KOREAN JOURNAL OF CROP SCIENCE (한국작물학회지)

The Korean Society of Crop Science (한국작물학회)
권호 표지

SSR Profiling and Its Variation in Soybean Germplasm

콩 유전자원의 SSR Profiling과 변이

  • Yoon, Mun-Sup (National Institute of Agricultural Biotechnology, RDA) ;
  • Lee, Jeong-Ran (National Institute of Agricultural Biotechnology, RDA) ;
  • Baek, Hyung-Jin (National Institute of Agricultural Biotechnology, RDA) ;
  • Cho, Gyu-Taek (National Institute of Agricultural Biotechnology, RDA) ;
  • Kim, Chang-Yung (National Institute of Agricultural Biotechnology, RDA) ;
  • Cho, Yang-Hee (National Institute of Agricultural Biotechnology, RDA) ;
  • Kim, Tae-San (National Institute of Agricultural Biotechnology, RDA) ;
  • Cho, Eun-Gi (Research & Development Bureau, RDA)
  • 윤문섭 (농촌진흥청 농업생명공학연구원) ;
  • 이정란 (농촌진흥청 농업생명공학연구원) ;
  • 백형진 (농촌진흥청 농업생명공학연구원) ;
  • 조규택 (농촌진흥청 농업생명공학연구원) ;
  • 김창영 (농촌진흥청 농업생명공학연구원) ;
  • 조양희 (농촌진흥청 농업생명공학연구원) ;
  • 김태산 (농촌진흥청 농업생명공학연구원) ;
  • 조은기 (농촌진흥청 연구개발국)
  • Published : 2007.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

The evaluation of soybean germplasm has mainly been carried out by morphological characters at Genetic Resources Division, Rural Development Administration (RDA). However, this information has been limited serving a diverse information for user and effectively managing the soybean germplasm. To resolve this problem, soybean collection conserved at RDA gene bank was profiled using nine soybean SSR (Simple Sequence Repeat) markers. Soybean SSR allele was confirmed using genescan and genotyper softwares of automatic sequencer for accurate genotyping of each accession and continuous accumulation of data. SSR profiling of soybean germplasm has been carried out from 2,855 (Satt458) to 4,368 (Satt197) accessions by locus. The number of allele revealed 267 with an average of 29.6 in total accession, and varied from a low of 21 (Satt532 and Satt141) to a high of 58 (Sat_074). Although the number of accessions of wild soybean is less than that of soybean landraces, Korean wild soybean is more variable than other soybean landraces populations in total number of alleles. However, Korean soybean landraces were more variable than Korean wild soybeans in 5 loci. In the allele frequency, wild soybean accessions showed an even distribution in all alleles and higher distribution in low ladder than in high ladder. Also, Korean soybean landraces revealed a high condensed frequency in Satt286 (202 bp, 232 bp), Chinese soybean landraces in Satt197 (171 bp) and Satt458 (173 bp), and Japanese soybean landraces in Sat_074 (244 bp) and Satt458 (170 bp). These SSR profile information will be provided as indications of redundancies or omissions of accessions and can aid in managing soybean collection held at RDA gene bank. The information on diversity analysis could help to enlarge the genetic diversity of materials in breeding program, and could be used to develop a core collection of soybean germplasm.

본 연구는 농진청 종자은행에 보존된 한국, 중국 및 일본 재래종 콩과 한국 야생콩의 SSR profile 작성과 그들의 유전적 구조 해석을 위해 9개의 SSR 마커에 의해 분석되었다. 1. DNA profiling은 유전자좌별로 2,855(Satt458)점$\sim$4,368(Satt197)점이 분석되어 35,655건이 데이터베이스화되었다. 2. 총 대립인자수는 267개였고 유전자좌당 평균 29.6개의 높은 다형성을 나타냈다. 유전자좌별 대립인자 수는 21개(Satt532 및 Satt141)부터 58개(Sat_074)까지 나타났다. 자원내력별 대립인자수는 한국 야생콩에서 196개로 가장 많은 것으로 나타난 반면, 일본 재래종 콩에서는 가장 적은 115개로 나타났다. 3. 집단에 따른 유전자좌별 대립인자의 범위로 한국 재래종 콩이 가장 많은 5개의 유전자좌(Sat_074, Satt141, Satt286, Satt545, Satt458)에서 다음으로는 한국 야생콩이 4개의 유전자좌(Satt187, Satt532, Satt245, Satt197)에서 가장 넓은 것으로 나타났다. 그러나 대립 인자수면에서는 한국 재래종 콩이 5개의 유전자좌(Sat_074, Satt141, Satt197, Satt545, Satt458)에서 가장 많은 대립인자수를 나타냈고, 한국 야생콩은 나머지 4개의 유전자좌(Satt187, Satt532, Satt245, Satt286)에서 가장 많은 대립인자수를 나타냈다. 4. 대립인자 분포에 있어 전체적으로 한국 야생콩 집단은 재래종 집단들에 비해 고른 분포를 나타냈고 대립인자의 크기가 큰쪽(high ladder)에서보다 작은쪽(low ladder)에서 높은 분포를 나타냈다. 5. 재래종 집단들 간에 대립인자 분포를 살펴보면, 한국 집단은 Satt286(202 bp, 232 bp)에서, 중국집단은 Satt197(171 bp)와 Satt458(173 bp)에서 그리고 일본집단은 Sat_074(244 bp)와 Satt458(170 bp)에서 매우 높은 것으로 나타났다.

Keywords

References

  1. Abe, J., D. H. Xu, Y. Suzuki, A. Kanazawa, and Y. Shimamoto. 2003. Soybean germp1asm pools in Asia revealed by nuclear SSRs. Theor. Appl. Genet. 106 : 445-453 https://doi.org/10.1007/s00122-002-1073-3
  2. Akkaya, M. S., A. A. Bhagwat, and P. B. Cregan. 1992. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics. 132 : 1131-1139
  3. Brown-Guedira, G. L., J. A. Thompson, R. L. Nelson, and M. L. Warburton. 2000. Evaluation of genetic diversity of soy­bean introductions and North American ancestors using RAPD and SSR markers. Crop Sci. 40 : 815-823 https://doi.org/10.2135/cropsci2000.403815x
  4. Cregan, P. B., M. S. Akkaya, A. A. Bhagwat, U. Lavi, and J. Rongwen. 1994. Length polymorphism of simple sequence repeat (SSR) DNA as molecular markers in plants. In Plant Genome Analysis. Current Topics in Plant Molecular Biology. Gresshoff P.M. (ed), CRC press, New York
  5. Cregan, P. B., T. Jarvik, A. L. Bush, R. C. Shoemaker, K. G. Lark, A. L. Kahler, N. Kaya, T. T. VanToai, D. G. Lohnes, J. Chung, and J. E. Specht. 1999. An integrated genetic linkage map of the soybean genome. Crop Sci. 39 : 1464-­1490 https://doi.org/10.2135/cropsci1999.3951464x
  6. Diwan, N. and P. B. Cregan. 1997. Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor. Appl. Genet. 95.: 723-733 https://doi.org/10.1007/s001220050618
  7. Dong, Y. S., L. M. Zhao, B. Liu, Z. W. Wang, Z. Q. Jin, and H. Sun. 2003. The genetic diversity of cultivated soybean grown in China. Theor. Appl. Genet. 108 : 931-936
  8. Dong, Y. S., B. C. Zhuang, L. M. Zhao, H. Sun, and M. Y. He. 2001. The genetic diversity of annual wild soybean grown in China. Theor. Appl. Genet. 103 : 98-103 https://doi.org/10.1007/s001220000522
  9. Gepts, P. and M. T. Clegg. 1989. Genetic diversity in pearl millet (Pennisetum. glaucum [L.] R. Br.) at the DNA sequence level. J. Heredity. 80 : 203-208 https://doi.org/10.1093/oxfordjournals.jhered.a110836
  10. Hong, E. H., S. D. Kim, Y. H. Lee, and R. K. Park. 1988. Results and perspectives of soybean varietal improvement. '88 RDA symposium. 3 : 31-57
  11. Kim, S. H., J. W. Jung, J. K. Moon, S. H. Woo, Y. G. Cho, S. K. Jong, and H. S. Kim. 2006. Genetic diversity and relationship by SSR markers of Korean soybean cultivars. Korean J. Crop Sci. 51(3) : 248-258
  12. Kwon, S. H., K. H. Im, and J. R. Kim. 1972. Studies on diversity of seed weight in the Korean soybean land races and wild soybean. Korean J. Breeding. 4(1) : 70-74
  13. Li, Z., L. Qiu, J. A. Thompson, M. M. Welsh, and R. L. Nelson. 2001. Molecular genetic analysis of U.S. and Chinese soybean ancestral lines. Crop Sci. 41 : 1330-1336 https://doi.org/10.2135/cropsci2001.4141330x
  14. Maughan, P. J., M. A. Saghai Maroof, and G. R. Buss. 1995. Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome. 38 : 715-723 https://doi.org/10.1139/g95-090
  15. Narvel, J. M., W. R. Fehr, W. C. Chu, D. Grant, and R. C. Shoemaker. 2000. Simple sequence repeat diversity among soybean plant introductions and elite geneotypes. Crop Sci. 40 : 1452-1458 https://doi.org/10.2135/cropsci2000.4051452x
  16. Perry, M. C. and M. S. Mcintosh. 1991. Geographical patterns of variation in the USDA soybean germplasm collection : I. Morphological traits. Crop Sci. 31 : 1350-1355 https://doi.org/10.2135/cropsci1991.0011183X003100050054x
  17. Perry, M. C., M. S. Mcintosh, and A. K. Stoner. 1991. Geo­graphical patterns of variation in the USDA soybean germ­plasm collection : II. Allozyme frequencies. Crop Sci. 31 : 1356-1360 https://doi.org/10.2135/cropsci1991.0011183X003100050055x
  18. Rongwen, J., M. S. Akkaya, A. A. Bhagwat, U. Lavi, and P. B. Cregan. 1995. The use of micro satellite DNA markers for soybean genotype identification. Theor. Appl. Genet. 90 : 43-48
  19. Saghai Maroof M. A., R. M. Biyashev, G. P. Yang, Q. Zhang, and R. W. Allard. 1994. Extraordinarily polymorphic micro­satellite DNA in barley : Species diversity, chromosomal locations and population dynamics. Pro. Natl. Acad. Sci. USA. 91 : 5466-5470
  20. Song, Q. J., C. V. Quigley, R. L. Nelson, T. E. Carter, H. R. Boerma, J. L. Strachan, and P. B. Cregan. 1999. A selected set of trinucleotide simple sequence repeat markers for soybean cultivar identification. Plant Varieties and Seeds. 12 : 207-220
  21. Song, Q. J., L. F. Marek, R. C. Shoemaker, K. G. Lark, V. C. Concibido, X. Delannay, J. E. Specht, and P. B. Cregan. 2004. A new integrated genetic linkage map of the soybean. Theor. Appl. Genet. 109 : 122-128 https://doi.org/10.1007/s00122-004-1602-3
  22. Yoon, M. S., J. W. Ahn, S. J. Park, H. J. Baek, N. K. Park, and Y. D. Rho. 2000a. Geographical patterns of morpho­logical variation in soybean (Glycine max (L.) Merrill) germ­plasm. Korean J. Crop Sci. 45(4) : 267-271
  23. Yoon, M. S., J. W. Ahn, J. H. Kang, H. J. Baek, N. K. Park, and Y. D. Rho. 2000b. Genotypic and geographical varia­tions of ${\beta}$-amylase isozyme in soybean land races by iso­electric focusing (IEF). Korean J. Crop Sci. 45(1) : 139­-142
  24. Park, K. S. and M. S. Yoon. 1997. Variation of leucine amino­peptidase isozyme in Korean land races and wild soybeans. Korean J. Crop Sci. 42(2) : 129-133