Identification of DNA Variations Using AFLP and SSR Markers in Soybean Somaclonal Variants

  • Lee, Suk-Ha (School of Plant Science, Seoul National University) ;
  • Jung, Hyun-Soo (School of Plant Science, Seoul National University) ;
  • Kyujung Van (School of Plant Science, Seoul National University) ;
  • Kim, Moon-Young (School of Plant Science, Seoul National University)
  • Published : 2004.03.01

Abstract

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

References

  1. Barwale, U. B., H. R. Kerns, and J. M. Widhalm. 1986. Plant regeneration from callus cultures of several soybean genotypes via embryogenesis and organogenesis. Planta 167 : 473-481 https://doi.org/10.1007/BF00391223
  2. Ellegren, H. 2000. Microsatellite mutations in the germline: Implications for evolutionary inference. Trends in Genet. 16 : 551-558 https://doi.org/10.1016/S0168-9525(00)02139-9
  3. Evans, D. A, W. R. Sharp, and H. P Medina-Filho. 1984. Somaclonal and gametoclonal variation. Am. J. Bot. 77 : 759-774
  4. Freytag, A. H., A. P.Rao-Arelli, S. C. Anand, J. A Wrather, and L. D. Owens. 1989. Somaclonal variation in soybean plants regenerated from tissue culture. Plant Cell Rep. 8 : 199-202 https://doi.org/10.1007/BF00778531
  5. Keim, P., T. C. Olson, and R. C. Shoemaker. 1988. A rapid protocol for isolating soybean DNA. Soybean Genet. Newsl. 15 : 150-154
  6. Kim, M. Y., B. -K. Ha, T. -H. Jun, E. -Y Hwang, K. Van, Y. I. Kuk, and S. -H. Lee. 2004. Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene $(Lx_2)$ in soybean. Euphytica 135 : 169-177 https://doi.org/10.1023/B:EUPH.0000014909.40136.20
  7. Larkin, P. J. and W. R. Scowcroft. 1981. Somaclonal variation a novel source of variability from plant cell cultures for plant improvements. Theor. Appl. Genet. 60: 197-214 https://doi.org/10.1007/BF02342540
  8. Levinson, G. and G. A Gutman. 1987. Slipped-strand mispairing: Amajor mechanism for DNA sequence evolution. Mol. BioI. Evol. 4 : 203-221
  9. Nguyen, M. V., C. D. Nickell, and J. M. Widhalm. 2001. Selection for high seed oil content in soybean families derived from plants regenerated from protoplasts and tissue cultures. Theor. Appl. Genet. 102 : 1072-1075 https://doi.org/10.1007/s001220000493
  10. Phillips, R. L., S. M. Kaeppler, and P. Olhoft. 1994. Genetic variability of plant tissue culture: Breakdown of normal controls. Proc. Natl. Acad. Sci. USA. 91 : 5222-5226 https://doi.org/10.1073/pnas.91.12.5222
  11. Stephens, P. A., U. Barwle-Sehr, C. D. Nickell, and J. M. Widholm. 1991. A cytoplasmically inherited, wrinkled-leaf mutant in soybean. J. Hered. 82: 71-73 https://doi.org/10.1093/jhered/82.1.71
  12. Van, K., B. -K. Ha, E. -Y. Hwang, M. Y. Kim, S. Heu, and S. -H. Lee. 2003. Molecular characterization of hypemodulation in soybean. Plant Pathol. J. 19 : 24-29 https://doi.org/10.5423/PPJ.2003.19.1.024
  13. Vos, P., R. Hogers, M. Bleeker, and M. Zabeau. 1995. AFLP: A new technique for DNA fingerprinting. Nucl. Acids Res. 23 : 4407-4414 https://doi.org/10.1093/nar/23.21.4407
  14. Weaver, R. F. and P. W. Hedrick. 1997. Genetics, 3rd ed. The McGraw-Hill Companies, Inc. Dubuque, lA, USA.
  15. Ziegle, J. S., Y. Su, K. P. Corcoran, L. Nie, P. E. Mayrand, L. B. Hoff, L. J. McBride, M. N. Kronick, and S. R. Kiehl. 1992. Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics 14 : 1026-1031 https://doi.org/10.1016/S0888-7543(05)80126-0