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Journal of Nucleic Acids
Volume 2017, Article ID 6590902, 9 pages
https://doi.org/10.1155/2017/6590902
Research Article

Systemic Identification of Hevea brasiliensis EST-SSR Markers and Primer Screening

1College of Agriculture, Hainan University, Haikou 570228, China
2Institute of Cereal Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China
3Hainan Tropical Ocean University, Sanya 572202, China
4Key Laboratory of Tropical Crop Molecular Breeding of Sanya, Sanya 572202, China

Correspondence should be addressed to Yaoting Wu; nc.gro.auhgnist@gnitoayuw

Received 4 August 2016; Revised 26 October 2016; Accepted 23 November 2016; Published 23 January 2017

Academic Editor: Yanfeng Zhang

Copyright © 2017 Benjun Hou et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. K. Varshney, K. Chabane, P. S. Hendre, R. K. Aggarwal, and A. Graner, “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,” Plant Science, vol. 173, no. 6, pp. 638–649, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. J. R. Russell, J. D. Fuller, M. Macaulay et al., “Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs,” Theoretical and Applied Genetics, vol. 95, no. 4, pp. 714–722, 1997. View at Publisher · View at Google Scholar · View at Scopus
  3. M. S. Röder, V. Korzun, K. Wendehake et al., “A microsatellite map of wheat,” Genetics, vol. 149, no. 4, pp. 2007–2023, 1998. View at Google Scholar · View at Scopus
  4. T. Ujino, T. Kawahara, Y. Tsumura, T. Nagamitsu, H. Yoshimaru, and W. Ratnam, “Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species,” Heredity, vol. 81, no. 4, pp. 422–428, 1998. View at Publisher · View at Google Scholar · View at Scopus
  5. M. I. Uzunova and W. Ecke, “Abundance, polymorphism and genetic mapping of microsatellites in oilseed rape (Brassica napus L.),” Plant Breeding, vol. 118, no. 4, pp. 323–326, 1999. View at Publisher · View at Google Scholar · View at Scopus
  6. P. K. Gupta, S. Rustgi, S. Sharma, R. Singh, N. Kumar, and H. S. Balyan, “Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat,” Molecular Genetics and Genomics, vol. 270, no. 4, pp. 315–323, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. J.-K. Yu, M. La Rota, R. V. Kantety, and M. E. Sorrells, “EST derived SSR markers for comparative mapping in wheat and rice,” Molecular Genetics and Genomics, vol. 271, no. 6, pp. 742–751, 2004. View at Google Scholar · View at Scopus
  8. V. Poncet, M. Rondeau, C. Tranchant et al., “SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus,” Molecular Genetics and Genomics, vol. 276, no. 5, pp. 436–449, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. T. Yamamoto, T. Kimura, Y. Sawamura et al., “SSRs isolated from apple can identify polymorphism and genetic diversity in pear,” Theoretical and Applied Genetics, vol. 102, no. 6-7, pp. 865–870, 2001. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Kumar Yadav, A. Ranjan, M. H. Asif, S. Mantri, S. V. Sawant, and R. Tuli, “EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera,” Tree Genetics and Genomes, vol. 7, no. 1, pp. 207–219, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. R. K. Varshney, R. Sigmund, A. Börner et al., “Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice,” Plant Science, vol. 168, no. 1, pp. 195–202, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. W. Ramakrishna, A. P. Davierwala, V. S. Gupta, and P. K. Ranjekar, “Expansion of a (GA) dinucleotide at a microsatellite locus associated with domestication in rice,” Biochemical Genetics, vol. 36, no. 9-10, pp. 323–327, 1998. View at Publisher · View at Google Scholar · View at Scopus
  13. A. P. Davierwala, W. Ramakrishna, V. Chowdari, P. K. Ranjekar, and V. S. Gupta, “Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies,” BMC Evolutionary Biology, vol. 1, article no. 7, 2001. View at Publisher · View at Google Scholar · View at Scopus
  14. A. Wünsch and J. I. Hormaza, “Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences,” Heredity, vol. 89, no. 1, pp. 56–63, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. F. L. Luro, G. Costantino, J. Terol et al., “Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other citrus species and their effectiveness for genetic mapping,” BMC Genomics, vol. 9, article 287, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. E. Vendramin, M. T. Dettori, J. Giovinazzi, S. Micali, R. Quarta, and I. Verde, “A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species,” Molecular Ecology Notes, vol. 7, no. 2, pp. 307–310, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. N. Bassil and J. D. Postman, “Identification of European and Asian pears using EST-SSRs from Pyrus,” Genetic Resources and Crop Evolution, vol. 57, no. 3, pp. 357–370, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. E. Inoue, Y. Matsuki, H. Anzai, and K. Evans, “Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai): primer note,” Molecular Ecology Notes, vol. 7, no. 3, pp. 445–447, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. L. G. Fraser, P. M. Datson, G. K. Tsang, K. I. Manako, E. H. Rikkerink, and M. A. McNeilage, “Characterisation, evolutionary trends and mapping of putative resistance and defence genes in Actinidia (kiwifruit),” Tree Genetics & Genomes, vol. 11, article 21, 2015. View at Publisher · View at Google Scholar · View at Scopus
  20. Y. Na-ek, A. Wongkaew, T. Phumichai et al., “Genetic diversity of physic nut (Jatropha curcas L.) revealed by SSR markers,” Journal of Crop Science and Biotechnology, vol. 14, no. 2, pp. 105–110, 2011. View at Publisher · View at Google Scholar
  21. V. Decroocq, M. G. Favé, L. Hagen, L. Bordenave, and S. Decroocq, “Development and transferability of apricot and grape EST microsatellite markers across taxa,” Theoretical and Applied Genetics, vol. 106, no. 5, pp. 912–922, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. R. M. Marius, “Ekué & oliver gailing & reiner finkeldey transferability of Simple Sequence Repeat (SSR) markers. Developed in Litchi chinensis to Blighia sapida (Sapindaceae),” Plant Molecular Biology Reporter, vol. 27, pp. 570–574, 2009. View at Google Scholar
  23. M. A. Viruel and J. I. Hormaza, “Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae),” Theoretical and Applied Genetics, vol. 108, no. 5, pp. 896–902, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. R. E. C. Mba, P. Stephenson, K. Edwards et al., “Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava,” Theoretical and Applied Genetics, vol. 102, no. 1, pp. 21–31, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. D. W. Peng, L. C. Zheng, and H. B. Zhu, “Analysis of SSR information in EST resource of cassava,” Chinese Agricultural Science Bulletin, vol. 24, no. 2, pp. 433–436, 2008. View at Google Scholar
  26. M. L. Zhou, Z. Q. Xia, J. R. Chen, and W. Q. Wang, “Analysis of SSR information and annotation in EST resource of Caster Bean (Ricinus communis),” Chinese Journal of Tropical Crops, vol. 33, no. 12, pp. 2138–2143, 2012. View at Google Scholar
  27. K. Laosatit, P. Tanya, P. Somta et al., “De novo transcriptome analysis of apical meristem of Jatropha spp. using 454 pyrosequencing platform, and identification of SNP and EST-SSR markers,” Plant Molecular Biology Reporter, vol. 34, no. 4, pp. 786–793, 2016. View at Publisher · View at Google Scholar · View at Scopus
  28. B. G. Jia, Q. Lin, X. F. Tan et al., “Development of EST-SSR markers and their use for genetic diversity analysis in tung tree(vernicia fordii),” Journal of Plant Genetic Resources, vol. 17, no. 4, pp. 625–636, 2016. View at Google Scholar
  29. W. Xu, Q. Yang, H. Huai, and A. Liu, “Development of EST-SSR markers and investigation of genetic relatedness in tung tree,” Tree Genetics & Genomes, vol. 8, no. 4, pp. 933–940, 2012. View at Publisher · View at Google Scholar · View at Scopus
  30. Y. W. Hu, Y. Lu, Q. Y. Long, X. Zeng, Y. S. Hu, and H. X. Huang, “Development of EST-SSRS using public ESTs in hevea,” Chinese Journal of Tropical Crops, vol. 29, no. 5, pp. 583–588, 2008. View at Google Scholar
  31. Z.-W. An, Y.-H. Zhao, H. Cheng, W.-G. Li, and H.-S. Huang, “Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg,” Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji, vol. 31, no. 3, pp. 311–319, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. D. J. Li, Z. Deng, H. N. Guo, and Z. H. Xia, “Development and characterizations of EST-SSR markers in rubber tree (Hevea brasiliensis),” Agricultural Science & Technology, vol. 15, no. 5, pp. 733–737, 2014. View at Google Scholar
  33. S. P. Feng, W. G. Li, H. S. Huang, J. Y. Wang, and Y. T. Wu, “Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis),” Molecular Breeding, vol. 23, no. 1, pp. 85–97, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. D. Li, Z. Deng, B. Qin, X. Liu, and Z. Men, “De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.),” BMC Genomics, vol. 13, no. 1, article 192, 2012. View at Publisher · View at Google Scholar · View at Scopus
  35. N.-C. Ting, N. M. Zaki, R. Rosli et al., “SSR mining in oil palm EST database: application in oil palm germplasm diversity studies,” Journal of Genetics, vol. 89, no. 2, pp. 135–145, 2010. View at Publisher · View at Google Scholar · View at Scopus
  36. P. Hu, C. L. Zhong, Y. Zhang et al., “Distribution and molecular marker of SSR in EST resourch of Casuarinaceae,” Bulletin of Botanical Research, vol. 36, no. 1, pp. 116–122, 2016. View at Google Scholar
  37. M. M. Yan, X. G. Dai, and S. X. Li, “Sequence analysis and comparison of EST-SSRs in Pine, Poplar and Eucalyptus,” Genomics and Applied Biology, no. 1, pp. 23–24, 2011. View at Google Scholar
  38. H. H. Fan, Y. C. Li, Y. P. Li, Y. Lin, and Y. P. Cai, “Characteristics of EST-SSR distribution in Ginkgo ESTs,” Genomics and Applied Biology, vol. 28, no. 5, pp. 869–873, 2009. View at Google Scholar
  39. H. Yang, Q. Chen, C. L. Wei, C. Y. Shi, C. B. Fang, and C. X. Wan, “Analysis on SSR information in Camellia sinensis transcriptome,” Journal of Anhui Agricultural University, vol. 38, no. 6, pp. 882–886, 2011. View at Google Scholar
  40. C. Chen, P. Zhou, Y. A. Choi, S. Huang, and F. G. Gmitter Jr., “Mining and characterizing microsatellites from citrus ESTs,” Theoretical and Applied Genetics, vol. 112, no. 7, pp. 1248–1257, 2006. View at Publisher · View at Google Scholar · View at Scopus
  41. R. K. Varshney, A. Graner, and M. E. Sorrells, “Genic microsatellite markers in plants: features and applications,” Trends in Biotechnology, vol. 23, no. 1, pp. 48–55, 2005. View at Publisher · View at Google Scholar · View at Scopus
  42. V. Camasamudram, J.-K. Fang, and N. G. Avadhani, “Transcription termination at the mouse mitochondrial H-strand promoter distal site requires an A/T rich sequence motif and sequence specific DNA binding proteins,” European Journal of Biochemistry, vol. 270, no. 6, pp. 1128–1140, 2003. View at Publisher · View at Google Scholar · View at Scopus
  43. W. Pootakham, J. Chanprasert, N. Jomchai et al., “Development of genomic-derived simple sequence repeat markers in Hevea brasiliensis from 454 genome shotgun sequences,” Plant Breeding, vol. 131, no. 4, pp. 555–562, 2012. View at Publisher · View at Google Scholar · View at Scopus
  44. S. X. Li, X. Y. Zhang, Y. Y. Wang et al., “Content and characteristics of microsatellites detected in expressed sequence tag sequences in eucalyptu,” Chinese Bulletin of Botany, vol. 45, no. 3, pp. 363–371, 2010. View at Google Scholar