Skip to main content
SpringerLink
Log in

Genetic diversity of wild soybean (Glycine soja Sieb. et Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Wild soybeans, Glycine soja, are a source of genetic variation to improve soybeans. To improve the efficiency evaluation of conserved germplasm a core or mini-core collection approach that maximizes allelic diversity in a proportion of the whole collection has frequently been advocated. The genetic diversity of a wild soybean collection (1,305 accessions) plus Japanese cultivated soybeans (53 accessions) were analyzed at 20 SSR marker loci. Higher levels of allelic diversity were found in wild soybeans (28 alleles per locus) than Japanese cultivated soybean (five alleles per locus). The genetic distance between wild soybeans from different regions reflected their proximity. Accessions from Russia consisted of a diverse array of alleles resulting in accessions being spread further apart in a PCA plot than accessions from other regions. Accessions of wild soybean from Korea included many rare alleles and thus had a high representation in the core collection. The two core collections developed here, traditional and mini, consisted of 192 accessions with 97% of the allelic diversity (14% of the whole collection) and 53 accessions with 62.4% of the allelic diversity (5% of the whole collection), respectively.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Abe J (2000) The genetic structure of natural populations of wild soybean revealed by isozymes and RFLPs of mitochondrial DNAs: possible influence of seed dispersal, cross-pollination and demography. In: K. Oono (ed) 7th MAFF International Workshop Genetic Resources, pp 143–158. AFFRC and NIAR, Tsukuba, Japan

  • Abe J, Hasegawa A, Fukushi H, Mikami T, Ohara M, Shimamoto Y (1999) Introgression between wild and cultivated soybeans of Japan revealed by RFLP analysis of chloroplast DNAs. Econ Bot 53:285–291

    Google Scholar 

  • Abe J, Xu DH, Suzuki Y, Kanazawa A, Shimamoto Y (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theor Appl Genet 106:445–453

    CAS  PubMed  Google Scholar 

  • Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824

    Google Scholar 

  • Brown AHD, Grace JP, Speer SS (1987) Designation of a ‘core’ collection of perennial Glycine. Soybean Genet Newsl 14:59–70

    Google Scholar 

  • Excoffier L, Smouse P, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  Google Scholar 

  • Gizlice Z, Carter TE, Burton JW (1994) Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci 34:1143–1151

    Google Scholar 

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html. Updated from Goudet (1995). Accessed Mar 2009

  • Hodgkin T, Brown AHD, van Hintum ThJL, Morales EAV (eds) (1995) Core collections of plant genetic resources. Wiley, Chichester, p 269

    Google Scholar 

  • Hyten DL, Song Q, Zhu Y, Choi YI, Nelson RL, Costa JM, Specht JE, Shoemaker RL, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671. doi:10.1073/pnas.0604379103

    Article  CAS  PubMed  Google Scholar 

  • Jin Y, He T, Lu BR (2003) Fine scale genetic structure in a wild soybean (Glycine soja) population and the implications for conservation. New Phytol 159:513–519. doi:10.1046/j.1469-8137.2003.00824.x

    Article  Google Scholar 

  • Kuroda Y, Kaga A, Tomooka N, Vaughan DA (2006) Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Mol Ecol 15:959–974. doi:10.1111/j.1365-294X.2006.02854.x

    Article  CAS  PubMed  Google Scholar 

  • Kuroda Y, Kaga A, Tomooka N, Vaughan DA (2008) Geneflow and genetic structure of wild soybean (Glycine soja) in Japan. Crop Sci 48:1071–1079. doi:10.2135/cropsci2007.09.0496

    Article  Google Scholar 

  • Lee J-D, Yu J-K, Hwang Y-H, Blake S, So Y-S, Lee G-J, Nguyen HT, Shannon JG (2008) Genetic diversity of wild soybean (Glycine soja Sieb. & Zucc.) accessions from South Korea and other countries. Crop Sci 48:606–616. doi:10.2135/cropsci2007.05.0257

    Article  Google Scholar 

  • Liu K, Muse S (2005) PowerMarker: new genetic data analysis software. Version 3.23, 2005. Available at http://powermarker.net. Accessed Mar 2009

  • Meilleur BA, Hodgkin T (2004) In situ conservation of crop wild relatives. Biodivers Conserv 13:663–684. doi:10.1023/B:BIOC.0000011719.03230.17

    Article  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nei M, Tajima N, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170. doi:10.1007/BF02300753

    Article  CAS  PubMed  Google Scholar 

  • Powell W, Morgante M, Andre C, McNicol JW, Machray GC, Doyle JJ, Tingey SV, Rafalski JA (1995) Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol 5:1023–1029. doi:10.1016/S0960-9822(95)00206-5

    Article  CAS  PubMed  Google Scholar 

  • Powell W, Morgante M, Doyle JJ, McNicol JW, Tingey SV, Rafalski JA (1996) Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics 144:793–803

    CAS  PubMed  Google Scholar 

  • Priolli RHG, Mendes-Junior CT, Arantes NE, Contel EPB (2002) Characterization of Brazilian soybean cultivars using microsatellite markers. Genet Mol Biol 25:185–193

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  • Qiu L, Guan R, Li Y, Wang L, Guan Y, Zhe Y, et al. (2004) The basis of sustainable soybean production: establishment and application of Chinese soybean core collections revealed by both agronomic characters and SSR markers. Fourth International Crop Science Congress (online)

  • Rohlf FJ (2000) NTSYS PC, version 2.02j. Exeter Software, Setauket

    Google Scholar 

  • Sangiri C, Kaga A, Tomooka N, Vaughan DA, Srinives P (2007) Genetic diversity of the mungbean (Vigna radiata, Leguminosae) genepool based on microsatellite analysis. Aust J Bot 55:837–847. doi:10.1071/BT07105

    Article  CAS  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetic data. Genetics and Biometry Laboratory, University of Geneva, Switzerland

    Google Scholar 

  • Shimamoto Y, Fukushi H, Abe J, Kanazawa A, Gai JY, Gao Z, Xu DH (1998) RFLPs of chloroplast and mitochondrial DNA in wild soybean, Glycine soja, growing in China. Genet Resour Crop Evol 45:433–439. doi:10.1023/A:1008693603526

    Article  Google Scholar 

  • Singh RJ, Nelson RL, Chung GH (2007) Soybean (Glycine max (L.) Merr.). In: Singh RJ (ed) Genetic resources, chromosome engineering, and crop improvement. Oilseed crops, vol 4. CRC Press, Boca Raton, pp 13–50

    Google Scholar 

  • Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399

    CAS  PubMed  Google Scholar 

  • Tozuka A, Fukushi H, Hirata T, Ohara M, Kanazawa A, Mikami T, Abe J, Shimamoto Y (1998) Composite and clinal distribution of Glycine soja in Japan revealed by RFLP analysis of mitochondrial DNA. Theor Appl Genet 96:170–176. doi:10.1007/s001220050724

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102:1292–1298. doi:10.1007/s00122-001-0556-y

    Article  Google Scholar 

  • Xu DH, Abe J, Gai JY, Shimamoto Y (2002) Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated cultivated soybeans. Theor Appl Genet 105:645–653. doi:10.1007/s00122-002-0972-7

    Article  CAS  PubMed  Google Scholar 

  • Yaklich RW, Helm RM, Cockrell G, Herman EM (1999) Analysis of the distribution of the major soybean seed allergens in a core collection of Glycine max accessions. Crop Sci 39:1444–1447

    Article  CAS  Google Scholar 

  • Zhao L, Dong Y, Liu B, Hao S, Wang K, Li X (2005) Establishment of a core collection for the Chinese annual wild soybean (Glycine soja). Chin Sci Bull 50:989–996. doi:10.1360/982004-657

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank the USDA for furnishing germplasm of wild soybeans from China, the Republic of Korea and Russia. The authors also thank the following research centers in Japan for supply of some of the cultivated soybean germplasm used in this experiment: Tokachi Agricultural Experiment Station, National Agricultural Research Center for Tohoku Region, Chushin Agricultural Experiment Station, National Agricultural Research Center for Kyushu Okinawa Region and Saga Agricultural Experiment Station.

Author information

Author notes

  1. Yosuke Kuroda

    Present address: National Agricultural Research Center for Hokkaido Region, National Agriculture and Food Research Organization, 9-4 Shinsei-minami Memuro-cho, Kasai-gun, Hokkaido, 082-0081, Japan

Authors and Affiliations

  1. Genebank, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Yosuke Kuroda, Norihiko Tomooka, Akito Kaga & Duncan A. Vaughan

  2. Plant Genetic Resources Center, P.O. Box 59, Gannoruwa, Peradeniya, Sri Lanka

    S. M. S. W. Wanigadeva

  3. FAO Regional Office for Asia and the Pacific, Maliwan Mansion, 39 Phra Atit Road, Bangkok, 10200, Thailand

    Duncan A. Vaughan

Authors
  1. Yosuke Kuroda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Norihiko Tomooka
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Akito Kaga
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. M. S. W. Wanigadeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Duncan A. Vaughan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Duncan A. Vaughan.

Additional information

All authors contributed equally to this research.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuroda, Y., Tomooka, N., Kaga, A. et al. Genetic diversity of wild soybean (Glycine soja Sieb. et Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection. Genet Resour Crop Evol 56, 1045–1055 (2009). https://doi.org/10.1007/s10722-009-9425-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-009-9425-3

Keywords

Search

Navigation