Skip to main content
SpringerLink
Log in

Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers

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

Abstract

Vegetable soybean is a kind of value-added specialty soybean serving as vegetable or snacks. Understanding the genetic structure of vegetable soybean is a key point for further utilization in breeding programs. In the present study, the genetic structure and diversity of 100 vegetable soybean accessions planted in China was analyzed using 53 simple sequence repeat (SSR) markers. A total of 296 alleles were detected with an average of 5.6 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.074 to 0.831, with an average of 0.573. Nei’s genetic distance between accessions ranged from 0 to 0.9434 with an average of 0.6286. These vegetable soybean germplasms could be divided into 8 subgroups based on STRUCTURE analysis, or 11 subgroups based on unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups were in fact highly consistent. Germplasms in each classified groups showed great consistency with their origins, seed coat colors or pedigrees. Genetic relationships among germplasm panels that initially came from different geographical regions were also analyzed. Germplasm panels from China Mainland, Taiwan Island and Japan were highly similar to each other with the similarities of over 98 %. Molecular data and cluster analysis also showed that germplasms from China Mainland are more diverse than those from other areas. These results gave us a deep insight into the genetic structure of vegetable soybeans in China and will help us to improve the breeding strategies.

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
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

AVRDC:

Asian Vegetable Research and Development Center

MAS:

Marker assisted selection

PAGE:

Polyacrylamide gel electrophoresis

PCA:

Principal coordinate analysis

PCR:

Polymerase chain reaction

PIC:

Polymorphism information content

SSR:

Simple sequence repeat

UPGMA:

Unweighted pair group method with arithmetic average

References

  • Bhat KV, Satyavathi CT, Bharadwaj C, Tiwari SP, Chaudhury VK (2006) AFLP analysis of genetic diversity in Indian soybean [Glycine max (L.) Merr.] varieties. Genet Resour Crop Evol 53(5):1069–1079. doi:10.1007/s10722-005-0779-x

    Article  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chakraborty R, Jin L (1993) Determination of relatedness between individuals using DNA fingerprinting. Hum biol 65(6):875–895

    Google Scholar 

  • Chen YW, Nelson RL (2005) Relationship between origin and genetic diversity in Chinese soybean germplasm. Crop Sci 45(4):1645–1652. doi:10.2135/cropsci2004.0071

    Article  CAS  Google Scholar 

  • Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE (1999) An integrated genetic linkage map of the soybean genome. Crop Sci 39(5):1464–1490. doi:10.2135/cropsci1999.3951464x

    Article  CAS  Google Scholar 

  • Dong YS, Zhao LM, Liu B, Wang ZW, Jin ZQ, Sun H (2004) The genetic diversity of cultivated soybean grown in China. Theor Appl Genet 108(5):931–936. doi:10.1007/s00122-003-1503-x

    Article  CAS  PubMed  Google Scholar 

  • Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development description for soybean (Glycine max L. Merrill). Crop Sci 11(6):929–931

    Google Scholar 

  • He SL, Wang YS, Volis S, Li DZ, Yi TS (2012) Genetic diversity and population structure: implications for conservation of wild soybean (Glycine soja Sieb. et Zucc.) based on nuclear and chloroplast microsatellite variation. Int J Mol Sci 13(10):12608–12628. doi:10.3390/ijms131012608

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hymowitz T, Kaizuma N (1979) Dissemination of soybeans (Glycine max): seed protein electrophoresis profiles among Japanese cultivars. Econ Bot 33(3):311–319

    Google Scholar 

  • Hymowitz T, Newell CA (1981) Taxonomy of the genus Glycine, domestication and uses of soybeans. Econ Bot 35(3):272–288

    Google Scholar 

  • Katou T, Fukushirna T, Akazawa T (1982) Differences in contents of amino acid, sugar and composition of fatty acids between edamame and normal soybean. J Jpn Soc Hortic Sci 51(supp 1.2):537

    Google Scholar 

  • Kumar V, Rani A, Goyal L, Pratap D, Billore SD, Chauhan GS (2011) Evaluation of vegetable-type soybean for sucrose, taste-related amino acids, and isoflavones contents. Int J Food Prop 14(5):1142–1151. doi:10.1080/10942911003592761

    Article  CAS  Google Scholar 

  • Kuroda Y, Tomooka N, Kaga A, Wanigadeva SMSW, Vaughan DA (2009) 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(8):1045–1055. doi:10.1007/s10722-009-9425-3

    Article  CAS  Google Scholar 

  • Lam HM, Xu X, Liu X, Chen WB, Yang GH, Wong FL, Li MW, He WM, Qin N, Wang B, Li J, Jian M, Wang JA, Shao GH, Wang J, Sun SSM, Zhang GY (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42(12):1053–1059. doi:10.1038/Ng.715

    Article  CAS  PubMed  Google Scholar 

  • Li W, Han Y, Zhang D, Yang M, Teng W, Jiang Z, Qiu L, Sun G (2008a) Genetic diversity in soybean genotypes from North-Eastern China and identification of candidate markers associated with maturity rating. Plant Breed 127(5):494–500. doi:10.1111/j.1439-0523.2008.01489.x

    Article  CAS  Google Scholar 

  • Li YH, Guan RX, Liu ZX, Ma YS, Wang LX, Li LH, Lin FY, Luan WJ, Chen PY, Yan Z, Guan Y, Zhu L, Ning XC, Smulders MJM, Li W, Piao RH, Cui YH, Yu ZM, Guan M, Chang RZ, Hou AF, Shi AN, Zhang B, Zhu SL, Qiu LJ (2008b) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor App Genet 117(6):857–871. doi:10.1007/s00122-008-0825-0

    Article  CAS  Google Scholar 

  • Li YH, Smulders MJM, Chang RZ, Qiu LJ (2011) Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis. Conserv Genet 12(5):1145–1157. doi:10.1007/s10592-011-0216-y

    Article  Google Scholar 

  • Liu SS, Ohta K, Dong CP, Thanh VC, Ishimoto M, Qin ZW, Hirata Y (2006) Genetic diversity of soybean (Glycine max (L.) Merrill) 7S globulin protein subunits. Genet Resour Crop Evol 53(6):1209–1219. doi:10.1007/s10722-005-2434-y

    Article  CAS  Google Scholar 

  • Lumpkin TA, Konovsky JC, Larson KJ, McClary DC (1993) Potential new specialty crops from Asia: Azuki bean, edamame soybean, and astragalus. In: Janick J, Simon JE (eds) New crops. Wiley, New York

    Google Scholar 

  • MAFF (2012) The 86th Statistical Yearbook of Ministry of Agriculture, Forestry and Fisheries (2010–2011). http://www.maff.go.jp/e/tokei/kikaku/nenji_e/86nenji/index.html

  • Mebrahtu T, Mohamed A, Wang CY, Andebrhan T (2004) Analysis of isoflavone contents in vegetable soybeans. Plant Food Hum Nutr 59(2):55–61. doi:10.1007/s11130-004-0023-4

    Article  CAS  Google Scholar 

  • Mimura M, Coyne CJ, Bambuck MW, Lumpkin TA (2007) SSR diversity of vegetable soybean [Glycine max (L.) Merr.]. Genet Resour Crop Evol 54(3):497–508. doi:10.1007/s10722-006-0006-4

    Article  CAS  Google Scholar 

  • Morse WJ (1950) History of soybean production. In: Markley KS (ed) Soybean and soybean products. Interscience, New York

    Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4325

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106(949):283–292

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genet 155(2):945–959

    Google Scholar 

  • Qiu LJ, Ma YS, Wang WH, Wang LX, Ma FM, Wang PW, Chang RZ (2006) Genetic diversity of soybean and the establishment of a core collection focused on resistance to soybean cyst nematode. J Integr Plant Biol 48(6):722–731

    Article  Google Scholar 

  • Shurtleff W, Aoyagi A (2009) History of Edamame, Green vegetable soybeans, and vegetable-type soybeans: bibliography and sourcebook. Soyinfo Center P.O. Box 234, Lafayette, CA 94549-0234 USA

  • Song ZQ (1987) Soybean of Ancient China. Agricultural History of China (3):50–57

  • Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang E-Y, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50(5):1950–1960. doi:10.2135/cropsci2009.10.0607

    Article  CAS  Google Scholar 

  • Ude GN, Kenworthy WJ, Costa JM, Cregan PB, Alvernaz J (2003) Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci 43(5):1858–1867

    Article  CAS  Google Scholar 

  • Vaughan DA, Kuroda Y, Tomooka N, Kaga A, Wanigadeva SMSW (2009) 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(8):1045–1055. doi:10.1007/s10722-009-9425-3

    Article  Google Scholar 

  • Wang KJ, Li XH (2011) Genetic differentiation and diversity of phenotypic characters in Chinese wild soybean (Glycine soja Sieb. et Zucc.) revealed by nuclear SSR markers and the implication for intraspecies phylogenic relationship of characters. Genet Resour Crop Evol 58(2):209–223. doi:10.1007/s10722-010-9563-7

    Article  Google Scholar 

  • Wang ZQ, Senga EFB, Wang DY (2005) Vegetable soy bean (Glycine max (L.) Merrill) from production to processing. Outlook Agric 34(3):167–172. doi:10.5367/000000005774378766

    Article  Google Scholar 

  • Wang LX, Guan RX, Liu ZX, Chang RZ, Qiu LJ (2006) Genetic diversity of chinese cultivated soybean revealed by SSR markers. Crop Sci 46(3):1032–1038. doi:10.2135/cropsci2005.0051

    Article  Google Scholar 

  • Wang KJ, Li XH, Jia JZ (2009) Genetic diversity and differentiation of Chinese wild soybean germplasm (G-soja Sieb. & Zucc.) in geographical scale revealed by SSR markers. Plant Breed 128(6):658–664. doi:10.1111/j.1439-0523.2009.01625.x

    Article  Google Scholar 

  • Wen ZX, Ding YL, Zhao TJ, Gai JY (2009) Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. et Zucc) from various eco-regions in China. Theore Appl Genet 119(2):371–381. doi:10.1007/s00122-009-1045-y

    Article  CAS  Google Scholar 

  • Xie H, Chang RZ, Cao YS, Zhang MH, Feng ZF, Qiu LJ (2003) Selection of core SSR loci by using Chinese autumn soybean. Scientia Agricultura Sinica 36:360–366

    CAS  Google Scholar 

  • Xu SB, Tao YF, Yang ZQ, Chu JY (2002) A Simple and rapid methods used for silver staining and gel preservation. Hereditas (Beijing) 24(5):335–336

    CAS  Google Scholar 

  • Yanagisawa Y, Akazawa T, Abe T, Sasahara T (1997) Changes in free amino acid and Kjeldahl N concentrations in seeds from vegetable-type and grain-type soybean cultivars during the cropping season. J Agr Food Chem 45(5):1720–1724. doi:10.1021/jf960594i

    Article  CAS  Google Scholar 

  • Young G, Mebrahtu T, Johnson J (2000) Acceptability of green soybeans as a vegetable entity. Plant Food Hum Nutr 55(4):323–333. doi:10.1023/A:1008164925103

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by “Genetically Modified Organisms Breeding Major Projects of China (2012ZX08009004, 2013ZX08004002)” and “Science and Technology Major Projects of Zhejiang Province (2012C12902)”.

Author information

Authors and Affiliations

  1. Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198#, Shiqiao Rd, Hangzhou, 310021, Zhejiang, People’s Republic of China

    Dekun Dong, Xujun Fu, Fengjie Yuan, Shenlong Zhu, Baiquan Li, Qinghua Yang, Xiaomin Yu & Danhua Zhu

  2. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    Pengyin Chen

Authors
  1. Dekun Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xujun Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fengjie Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pengyin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shenlong Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Baiquan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Qinghua Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiaomin Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Danhua Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Danhua Zhu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dong, D., Fu, X., Yuan, F. et al. Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers. Genet Resour Crop Evol 61, 173–183 (2014). https://doi.org/10.1007/s10722-013-0024-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-013-0024-y

Keywords

Search

Navigation