Legume Research

  • Chief EditorJ. S. Sandhu

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Legume Research, volume 43 issue 1 (february 2020) : 8-17

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

X.J. Fu, J.X. Pei, Y.T. Zheng, D.D. Guo, Q.H. Yang, H.X. Jin, D.H. Zhu, D.K. Dong, S.C. Xu
1Hangzhou National Sub-center of Soybean Improvement, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences. Hangzhou, Zhejiang 310021, P.R. China.
  • Submitted10-10-2018|

  • Accepted29-06-2019|

  • First Online 09-11-2019|

  • doi 10.18805/LR-456

Cite article:- Fu X.J., Pei J.X., Zheng Y.T., Guo D.D., Yang Q.H., Jin H.X., Zhu D.H., Dong D.K., Xu S.C. (2019). DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers. Legume Research. 43(1): 8-17. doi: 10.18805/LR-456.
Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar ‘Zhexian No.9’ with ‘Williams 82’ as reference. 33.7% of these markers were polymorphic between ‘Zhexian No.9’ and ‘Williams 82’. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing ‘Zhexian No.9’ and ‘Williams 82’. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of ‘Zhexian No.9’. The described marker-developing methodology could be used in other crops with known genomic information. 
  1. Colasuonno, P., Incerti, O., Lozito, M.L., Simeone, R., Gadaleta, A., Blanco, A. (2016). DHPLC technology for high-throughput detection of mutations in a durum wheat TILLING population. Bmc Genetics, 17(1):43. 
  2. De Koeyer, D., Douglass, K., Murphy, A., Whitney, S., Nolan, L., Song, Y., De Jong, W. (2010). Application of high-resolution DNA melting for genotyping and variant scanning of diploid and autotetraploid potato. Molecular Breeding, 25(1):67-90. 
  3. Distefano, G., La Malfa, S., Gentile, A., Wu, S.B. (2013). EST-SNP genotyping of citrus species using high-resolution melting curve analysis. Tree Genetics and Genomes, 9(5):1271-1281. 
  4. Dong, D.K., Fu, X.J., Yuan, F.J., Chen, P.Y., Zhu, S.L., Li, B.Q., Yang, Q.H., Yu, X.M., Zhu, D.H. (2014). Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers. Genetic Resources and Crop Evolution, 61(1):173-183. 
  5. Ganopoulos, I., Tsaballa, A., Xanthopoulou, A., Madesis, P., Tsaftaris, A. (2013). Sweet Cherry Cultivar Identification by High-Resolution-Melting (HRM) Analysis Using Gene-Based SNP Markers. Plant Molecular Biology Reporter, 31(3):763-768.
  6. Guldberg, P., Romano, V., Ceratto, N., Bosco, P., Ciuna, M., Indelicato, A., Mollica, F., et al. (1993). Mutational spectrum of phenylalanine hydroxylase deficiency in Sicily: implications for diagnosis of hyperphenylalaninemia in southern Europe. Human Molecular Genetics, 2(10):1703-1707. 
  7. Gupta, P.K., Roy, J.K. and Prasad, M. (2001). Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science, 80(4):524–535.
  8. Han, Y.H., Khu, D.M. and Monteros, M.J. (2012). High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.). Molecular Breeding, 29(2): 489- 501.
  9. Hayashi, K., Hashimoto, N., Daigen, M. and Ashikawa, I. (2004). Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theoretical and Applied Genetics, 108(7):1212-1220. 
  10. Hisano, H., Sato, S., Isobe, S., Sasamoto, S., Wada, T., Matsuno, A., Fujishiro, T., et al. (2007). Characterization of the soybean genome using EST-derived microsatellite markers. DNA Research, 14(6):271-281.
  11. Jeong, H.J., Jo, Y.D., Park, S.W. and Kang, B.C. (2010). Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome, 53(12):1029-1040.
  12. Kim, B., Kim, N., Kim, J.Y., Kim, B.S., Jung, H.J., Hwang, I., Noua, I.S., Sim, S.C. and Park, Y. (2016). Development of a high-    resolution melting marker for selecting Fusarium crown and root rot resistance in tomato. Genome, 59(3):173-183.
  13. Korir, N.K., Han, J., Shangguan, L.F., Wang, C., Kayesh, E., Zhang, Y.Y. and Fang, J.G. (2013). Plant variety and cultivar identification: advances and prospects. Critical Reviews in Biotechnology, 33(2):111-125. 
  14. Kozlowski, P. and Krzyzosiak, W.J. (2001). Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection. Nucleic Acids Research, 29(14):e71. 
  15. Li, A.Q., Zhao, C.Z., Wang, X.J., Liu, Z.J., Zhang, L.F., Song, G.Q., Yin, J., Li, C.S., Xia, H., Bi, Y.P. (2010). Identification of SSR markers using soybean (Glycine max) ESTs from globular stageembryos. Electronic Journal of Biotechnology, 13(5):1-11.
  16. Li, D.D., Lewis, R.S., Jack, A.M., Dewey, R.E., Bowen, S.W. and Miller, R.D. (2012). Development of CAPS and dCAPS markers for CYP82E4, CYP82E5v2 and CYP82E10 gene mutants reducing nicotine to nornicotine conversion in tobacco. Molecular Breeding, 29(3):589-599. 
  17. Li, W.G., Liu, S., Jiang, S.T., Li, X.L. and Li, G. (2018). Development of 30 SNP markers for the endangered plant Taihangia rupestris based on transcriptome database and high resolution melting analysis. Conservation Genetics Resources, 10(4):775-778.
  18. Liew, M., Johnson, M., Graham, R., Meadows, C., Erali, M., Mao, R., Lyon, E., Wittwer, C. (2004). Fluorescent SNP genotyping by high-resolution melting analysis without probes. Clinical Chemistry, 50(11):2227-2227.
  19. Lopez, C.M.R., Croxford, A.E. and Wilkinson, M.J. (2008). High-resolution melt analysis for SNP discovery, linkage mapping and analysis of DNA methylation. Comparative Biochemistry and Physiology A, 150(3):S49-S50.
  20. Montgomery, J., Wittwer, C.T., Palais, R. and Zhou, L.M. (2007). Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nature Protocols, 2(1): 59- 66. 
  21. Nguyen, Q., Mckinney, J., Johnson, D.J., Roberts, K.A. and Hardy, W.R. (2012). STR melting curve analysis as a genetic screening tool for crime scene samples. Journal of Forensic Sciences, 57(4):887-899. 
  22. Park, J.H., Jang, H., Jung, Y.K., Jung, Y.L., Shin, I., Cho, D.Y. and Park, H.G. (2017). A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosensors and Bioelectronics, 91:122-127. 
  23. Permingeat, H.R., Romagnoli, M.V., Sesma, J.I. and Vallejos, R.H. (1998). A simple method for isolating DNA of high yield and quality from cotton (Gossypium hirsutum L.) leaves. Plant Molecular Biology Reporter, 16(1):89.
  24. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2(3):225-238. 
  25. Singh, N., Choudhury, D.R., Tiwari, G., Singh, A.K., Kumar, S., Srinivasan, K., Tyagi, R.K., Sharma, A.D., Singh, N.K. and Singh, R. (2016). Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genetics, 17(1):127. 
  26. Singh, N., Jayaswal, P.K., Panda, K., Mandal, P., Kumar, V., Singh, B., Mishra, S., et al. (2015). Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Scientific Reports, 5:11600. 
  27. Villano, C., Miraglia, V., Iorizzo, M., Aversano, A. and Carputo, D. (2016). Combined use of molecular markers and high-resolution melting (HRM) to assess chromosome dosage in potato hybrids. Journal of Heredity, 107(2):187-192. 
  28. Wolford, J.K., Blunt, D., Ballecer, C. and Prochazka, M. (2000). High-throughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DHPLC). Human Genetics, 107(5):483-487. 
  29. Wu, X.H., Wang, B.G., Lu, Z.F., Wu, X.Y., Li, G.J. and Xu, P. (2014). Identification and Mapping of a Powdery Mildew Resistance Gene Vu-Pm1 in the Chinese Asparagus Bean Landrace Zn016. Legume Research, 37(1):32-36.
  30. Wu, X.Y., Wang, B.G., Wu, X.H., Lu, Z.F., Li, G.J. and Xu, P. (2018). SNP marker-based genetic mapping of rust resistance gene in the vegetable cowpea landrace ZN016. Legume Research, 41(2):222-225.
  31. Young, G., Mebrahtu, T. and Johnson, J. (2000). Acceptability of green soybeans as a vegetable entity. Plant Foods for Human Nutrition, 55(4):323-333. 
  32. Zhang, G.W., Xu, S.C., Mao, W.H., Hu, Q.Z. and Gong, Y.M. (2013). Determination of the genetic diversity of vegetable soybean Glycine max (L.) Merr. using EST-SSR markers. Journal of Zhejiang University-Science B, 14(4):279-288. 

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