Genetic architecture of wild soybean (Glycine soja Sieb. and Zucc.) populations originating from different East Asian regions

Abstract

East Asian region is home to wild soybean and has high topographic complexity. Measuring genetic diversity and geographical distribution patterns are essential steps to expand the germplasm base. We used SoySNP6K to determine the genetic diversity and population genetic structure of the wild soybean populations from four East-Asian geographies i.e. China, Japan, Korea, and Russian Far East. The wild soybean populations from China, Japan, and Korea are distinct from one another based on genetic structure, whereas the one from Russian Far East was not distinguishable from the Chinese wild soybeans. These populations share three ancestral populations and have a large number of common SNPs. Despite the low genetic diversity scores between the populations, the Chinese accessions had the highest genetic diversity values while the accession from Russian Far East had the lowest. Our analysis also showed that the population is showing a departure from the Hardy–Weinberg equilibrium and there is a possibility of inbreeding for most of the loci. The results showed that the genetic variation follows the geographic distribution within each geographically distinct wild soybeans population. Therefore, a diverse collection of wild soybeans representing all-natural habitats should include representatives from each of these sub-centers. This population would provide important breeding materials to expand the allelic pool of cultivated soybeans through introgression. Based on these criteria, the Chung’s wild legume germplasm collection from Korea provides a good representation of the genetic diversity in wild soybeans for use in soybean breeding programs.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Availability of materials

The wild soybean germplasms used in this study are available for distribution to researchers who are interested in collaborating with our group. Requests for material should be sent to G.C. (chung@chonnam.ac.kr).

References

  1. Akond M, Liu S, Schoener L, Anderson JA, Kantartzi SK, Meksem K, Song Q, Wang D, Wen Z, Lightfoot DA (2013) A SNP-based genetic linkage map of soybean using the SoySNP6K Illumina Infinium BeadChip genotyping array. Plant Genet Genom Biotechnol 1:80–89

    Article  Google Scholar 

  2. Aleem M, Raza MM, Haider MS, Atif RM, Ali Z, Bhat JA, Zhao T (2020) Comprehensive RNA‐seq analysis revealed molecular pathways and genes associated with drought tolerance in wild soybean (Glycine soja Sieb. & Zucc.). Physiol Plant. https://doi.org/10.1111/ppl.13219

    Article  PubMed  PubMed Central  Google Scholar 

  3. Bandillo NB, Anderson JE, Kantar MB, Stupar RM, Specht JE, Graef GL, Lorenz AJ (2017) Dissecting the genetic basis of local adaptation in soybean. Sci Rep 7:1–12

    CAS  Article  Google Scholar 

  4. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  5. Chen B, Cole JW, Grond-Ginsbach C (2017) Departure from Hardy Weinberg equilibrium and genotyping error. Front Genet 8:167

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  6. Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Dashti MJS, Mulder N, Tiffin N, Ramsay M (2014) Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genom 15:437

    Article  Google Scholar 

  7. Chung G, Singh RJ (2008) Broadening the genetic base of soybean: a multidisciplinary approach. Crit Rev Plant Sci 27:295–341

    CAS  Article  Google Scholar 

  8. Chung YM, Son S, Suh GU, Herrando-Moraira S, Lee CH, López-Pujol J, Chung MG (2018) The Korean Baekdudaegan Mountains: a glacial refugium and a biodiversity hotspot that needs to be conserved. Front Genet 9:489

    PubMed  PubMed Central  Article  Google Scholar 

  9. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6:80–92

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. Diniz-Filho JAF, Soares TN, Lima JS, Dobrovolski R, Landeiro VL, Telles MPDC, Rangel TF, Bini LM (2013) Mantel test in population genetics. Genet Mol Biol 36:475–485

    PubMed  PubMed Central  Article  Google Scholar 

  11. Dobson M, Kawamura Y (1998) Origin of the Japanese land mammal fauna. Quat Res (Daiyonki-Kenkyu) 37:385–395

    Article  Google Scholar 

  12. Earl DA (2012) Structure harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  13. Eickholt D, Carter TE, Taliercio E, Dickey D, Dean LO, Delheimer J, Li Z (2019) Registration of USDA-max × soja Core Set-1: recovering 99% of wild soybean genome from PI 366122 in 17 agronomic interspecific germplasm lines. J Plant Regist 13:217–236

    Article  Google Scholar 

  14. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  Article  PubMed  Google Scholar 

  15. Ferguson ME, Ford-Lloyd B, Robertson L, Maxted N, Newbury H (1998) Mapping the geographical distribution of genetic variation in the genus Lens for the enhanced conservation of plant genetic diversity. Mol Ecol 7:1743–1755

    Article  Google Scholar 

  16. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2011) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  17. Goudet J (2005) Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes 5:184–186

    Article  Google Scholar 

  18. Guo Juan, Liu Y, Wang Y, Chen J, Li Y, Huang H, Qiu L, Wang Y (2012) Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses. Ann Bot 110:777–785

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. Guo Peng Zhu, Niu Bo, Wang Hong, Liang Zezhao, Chen Yonghu, Zhang Yan, Ni Lupei, Guo Hemin, Yong El Hamidi AH (2018) Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis. BMC Bioinformatics 19:1–11

    Article  CAS  Google Scholar 

  20. Hao D, Cheng H, Yin Z, Cui S, Zhang D, Wang H, Yu D (2012) Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments. Theor Appl Genet 124:447–458

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  21. He S, Wang Y, Volis S, Li D, Yi T (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 13:12608–12628

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. He SL, Wang YS, Li DZ, Yi TS (2016) Environmental and historical determinants of patterns of genetic differentiation in wild soybean (Glycine soja Sieb. et Zucc). Sci Rep 6:1–11

    Article  CAS  Google Scholar 

  23. Hu D, Zhang H, Du Q, Hu Z, Yang Z, Li X, Wang J, Huang F, Yu D, Wang H (2020) Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.). Planta 251:39

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  24. Hyten DL, Song Q, Zhu Y, Choi I-Y, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci 103:16666–16671

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  25. Jeong S-C, Moon J-K, Park S-K, Kim M-S, Lee K, Lee SR, Jeong N, Choi MS, Kim N, Kang S-T (2019) Genetic diversity patterns and domestication origin of soybean. Theor Appl Genet 132:1179–1193

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  26. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  27. Kitada S, Nakamichi R, Kishino H (2020) Population-specific FST and pairwise FST: history and environmental pressure. bioRxiv

  28. Kuroda Y, Kaga A, Tomooka N, Vaughan D (2006) Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Mol Ecol 15:959–974

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  29. La T, Large E, Taliercio E, Song Q, Gillman JD, Xu D, Nguyen HT, Shannon G, Scaboo A (2019) Characterization of select wild soybean accessions in the USDA germplasm collection for seed composition and agronomic traits. Crop Sci 59:233–251

    CAS  Article  Google Scholar 

  30. Lam H-M, Xu X, Liu X, Chen W, Yang G, Wong F-L, Li M-W, He W, Qin N, Wang B (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  31. Leppik EE (1971) Assumed gene centers of peanuts and soybeans. Econ Bot 25:188–194

    Article  Google Scholar 

  32. Muñoz N, Liu A, Kan L, Li M-W, Lam H-M (2017) Potential uses of wild germplasms of grain legumes for crop improvement. Int J Mol Sci 18:328

    PubMed Central  Article  CAS  Google Scholar 

  33. Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F (2018) Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS ONE 13:e0205363

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  34. Nawaz MA, Baloch FS, Rehman HM, Le B, Akther F, Yang SH, Gyuhwa C (2016) Development of a competent and trouble free DNA isolation protocol for downstream genetic analyses in Glycine species. Turk J Agric-Food Sci Technol 4:700–705

    Google Scholar 

  35. Nawaz MA, Yang SH, Chung G (2018) Wild soybeans: an opportunistic resource for soybean improvement. In: Rediscovery of landraces as a resource for the future. IntechOpen

  36. Nawaz MA, Lin X, Chan T-F, Ham J, Shin T-S, Ercisli S, Golokhvast KS, Lam HM, Gyuhwa C (2020) Korean wild soybeans (Glycine soja Sieb & Zucc.): geographic distribution and germplasm conservation. Agronomy 10:214

    Article  Google Scholar 

  37. Oliveira HR, Tomás D, Silva M, Lopes S, Viegas W, Veloso MM (2016) Genetic diversity and population structure in Vicia faba L. landraces and wild related species assessed by nuclear SSRs. PLoS ONE 11:154

    Google Scholar 

  38. Pavan S, Bardaro N, Fanelli V, Marcotrigiano AR, Mangini G, Taranto F, Catalano D, Montemurro C, De Giovanni C, Lotti C (2019) Genotyping by sequencing of cultivated lentil (Lens culinaris Medik.) highlights population structure in the Mediterranean gene pool associated with geographic patterns and phenotypic variables. Front Genet 10:872

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Prince SJ, Vuong TD, Wu X, Bai Y, Lu F, Kumpatla SP, Valliyodan B, Shannon JG, Nguyen HT (2020) Mapping quantitative trait loci for soybean seedling shoot and root architecture traits in an inter-specific genetic population. Front Plant Sci 11:1284

    PubMed  PubMed Central  Article  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Qiu Y-X, Fu C-X, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora. Mol Phylogenet Evol 59:225–244

    PubMed  Article  Google Scholar 

  42. Ren Hai, Jian S, Liu H, Zhang Q, Lu H (2014) Advances in the reintroduction of rare and endangered wild plant species. Sci China Life Sci 57:603–609

    PubMed  Article  PubMed Central  Google Scholar 

  43. Scheiner SM (1993) Genetics and evolution of phenotypic plasticity. Annu Rev Ecol Syst 24:35–68

    Article  Google Scholar 

  44. Sharmin RA, Bhuiyan MR, Lv W, Yu Z, Chang F, Kong J, Bhat JA, Zhao T (2020) RNA-Seq based transcriptomic analysis revealed genes associated with seed-flooding tolerance in wild soybean (Glycine soja Sieb. & Zucc.). Environ Exp Bot 171:103906

    CAS  Article  Google Scholar 

  45. Singh RJ (2019) Cytogenetics and genetic introgression from wild relatives in soybean. Nucleus 62:3–14

    Article  Google Scholar 

  46. Singh RJ, Hymowitz T (1999) Soybean genetic resources and crop improvement. Genome 42:605–616

    CAS  Article  Google Scholar 

  47. Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE 8:e54985

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. Team RC (2013) R: a language and environment for statistical computing

  49. Thioulouse J, Dray S, Dufour A-B, Siberchicot A, Jombart T, Pavoine S (2018) Multivariate analysis of ecological data with ade4. Springer, Berlin

    Google Scholar 

  50. Thormann I, Reeves P, Reilley A, Engels JM, Lohwasser U, Börner A, Pillen K, Richards CM (2016) Geography of genetic structure in barley wild relative Hordeum vulgare subsp. spontaneum in Jordan. PLoS ONE 11:e0160745

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  51. Wang K-J, Takahata Y (2007) A preliminary comparative evaluation of genetic diversity between Chinese and Japanese wild soybean (Glycine soja) germplasm pools using SSR markers. Genet Resour Crop Evol 54:157–165

    CAS  Article  Google Scholar 

  52. Wang L-X, Lin F-Y, Li L-H, Wei L, Zhe Y, Luan W-J, Piao R-H, Yuan G, Ning X-C, Li Z (2016) Genetic diversity center of cultivated soybean (Glycine max) in China-new insight and evidence for the diversity center of Chinese cultivated soybean. J Integr Agric 15:2481–2487

    Article  Google Scholar 

  53. Wright S (1921) Systems of mating. I. The biometric relations between parent and offspring. Genetics 6:111

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Yousef EA, Mueller T, Boerner A, Schmid KJ (2018) Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks. PloS one 13:19

    Google Scholar 

  55. Yu G, Smith DK, Zhu H, Guan Y, Lam TTY (2017) ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 8:28–36

    Article  Google Scholar 

  56. Zhao H, Wang Y, Xing F, Liu X, Yuan C, Qi G, Guo J, Dong Y (2018) The genetic diversity and geographic differentiation of the wild soybean in Northeast China based on nuclear microsatellite variation. Int J Genom 2018:8561458

    Google Scholar 

  57. Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 33:408–414

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

Ms. Jee Chu copy-edited the manuscript.

Funding

This study was financially supported by Cooperative Research Program for Agricultural Science and Technology Development, Rural Development Administration, Republic of Korea (Project no. PJ013215012020), and the Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M-403/16).

Author information

Affiliations

Authors

Contributions

Conceptualization, M.A.N. and G.C.; methodology, M.A.N., S.H.Y, and H.M.L.; software, X.L., and T.F.C; validation, M.A.A., F.S.B., K.S.G and G.C..; formal analysis, M.A.N.; investigation, M.A.N., G.C., S.H.Y.; resources, G.C. and S.H.Y; data curation, M.A.N., K.S.G., and X.L.,; writing—original draft preparation, M.A.N.; writing—review and editing, G.C., H.M.L., M.A.A.; visualization, G.C. and F.S.B.; supervision, G.C. and S.H.Y.; project administration, G.C.; funding acquisition, G.C., S.H.Y., H.M.L.”.

Corresponding authors

Correspondence to Seung Hwan Yang or Gyuhwa Chung.

Ethics declarations

Conflicts of interest

The authors declare no conflict of interest.

Ethical approval

No approval required for the study.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Gyuhwa Chung and Seung Hwan Yang are equal corresponding authors.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 289 kb)

Supplementary material 2 (XLSX 30 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nawaz, M.A., Lin, X., Chan, TF. et al. Genetic architecture of wild soybean (Glycine soja Sieb. and Zucc.) populations originating from different East Asian regions. Genet Resour Crop Evol (2021). https://doi.org/10.1007/s10722-020-01087-z

Download citation

Keywords

  • Array-based genotyping
  • CWLGC
  • East Asian wild soybeans
  • Genetic diversity
  • Glycine soja Sieb. and Zucc
  • SNP genotyping