Many leguminous species have adapted their seed coat with a layer of powdery bloom that contains hazardous allergens and makes the seeds less visible, offering duel protection against potential predators1. Nevertheless, a shiny seed surface without bloom is desirable for human consumption and health, and is targeted for selection under domestication. Here we show that seed coat bloom in wild soybeans is mainly controlled by Bloom1 (B1), which encodes a transmembrane transporter-like protein for biosynthesis of the bloom in pod endocarp. The transition from the ‘bloom’ to ‘no-bloom’ phenotypes is associated with artificial selection of a nucleotide mutation that naturally occurred in the coding region of B1 during soybean domestication. Interestingly, this mutation not only ‘shined’ the seed surface, but also elevated seed oil content in domesticated soybeans. Such an elevation of oil content in seeds appears to be achieved through b1-modulated upregulation of oil biosynthesis in pods. This study shows pleiotropy as a mechanism underlying the domestication syndrome2, and may pave new strategies for development of soybean varieties with increased seed oil content and reduced seed dust.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Corner, E. J. H. The leguminous seed. Phytomorphology 12, 117–150 (1951).

  2. 2.

    Olsen, K. M. & Wendel, J. F. A bountiful harvest: genomic insights into crop domestication phenotypes. Annu. Rev. Plant. Biol. 64, 47–70 (2013).

  3. 3.

    Carter, T. E., Nelson, R., Sneller, C. H. & Cui, Z. in Soybeans: Improvement, Production and Uses 3 edn. (eds. Boerma, H. R. & Specht, J. E.) pp. 303-416 (American Society of Agronomy-Crop Science Society of America-Soil Science Society of America, 2004).

  4. 4.

    Liu, B. et al. QTL mapping of domestication-related traits in soybean (Glycine max). Ann. Bot. 100, 1027–1038 (2007).

  5. 5.

    Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).

  6. 6.

    Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408–414 (2015).

  7. 7.

    Wolf, W. J., Baker, F. L. & Bernard, R. L. Soybean seed-coat structural features: pits, deposits and cracks. Scanning Electron Microsc. 3, 531–544 (1981).

  8. 8.

    Gijzen, M. et al. Hydrophobic protein synthesized in the pod endocarp adheres to the seed surface. Plant. Physiol. 120, 951–960 (1999).

  9. 9.

    Juvik, G. A., Bernard R. L., Chang R. Z. & Cavins J. F. Evaluation of the USDA wild soybean germplasm collection: maturity groups 000 to IV (PI-655.49 to PI-48.3464). Technical Bulletin 1761 (U.S. Govt. Print Office, U.S. Department of Agriculture, Washington, D.C., 1989).

  10. 10.

    Gijzen, M., Weng, C., Kuflu, K., Woodrow, L., Yu, K. & Poysa, V. Soybean seed lustre phenotype and surface protein cosegregate and map to linkage group E. Genome 46, 659–664 (2003).

  11. 11.

    Guodong, Z. et al. Inheritance of bloom on seed coat in soybean. Soybean Genet. Newsl. 14, 91–93 (1987).

  12. 12.

    Palmer, R. G. & Kilen, T. C. Qualitative genetics and cytogenetics. (American Society of Agronomy, Madison, WI, 1987).

  13. 13.

    Chen, Z. & Shoemaker, R. C. Four genes affecting seed traits in soybeans map to linkage group F. J. Hered. 89, 211–215 (1998).

  14. 14.

    Wang, W. et al. Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean (Glycine soja Sieb. & Zucc.). Euphytica 208, 101–111 (2016).

  15. 15.

    Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183 (2010).

  16. 16.

    Hyten, D. L. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl Acad. Sci. USA 103, 16666–16671 (2006).

  17. 17.

    Song, Q. et al. Fingerprinting soybean germplasm and its utility in genomic research. G3 (Bethesda). 5, 1999–2006 (2015).

  18. 18.

    Zhang, D., Zhao, M., Li, S., Sun, L., Wang, W., Cai, C., Dierking, E. C. & Ma, J. Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean.Plant J. 90, 1120–1133 (2017).

  19. 19.

    Doust, A. N., Lukens, L., Olsen, K. M., Mauro-Herrera, M., Meyer, A. & Rogers, K. Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication. Proc. Natl Acad. Sci. USA 111, 6178–6183 (2014).

  20. 20.

    Wu, W. et al. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat. Plants 3, 17064 (2017).

  21. 21.

    Sun, L. et al. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat. Genet. 47, 939–943 (2015).

  22. 22.

    Bilyeu, K., Palavalli, L., Sleper, D. & Beuselinck, P. Mutations in soybean microsomal omega-3 fatty acid desaturase genes reduce linolenic acid concentration in soybean seeds. Crop. Sci. 45, 1830–1836 (2005).

  23. 23.

    To, A. et al. WRINKLED transcription factors orchestrate tissue-specific regulation of fatty acid biosynthesis in Arabidopsis. Plant Cell. 24, 5007–5023 (2012).

  24. 24.

    Ping, J. et al. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell. 26, 2831–2842 (2014).

  25. 25.

    Poland, J. A., Brown, P. J., Sorrells, M. E. & Jannink, J. L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7, e32253 (2012).

  26. 26.

    Broman, K. W., Wu, H., Sen, Ś. & Churchill, G. A. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 19, 889–890 (2003).

  27. 27.

    Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001).

  28. 28.

    Yang, J. et al. The I-TASSER suite: protein structure and function prediction. Nat. Methods 12, 7–8 (2014).

  29. 29.

    Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 23, 2633–2635 (2007).

  30. 30.

    Zhang, Z. et al. Mixed linear model approach adapted for genome-wide association studies. Nat. Genet. 42, 355–360 (2010).

Download references


This work was mainly supported by soybean checkoff funds from the North Central Soybean Research Program and Indiana Soybean Alliance, and partially supported by the Agriculture and Food Research Initiative competitive grant (2015-67013-22811) of the USDA National Institute of Food and Agriculture, the Republic of Korea Rural Development Administration (RDA) Research Program (Grant no. PJ0122112017), Taishan Scholarship and Purdue University AgSEED Program.

Author information

Author notes

    • Lianjun Sun
    •  & Linghong Li

    Present address: Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China

  1. Dajian Zhang, Lianjun Sun, Shuai Li, Weidong Wang and Yanhua Ding contributed equally to this work.


  1. Department of Agronomy, Purdue University, West Lafayette, IN, USA

    • Dajian Zhang
    • , Lianjun Sun
    • , Weidong Wang
    • , Linghong Li
    • , Xutong Wang
    •  & Jianxin Ma
  2. College of Life Sciences, Qingdao Agricultural University, Qingdao, China

    • Shuai Li
    • , Yanhua Ding
    • , Xuemin Tang
    •  & Chunmei Cai
  3. Department of Crop Sciences, University of Illinois, Urbana, IL, USA

    • Stephen A. Swarm
    • , Patrick J. Brown
    •  & Randall L. Nelson
  4. Institute of Genetics and Developmental Biology, Beijing, China

    • Zhifang Zhang
    •  & Zhixi Tian
  5. Center for Plant Biology, Purdue University, West Lafayette, IN, USA

    • Jianxin Ma


  1. Search for Dajian Zhang in:

  2. Search for Lianjun Sun in:

  3. Search for Shuai Li in:

  4. Search for Weidong Wang in:

  5. Search for Yanhua Ding in:

  6. Search for Stephen A. Swarm in:

  7. Search for Linghong Li in:

  8. Search for Xutong Wang in:

  9. Search for Xuemin Tang in:

  10. Search for Zhifang Zhang in:

  11. Search for Zhixi Tian in:

  12. Search for Patrick J. Brown in:

  13. Search for Chunmei Cai in:

  14. Search for Randall L. Nelson in:

  15. Search for Jianxin Ma in:


J.M. and R.L.N. conceived and designed the research; D.Z., L.S., S.L., W.W., Y.D., S.A.S., L.L., X.W. X.T. and Z.Z. performed the research; D.Z., L.S., S.L., W.W., Z.T., P.B., C.C., R.L.N. and J.M. analysed the data; J.M. wrote the manuscript with input from D.Z., W.W., S.A.S. and R.L.N.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jianxin Ma.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1 & 2, Supplementary Tables 1–4.

  2. Life Sciences Reporting Summary

  3. Supplementary Data 1

    SNP genotyping data generated in this study.

About this article

Publication history






Further reading