Legume Research

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Research Article

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.

ABSTRACT

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. 

REFERENCES

  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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