Skip to main content
SpringerLink
Log in

Molecular Evidence for Soybean Domestication

  • Chapter
  • First Online:
Genomics of Plant Genetic Resources

Abstract

Crop domestication is a good example of plant–human co-evolution. Seed gathering and human cultivation of crops were observed since the Neolithic period, as shown by archeological evidence. Numerous studies have been conducted to identify genes related to domestication. With the development of molecular techniques (molecular markers and next-generation sequencing) and bioinformatics, a greater understanding of crop domestication and improvement has been established, including the origins of crops, the numbers of independent domestication events, the molecular diversity of domestication-related traits (DRTs), and the selection pressures. A comparison of the genome sequences between wild species and cultivated crops may provide key information regarding the genetic elements involved in speciation and domestication. Therefore, sequencing projects of currently important crops and their wild relatives are in progress. Accordingly, whole genome sequencing of soybean could provide new knowledge about domestication of this important crop. In this review, we introduce the archaeological evidence of soybean domestication and summarize the DRTs in soybean populations of crosses between cultivated (Glycine max) and wild soybean (G. soja). Soybean domestication is discussed at the sequence level. The current hypothesis of soybean domestication considers that G. max was domesticated from G. soja. However, our previous work suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. This review explores soybean domestication history by focusing on nucleotide diversity using resequencing. Analysis of genes around DRTs at the population level may clarify the domestication history of soybean.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trend Plant Sci 8:554–560

    Article  CAS  Google Scholar 

  • Bailey MA, Mian MAR, Carter TE et al (1997) Pod dehiscence of soybean: identification of quantitative trait loci. J Hered 88:152–154

    Article  CAS  Google Scholar 

  • Barabaschi D, Guerra D, Lacrima K et al (2012) Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 50:250–266

    Article  CAS  PubMed  Google Scholar 

  • Bennett ST, Barnes C, Cox A et al (2005) Toward the 1,000 dollars human genome. Pharmacogenomics 6:373–382

    Article  CAS  PubMed  Google Scholar 

  • Boerma HR, Specht JE (2004) Soybeans: improvement, production and uses. Am Soc of Agro, Madison

    Google Scholar 

  • Buckler ES, Thornsberry JM, Kresovich S (2001) Molecular diversity, structure and domestication of grasses. Genet Res 77:213–218

    Article  CAS  PubMed  Google Scholar 

  • Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161:1257–1267

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cai HW, Morishima H (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100:840–846

    Article  CAS  Google Scholar 

  • Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228

    Article  CAS  PubMed  Google Scholar 

  • Carter TE Jr, Nelson R, Sneller CH, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production and uses. Am Soc of Agro, Madison, pp 303–416

    Google Scholar 

  • Choi I-Y, Hyten DL, Matukumalli LK et al (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Clarke J, Wu H-C, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnol 4:265–270

    Article  CAS  Google Scholar 

  • Concibido VC, La Vallee B, Mclaird P et al (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106:575–582

    CAS  PubMed  Google Scholar 

  • Crawford G (2005) East Asian plant domestication. In: Stark MT (ed) Archaeology of asia. Blackwell Publishing, Oxford, pp 77–95

    Google Scholar 

  • Crawford G, Lee G-A (2003) Agricultural origins in the Korean Peninsula. Antiquity 77:87–95

    Google Scholar 

  • Crawford GW, Underhill AP, Zhao J et al (2005) Late neolithic plant remains from northern China: preliminary results from Liangchengzhen, Shandong. Curr Anthropol 46:309–317

    Article  Google Scholar 

  • Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418:700–707

    Article  CAS  PubMed  Google Scholar 

  • Doebley JF (1989) Isozymic evidence and the evolution of crop plants. In: Soltis D, Soltis P (eds) Isozymes in plant biology. Dioscorides Press, Portland, pp 165–191

    Chapter  Google Scholar 

  • Doebley J, Stec A (1993) Inheritance of the morphological differences between maize and Teosinte—comparison of results for two F2 populations. Genetics 134:559–570

    CAS  PubMed Central  PubMed  Google Scholar 

  • Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize Teosinte F2 population—implications for the origin of maize. Proc Natl Acad Sci USA 87:9888–9892

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321

    Article  CAS  PubMed  Google Scholar 

  • Doganlar S, Frary A, Daunay MC et al (2002) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161:1713–1726

    CAS  PubMed Central  PubMed  Google Scholar 

  • Dong YS, Zhao LM, Liu B et al (2004) The genetic diversity of cultivated soybean grown in China. Theor Appl Genet 108:931–936

    Article  CAS  PubMed  Google Scholar 

  • Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  • Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trend Plant Sci 16:77–88

    Article  CAS  Google Scholar 

  • Frary A, Nesbitt TC, Frary A et al (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  CAS  PubMed  Google Scholar 

  • Fuller DQ (2002) Fifty years of archaeobotanical studies in India: laying a solid foundation. In: Settar S, Korisettar R (eds) Indian archaeology in retrospect: archaeology and interactive disciplines, vol III. Manohar, Delhi, pp 247–263

    Google Scholar 

  • Fuller DQ (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann Bot 100:903–924

    Article  PubMed Central  PubMed  Google Scholar 

  • Funatsuki H, Ishimoto M, Tsuji H et al (2006) Simple sequence repeat markers linked to a major QTL controlling pod shattering in soybean. Plant Breed 125:195–197

    Article  CAS  Google Scholar 

  • Grandillo S, Tanksley SD (1996) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951

    Article  CAS  PubMed  Google Scholar 

  • Gross BL, Olsen KM (2010) Genetic perspectives on crop domestication. Trend Plant Sci 15:529–537

    Article  CAS  Google Scholar 

  • Gunter C (2008) Plant genetics rice stands up. Nat Rev Genet 9:816–816

    Article  CAS  Google Scholar 

  • Guo J, Wang Y, Song C et al (2010) A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences. Ann Bot 106:505–514

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1–13

    Article  Google Scholar 

  • Harris DR (1998) The origins of agriculture in southwest Asia. Rev Archaeol 19:5–11

    Google Scholar 

  • Harris TD, Buzby PR, Babcock H et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109

    Article  CAS  PubMed  Google Scholar 

  • Henry RJ (2012) Next-generation sequencing for understanding and accelerating crop domestication. Brief Func Genom 11:51–56

    Article  CAS  Google Scholar 

  • Hymowitz T (1970) On the domestication of the soybean. Eco Bot 24:408–421

    Article  Google Scholar 

  • Hyten DL, Song Q, Zhu Y et al (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Iqbal SM, Bashir R (2011) Nanopores: sensing and fundamental biological interactions. Springer, New York

    Book  Google Scholar 

  • Jackson SA, Iwata A, Lee SH et al (2011) Sequencing crop genomes: approaches and applications. New Phytol 191:915–925

    Article  CAS  PubMed  Google Scholar 

  • Jin J, Huang W, Gao JP et al (2008) Genetic control of rice plant architecture under domestication. Nature Genet 40:1365–1369

    Article  CAS  PubMed  Google Scholar 

  • Jun T-H, Van K, Kim MY et al (2011) Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance. Genes Genom 33:391–397

    Article  CAS  Google Scholar 

  • Kang S-T, Kwak M, Kim H-K et al (2009) Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.]. Euphytica 166:15–24

    Article  Google Scholar 

  • Keim P, Diers BW, Olson TC, Shoemaker RC (1990a) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735–742

    CAS  Google Scholar 

  • Keim P, Diers BW, Shoemaker RC (1990b) Genetic analysis of soybean hard seededness with molecular markers. Theor Appl Genet 79:465–469

    Article  CAS  Google Scholar 

  • Kim MY, Lee S, Van K et al (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107:22032–22037

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim MY, Van K, Kang YJ et al (2012) Tracing soybean domestication history: from nucleotide to genome. Breed Sci 61:445–452

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36:1037–1045

    Article  Google Scholar 

  • Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trend Genet 23:578–587

    Article  CAS  Google Scholar 

  • Lam H-M, Xu X, Liu X et al (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genet 42:1053–1059

    Article  CAS  PubMed  Google Scholar 

  • Lauter N, Doebley J (2002) Genetic variation for phenotypically invariant traits detected in teosinte: implications for the evolution of novel forms. Genetics 160:333–342

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee G-A (2011) The transition from foraging to farming in prehistoric Korea. Curr Anthropol 52:S307–S329

    Google Scholar 

  • Lee Y-H, Park T-S (2006) Origin of legumes cultivation in Korean Peninsula by viewpoint of excavated grain remains and genetic diversity of legumes. Kor Agri Hist Assoc 5:1–31 (in Korean)

    CAS  Google Scholar 

  • Lee G-A, Crawford GW, Liu L, Chen X (2007) Plants and people from the early neolithic to shang periods in North China. Proc Natl Acad Sci USA 104:1087–1092

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lee JD, Yu JK, Hwang YH et al (2008) Genetic diversity of wild soybean (Glycine soja Sieb. and Zucc.) accessions from South Korea and other countries. Crop Sci 48:606–616

    Article  Google Scholar 

  • Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939

    Article  CAS  PubMed  Google Scholar 

  • Li DD, Pfeiffer TW, Cornelius PL (2008) Soybean QTL for yield and yield components associated with Glycine soja alleles. Crop Sci 48:571–581

    Article  Google Scholar 

  • Li YH, Guan RX, Liu ZX et al (2008) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 117:857–871

    Article  CAS  PubMed  Google Scholar 

  • Li YH, Li W, Zhang C et al (2010) Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol 188:242–253

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Fujita T, Yan Z-H et al (2007) QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot 100:1027–1038

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu B, Watanabe S, Uchiyama T et al (2010) The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol 153:198–210

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nagai YS, Sobrizal, Sanchez PL et al (2002) Sh3, a gene for seed shattering, commonly found in wild rices. Rice Genet Newsl 19:74–75

    Google Scholar 

  • Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39:197–218

    Article  CAS  PubMed  Google Scholar 

  • Parameswaran P, Jalili R, Tao L et al (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35:e130

    Article  PubMed Central  PubMed  Google Scholar 

  • Peng JH, Ronin Y, Fahima T et al (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Poncet V, Martel E, Allouis S et al (2002) Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet (Pennisetum glaucum L., Poaceae) crosses. Theor Appl Genet 104:965–975

    Article  CAS  PubMed  Google Scholar 

  • Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:843–848

    Article  CAS  PubMed  Google Scholar 

  • Ross-Ibarra J (2005) Quantitative trait loci and the study of plant domestication. Genetica 123:197–204

    Article  PubMed  Google Scholar 

  • Rusk N (2009) Cheap third-generation sequencing. Nat Methods 6:244–245

    Article  CAS  Google Scholar 

  • Sang T, Ge S (2007) The puzzle of rice domestication. J Integr Plant Biol 49:760–768

    Article  CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178–183

    Article  CAS  PubMed  Google Scholar 

  • Schulman AH (2007) Molecular markers to assess genetic diversity. Euphytica 158:313–321

    Article  CAS  Google Scholar 

  • Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18

    Article  CAS  PubMed  Google Scholar 

  • Sobrizal, Ikeda K, Sanchez PL, Yoshimura A (1999) RFLP mapping of a seed shattering gene on chromosome 4 in rice. Rice Genet Newslett 16:74–75

    Google Scholar 

  • Stupar RM (2010) Into the wild: the soybean genome meets its undomesticated relative. Proc Natl Acad Sci USA 107:21947–21948

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tang H, Sezen U, Paterson AH (2010) Domestication and plant genomes. Curr Opin Plant Biol 13:160–166

    Article  CAS  PubMed  Google Scholar 

  • Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21:1214–1225

    Article  CAS  PubMed  Google Scholar 

  • Tian Z, Wang X, Lee R et al (2010) Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107:8563–8568

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Van K, Hwang E-Y, Kim MY et al (2004) Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica 139:147–157

    Article  CAS  Google Scholar 

  • Van K, Hwang E-Y, Kim MY et al (2005) Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J Hered 96:529–535

    Article  CAS  PubMed  Google Scholar 

  • Van K, Kim D, Cai CM et al (2008) Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome. DNA Res 15:93–102

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Van K, Kim DH, Shin JH, Lee S-H (2011) Genomics of plant genetic resources: past, present and future. Plant Genet Resour 9:155–158

    Article  Google Scholar 

  • Van K, Rastogi K, Kim K-H, Lee S-H (2013) Next-generation sequencing technology for crop improvement. SABRAO J Breed Genet 45:84–99

    Google Scholar 

  • Vaughan DA, Balazs E, Heslop-Harrison JS (2007) From crop domestication to super-domestication. Ann Bot 100:893–901

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Vielle-Calzada JP, Martinez delaVO, Hernandez-Guzman G et al (2009) The Palomero genome suggests metal effects on domestication. Science 326:1078

    Article  CAS  PubMed  Google Scholar 

  • Wilson RF (2008) Soybean: market driven research needs. In: Stacey G (ed) Genetics and genomics of soybean. Plant genetics and genomics, vol 2. Springer, pp 3–15

    Google Scholar 

  • Xiong LX, Liu KD, Dai XK et al (1999) Identification of genetic factors controlling domestication-related traits of rice using an F-2 population of a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 98:243–251

    Article  CAS  Google Scholar 

  • Xu DH, Gai JY (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breed 122:503–506

    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 soybean. Theor Appl Genet 105:645–653

    Article  CAS  PubMed  Google Scholar 

  • Yuan C, Zhou G, Li Y, Wang K, Wang Z, Li X, Chang R, Qiu L (2008) Cloning and sequence diversity analysis of GmHs1 pro-1 in Chinese domesticated and wild soybeans. Mol Breed 22:593–602

    Google Scholar 

  • Zhu YL, Song QJ, Hyten DL et al (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008117) of the Rural Development Administration, Republic of Korea.

Author information

Authors and Affiliations

  1. Plant Genomics and Breeding Institute, Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, 151-921, Seoul, Korea

    Moon Young Kim & Dr. Suk-Ha Lee

  2. Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, 151-921, Seoul, Korea

    Kyujung Van, Jin Hee Shin, Kyung Do Kim & Yeong-Ho Lee

Authors
  1. Kyujung Van
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Moon Young Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jin Hee Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kyung Do Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yeong-Ho Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dr. Suk-Ha Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Suk-Ha Lee .

Editor information

Editors and Affiliations

  1. Agricultural Sciences, University of Bologna, Bologna, Italy

    Roberto Tuberosa

  2. Genebank, IPK, Gatersleben, Sachsen-Anhalt, Germany

    Andreas Graner

  3. Bioversity International, Rome, Italy

    Emile Frison

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Van, K., Kim, M., Shin, J., Kim, K., Lee, YH., Lee, SH. (2014). Molecular Evidence for Soybean Domestication. In: Tuberosa, R., Graner, A., Frison, E. (eds) Genomics of Plant Genetic Resources. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7572-5_19

Download citation

Publish with us

Policies and ethics

Search

Navigation