite markers in Cucumis. Theoretical and Applied Genetics, 2001, 102: 61-72.
[1] XU JiuKai, YUAN Liang, WEN YanChen, ZHANG ShuiQin, LI YanTing, LI HaiYan, ZHAO BingQiang. Nitrogen Fertilizer Replacement Value of Livestock Manure in the Winter Wheat Growing Season [J]. Scientia Agricultura Sinica, 2023, 56(2): 300-313.
[2] CHEN XiaoWei, WANG XiaoLong. Accounting Framework of Carbon Footprint on Integrated Cropping-Breeding Farming System: A Case on Maize-Cow-Recycling Manure Model [J]. Scientia Agricultura Sinica, 2023, 56(2): 314-332.
[3] XU Qian, WANG Han, MA Sai, HU QiuHui, MA Ning, SU AnXiang, LI Chen, MA GaoXing. Inhibition and Interaction of Pleurotus eryngii Polysaccharide and Its Digestion Products on Starch Digestive Enzymes [J]. Scientia Agricultura Sinica, 2023, 56(2): 357-367.
[4] WANG CaiXiang,YUAN WenMin,LIU JuanJuan,XIE XiaoYu,MA Qi,JU JiSheng,CHEN Da,WANG Ning,FENG KeYun,SU JunJi. Comprehensive Evaluation and Breeding Evolution of Early Maturing Upland Cotton Varieties in the Northwest Inland of China [J]. Scientia Agricultura Sinica, 2023, 56(1): 1-16.
[5] ZHAO HaiXuan,ZHANG YiTao,LI WenChao,MA WenQi,ZHAI LiMei,JU XueHai,CHEN HanTing,KANG Rui,SUN ZhiMei,XI Bin,LIU HongBin. Spatial Characteristic and Its Factors of Nitrogen Surplus of Crop and Livestock Production in the Core Area of the Baiyangdian Basin [J]. Scientia Agricultura Sinica, 2023, 56(1): 118-128.
[6] JIANG Hui,FENG Yu,QIN YuMing,ZHU LiangQuan,FAN XueZheng,DING JiaBo. Method Improvement and Its Application of Micro Complement Fixation Test for Brucellosis [J]. Scientia Agricultura Sinica, 2022, 55(8): 1676-1684.
[7] LIU Shuo,ZHANG Hui,GAO ZhiYuan,XU JiLi,TIAN Hui. Genetic Variations of Potassium Harvest Index in 437 Wheat Varieties [J]. Scientia Agricultura Sinica, 2022, 55(7): 1284-1300.
[8] WANG YangYang,LIU WanDai,HE Li,REN DeChao,DUAN JianZhao,HU Xin,GUO TianCai,WANG YongHua,FENG Wei. Evaluation of Low Temperature Freezing Injury in Winter Wheat and Difference Analysis of Water Effect Based on Multivariate Statistical Analysis [J]. Scientia Agricultura Sinica, 2022, 55(7): 1301-1318.
[9] GOU ZhiWen,YIN Wen,CHAI Qiang,FAN ZhiLong,HU FaLong,ZHAO Cai,YU AiZhong,FAN Hong. Analysis of Sustainability of Multiple Cropping Green Manure in Wheat-Maize Intercropping After Wheat Harvested in Arid Irrigation Areas [J]. Scientia Agricultura Sinica, 2022, 55(7): 1319-1331.
[10] WANG ShuHui,TAO Wen,LIANG Shuo,ZHANG XuBo,SUN Nan,XU MingGang. The Spatial Characteristics of Soil Organic Carbon Sequestration and N2O Emission with Long-Term Manure Fertilization Scenarios from Dry Land in North China Plain [J]. Scientia Agricultura Sinica, 2022, 55(6): 1159-1171.
[11] XIAO LuTing,LI XiuHong,LIU LiJun,YE FaYin,ZHAO GuoHua. Effects of Starch Granule Size on the Physical and Chemical Properties of Barley Starches [J]. Scientia Agricultura Sinica, 2022, 55(5): 1010-1024.
[12] QIAO Yuan,YANG Huan,LUO JinLin,WANG SiXian,LIANG LanYue,CHEN XinPing,ZHANG WuShuai. Inputs and Ecological Environment Risks Assessment of Maize Production in Northwest China [J]. Scientia Agricultura Sinica, 2022, 55(5): 962-976.
[13] GUO Yan, ZHANG ShuHang, LI Ying, ZHANG XinFang, WANG GuangPeng. Diversity Analysis of 36 Leaf Phenotypic Traits of Chinese Chestnut [J]. Scientia Agricultura Sinica, 2022, 55(5): 991-1009.
[14] HUANG ZhaoFu, LI LuLu, HOU LiangYu, GAO Shang, MING Bo, XIE RuiZhi, HOU Peng, WANG KeRu, XUE Jun, LI ShaoKun. Accumulated Temperature Requirement for Field Stalk Dehydration After Maize Physiological Maturity in Different Planting Regions [J]. Scientia Agricultura Sinica, 2022, 55(4): 680-691.
[15] LIU ZhenRong,ZHAO WuQi,HU XinZhong,HE LiuCheng,CHEN YueYuan. Optimization of Drying Process in Oat Noodle Production [J]. Scientia Agricultura Sinica, 2022, 55(24): 4927-4942.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd