Zhang Lei, Wang Guoliang, Liu Cui, Chi Shan, Liu Tao. Development and utility of EST-SSR markers in Ulva prolifera of the South Yellow Sea[J]. Acta Oceanologica Sinica, 2014, 33(10): 105-113. doi: 10.1007/s13131-014-0545-z
Citation: Zhang Lei, Wang Guoliang, Liu Cui, Chi Shan, Liu Tao. Development and utility of EST-SSR markers in Ulva prolifera of the South Yellow Sea[J]. Acta Oceanologica Sinica, 2014, 33(10): 105-113. doi: 10.1007/s13131-014-0545-z

Development and utility of EST-SSR markers in Ulva prolifera of the South Yellow Sea

doi: 10.1007/s13131-014-0545-z
  • Received Date: 2013-12-26
  • Rev Recd Date: 2014-05-20
  • Ulva species can grow rapidly in nutrient-rich habitats causing green tides and marine fouling. A more complete understanding of the reasons behind these outbreaks is urgently required. Accordingly, this study attempts to use microsatellite markers based expressed sequence tag (EST) to analyze the genetic variation of several Ulva prolifera populations in the South Yellow Sea of China. Two hundred and thirty-eight SSRs were identified from 8 179 unique ESTs (6 203 newly sequenced and 1 976 downloaded from NCBI database) and 37 primer pairs were successfully designed according to the ESTs; 11 pairs were selected to detect the genetic diversity and relationship of 69 attached U. prolifera samples and 13 free-floating samples collected from coastal and off-coast areas of the South Yellow Sea. The results of cross-species transferability showed that six of the 11 EST-SSR primers could give good amplification in other five Ulva species and the average allele number was 4.67. Genetic variation analysis indicated that all 82 U. prolifera samples were clearly divided and most samples collected from the same site clustered together as a group in the dendrogram tree produced by unweighted pair-group mean analysis (UPGMA) method and the cluster results showed some consistency with the geographical origins. In addition, 13 free-floating samples (except HT-001-2) were grouped as a single clade separated from the attached samples.
  • loading
  • Alström-Rapaport C, Leskinen E. 2002. Development of microsatellite markers in the green algae Enteromorpha intestinalis (Chlorophyta). Mol Ecol Notes, 2(4): 581-583
    Chen Junfang, Ren Zhenglong, Gao Lifeng, et al. 2005. Developing new SSR markers from EST of wheat. Acta Agron Sin (in Chinese), 31(2): 154-158
    Duan Weijun, Guo Lixin, Sun Dong, et al. 2011. Morphological and molecular characterization of free-floating and attached green macroalgae Ulva spp. in the Yellow Sea of China. J Appl Phycol, 24(1): 97-108
    Doyle J J, Doyle J L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12: 13-15
    Engel C R, Brawlev S H, Edwards K J, et al. 2003. Isolation and crossspecies amplification of microsatellite loci from the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum (Heterokontophyta, Fucaceae). Mol Ecol Notes, 3(2): 180-182
    Falush D, Stephens M, Pritchard J K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164(4): 1567-1587
    Fletcher R L. 1996. The occurrence of “green tides” a review. Marine benthic vegetation in Europe: recent changes and the effect of eutrophication. Heidelberg: Springer
    Hayden H S, Blomster J, Maggs C A, et al. 2003. Linnaeus was right all along: Ulva and Enteromorpha are not distinct genera. Eur J Phycol, 38(3): 277-294
    Hiraoka M, Ichihara K, Zhu W R, et al. 2011. Culture and hybridization experiments on an Ulva clade including the Qingdao strain blooming in the Yellow Sea. PLoS ONE, 6(5): e19371
    Hiraoka M, Ohno M, Kawaguchi S, et al. 2004. Crossing test among floating Ulva thalli forming ‘green-tide’ in Japan. Hydrobiologia, 512(1-3): 239-245
    Jiang Peng, Wang Jinfeng, Cui Yulin, et al. 2008. Molecular phylogenetic analysis of attached Ulvaceae species and free floating Enteromorpha from Qingdao coasts in 2007. Chin J Oceanol Limnol, 26(3): 276-279
    Keesing J K, Liu D Y, Fearns P, et al. 2011. Inter-and intra-annual patterns of Ulva prolifera green tides in the Yellow Sea during 2007-2009, their origin and relationship to the expansion of coastal seaweed aquaculture in China. Mar Pollut Bull, 62(6): 1169-1182
    Kostamo K, Blomster J, Korpelainen H, et al. 2008. New microsatellite markers for Ulva intestinalis (Chlorophyta) and the transferability of markers across species of Ulvaceae. Phycologia, 47(6): 580-587
    Kusumo H T, Pfister C A, Wooton J T. 2004. Dominant (AFLP) and codominant (microsatellite) markers for the kelp Postelsia palmaeformis (Laminariales). Mol Ecol Notes, 4(3): 372-375
    Leliaert F, Zhang Xiaowen, Ye Naihao, et al. 2009. Identity of the Qingdao algal bloom. Phycol Res, 57(2): 147-151
    Lewis J R. 1978. The Ecology of Rocky Shores. London: Hodder & Stoughton Liang Xuanqiang, Chen Xiaoping, Hong Yanbin, et al. 2009. Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol, 9: 35
    Liang Zongying, Lin Xiangzhi, Ma Mu, et al. 2008. A preliminary study of the Enteromorpha prolifera drift gathering causing the Green Tide phenomenon. J Ocean Univ China (in Chinese), 38(4): 601-604
    Liu Cui, Zhang Jing, Sun Xiaoyu, et al. 2011. Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP Marker. J Ocean Univ China, 10(3): 263-269
    Martínez E A, Cardenas L, Figueroa C, et al. 2005. Microsatellites of Laminaria digitata tested in Lessonia nigrescens: Evaluation and improvement of cross amplification between kelps of two different families. J Appl Phycol, 17(3): 245-253
    Merceron M, Antoine V, Auby I, et al. 2007. In situ growth potential of the subtidal part of green-tide forming Ulva spp.. Stocks. Sci Total Envir, 384(1-3): 293-305
    Miller M P. 1997. Tools for Population Genetic Analyses (TFPGA). Version 1.3: A Windows? program for the analysis of allozyme and molecular population genetic data. Flagstaff, AZ: Department of Biological Sciences, Northern Arizona University
    Niu Jianfeng, Hu Haiyan, Hu Songnian, et al. 2010. Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta). Chin J Oceanol Limnol, 28(1): 26-36
    Noah A R. 2007. Distruct: a program for the graphical display of population structure. Mol Ecol Notes, 4(1): 137-138
    Pang Shaojun, Liu Feng, Shan Tifeng, et al. 2010. Tracking the algal origin of the Ulva bloom in the Yellow Sea by a combination of molecular, morphological and physiological analyses. Mar Environ Res, 69(4): 207-215
    Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959
    Shimada S, Yokoyama N, Arai S, et al. 2008. Phylogeography of the genus Ulva (Ulvophyceae, Chlorophyta), with special reference to the Japanese freshwater and brackish taxa. J Appl Phycol, 20(5): 979-989
    Sun Jianwei, Liu Tao, Guo Baotai, et al. 2006. Development of SSR primers from EST sequences and their application in germplasm identification of Porphyra lines (Rhodophyta). Eur J Phycol, 41(3): 329-336
    Tseng C K. 2009. Seaweeds in Yellow Sea and Bohai Sea of China (in Chinese). Beijing: Science Press
    Varshney R K, Thiel T, Stein N, et al. 2002. In silico analysis of frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett, 7(2A): 537-546
    Villares R, Puente X, Carballeira A. 2001. Ulva and Enteromorpha as indicators of heavy metal pollution. Hydrobiologia, 462(1-3): 221-232
    Wang Jinfeng, Li Nan, Jiang Peng, et al. 2010. Ulva and Enteromorpha (Ulvaceae, Chlorophyta) from two sides of the Yellow Sea: analysis of nuclear rDNA ITS and plastid rbcL sequence data. Chin J Oceanol Limnol, 28(4): 762-768
    Wang Guoliang, Tan Xiaolong, Shen Junling, et al. 2011. Development of EST-SSR primers and their practicability test for Laminaria. Acta Oceanol Sin, 30(3): 112-117
    Xie Chaotian, Cheng Changsheng, Ji Dehua, et al. 2009. Characterization, development and exploitation of EST-derived microsatellites in Porphyra haitanensis Chang et Zheng (Bangiales, Rhodophyta). J Appl Phycol, 21(3): 367-374
    Xu Shaobin, Tao Yufen, Yang Zhaoqing, et al. 2002. A simple and rapid method used for silver staining and gel preservation. Hereditas (in Chinese), 24(3): 335-336
    Yeh F C, Yang R C, Boyle T. 1999. POPGENE, Version 1.31. Microsoft Window-based Freeware for Population Genetic Analysis: Quick User Guide. Edmonton, Alberta, Canada: University of Alberta
    Zhang Xiaowen, Wang Hongxia, Mao Yuze, et al. 2010. Somatic cells serve as a potential propagule bank of Enteromorpha prolifera forming a green tide in the Yellow Sea, China. J Appl Phycol, 22(2): 173-180
    Zhao Jin, Jiang Peng, Liu Zhengyi, et al. 2010. Genetic variation of Ulva (Enteromorpha) prolifera (Ulvales, Chlorophyta)—the causative species of the green tides in the Yellow Sea, China. J Appl Phycol, 23(2): 227-233
  • 加载中

Catalog

    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

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (1758) PDF downloads(1584) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return