Genes & Genomics

, Volume 41, Issue 11, pp 1315–1327 | Cite as

Comparative transcriptome analysis reveals higher expression of stress and defense responsive genes in dwarf soybeans obtained from the crossing of G. max and G. soja

  • Yong-Wook Ban
  • Neha Samir Roy
  • Heejung Yang
  • Hong-Kyu Choi
  • Jin-Hyun Kim
  • Prakash Babu
  • Keon-Soo Ha
  • Jin-Kwan Ham
  • Kyong Cheul Park
  • Ik-Young ChoiEmail author
Research Article



Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. Dwarfism in plants prevents lodging and therefore it’s a desired trait in crops.


To find differentially expressed genes to classify and understand the regulation of genes related to plant growth in mutant dwarf soybeans, which appeared in the F5 generation.


We obtained a few segregated dwarf soybeans in the populations derived from the crossing of Glycine max var. Peking and Glycine soja var. IT182936 in an F5 RIL population. These dwarf soybeans may be useful genetic resources for plant breeders, geneticists and biologists. Using the Illumina high-throughput platform, transcriptomes were generated and compared among normal and dwarf soybeans in triplicate.


We found complex relationship of the expressed genes to plant growth. There were highly significantly up-/downregulated genes according to the comparison of gene expression in normal and dwarf soybeans. The genes related to disease and stress responses were found to be upregulated in dwarf soybeans. Such over-expression of disease resistance and other immune response genes can be targeted to understand how the immune genes regulate the response of plant growth. In addition, photosynthesis-related genes showed very low expression in dwarf lines. The transcriptome expression and genes classified as related to plant growth may be useful resources to researchers studying plant growth.


DEG Dwarf Growth Soybean Transcriptome 



This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2017R1A2B4011198) and by a 2017 Research Grant from Kangwon National University.

Author contributions

I-YC conceived and designed the project and prepared the samples. Y-WB and NSR were major contributor to the data analysis and writing the manuscript. HY analyzed the metabolite. H-KC and J-HK, PB and KCP surveyed and analyzed the NGS data. K-SH and J-KH cultivated and surveyed the soybean population.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest in regards to the content of this manuscript.

Supplementary material

13258_2019_846_MOESM1_ESM.xlsx (174 kb)
Supplementary material 1 (XLSX 173 kb)


  1. Acquaah G (2012) Yield and morphological traits. In: Acquaah G (ed) Principles of plant genetics and breeding. Blackwell, Oxford. CrossRefGoogle Scholar
  2. Baldwin IT, Callahan P (1993) Autotoxicity and chemical defense: nicotine accumulation and carbon gain in solanaceous plants. Oecologia 94:534–541. CrossRefPubMedGoogle Scholar
  3. Belkhadir Y, Subramaniam R, Dangl JL (2004) Plant disease resistance protein signaling: NBS–LRR proteins and their partners. Curr Opin Plant Biol 7:391–399CrossRefGoogle Scholar
  4. Bilgin DD, Zavala JA, Zhu J, Clough SJ, Ort DR, DeLucia EH (2010) Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ 33:1597–1613. CrossRefPubMedGoogle Scholar
  5. Bogorad IW, Lin TS, Liao JC (2013) Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502:693–697. CrossRefPubMedGoogle Scholar
  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Boutraa T, Akhkha A, Al-Shoaibi AA, Alhejeli AM (2010) Effect of water stress on growth and water use efficiency (WUE) of some wheat cultivars (Triticum durum) grown in Saudi Arabia. J Taibah Univ Sci 3:39–48CrossRefGoogle Scholar
  8. Cooper R, Martin R, Schmitthenner A, McBlain B, Fioritto R, St Martin S, Calip-DuBois A (1991) Registration of’ Hobbit 87’ soybean. Crop Sci (USA) 31:1093Google Scholar
  9. Cooper R, Martin R, St Martin S, Calip-DuBois A, Fioritto R, Schmitthenner A (1995) Registration of’ Charleston’ soybean. Crop Sci 35:593CrossRefGoogle Scholar
  10. Cooper R, Mendiola T, Martin SS, Fioritto R, Schmitthenner A, Dorrance A (2001) Registration of strong’ soybean. Crop Sci 41:921CrossRefGoogle Scholar
  11. Cooper R, Mendiola T, St Martin S, Fioritto R, Dorrance A (2003) Registration of ‘Apex’ soybean (Registration Of Cultivars). Crop Sci 43:1563–1564CrossRefGoogle Scholar
  12. Crawford NM (1995) Nitrate: nutrient and signal for plant growth. Plant Cell 7:859–868. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Daft MJ, Nicolson T (1966) Effect of endogone mycorrhiza on plant growth. New Phytol 65:343–350. CrossRefGoogle Scholar
  14. de Souza IR, MacAdam JW (2001) Gibberellic acid and dwarfism effects on the growth dynamics of B73 maize (Zea mays L.) leaf blades: a transient increase in apoplastic peroxidase activity precedes cessation of cell elongation. J Exp Bot 52:1673–1682. CrossRefPubMedGoogle Scholar
  15. Dempsey DMA, Shah J, Klessig DF (1999) Salicylic acid and disease resistance in plants. Crit Rev Plant Sci 18:547–575. CrossRefGoogle Scholar
  16. Giri AP, Wunsche H, Mitra S, Zavala JA, Muck A, Svatos A, Baldwin IT (2006) Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. VII. Changes in the plant’s proteome. Plant Physiol 142:1621–1641. CrossRefPubMedPubMedCentralGoogle Scholar
  17. Greenberg JT (1997) Programmed cell death in plant-pathogen interactions. Annu Rev Plant Physiol Plant Mol Biol 48:525–545. CrossRefPubMedGoogle Scholar
  18. Heil M, Hilpert A, Kaiser W, Linsenmair KE (2000) Reduced growth and seed set following chemical induction of pathogen defence: does systemic acquired resistance (SAR) incur allocation costs? J Ecol 88:645–654CrossRefGoogle Scholar
  19. Herrera-Vasquez A, Salinas P, Holuigue L (2015) Salicylic acid and reactive oxygen species interplay in the transcriptional control of defense genes expression. Front Plant Sci 6:171. (ARTN 171) CrossRefPubMedPubMedCentralGoogle Scholar
  20. Huot B, Yao J, Montgomery BL, He SY (2014) Growth-defense tradeoffs in plants: a balancing act to optimize fitness. Mol Plant 7:1267–1287. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Hutchings MJ, de Kroon H (1994) Foraging in plants: the role of morphological plasticity in resource acquisition. In: Advances in ecological research, vol 25. Elsevier, pp 159–238. Google Scholar
  22. Hwang WJ, Kim MY, Kang YJ, Shim S, Stacey MG, Stacey G, Lee SH (2015) Genome-wide analysis of mutations in a dwarf soybean mutant induced by fast neutron bombardment. Euphytica 203:399–408. CrossRefGoogle Scholar
  23. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirement. Nat Methods 12:357–360. CrossRefPubMedPubMedCentralGoogle Scholar
  24. Korner C (2016) Plant adaptation to cold climates. F1000Research 25:1754–1760. CrossRefGoogle Scholar
  25. Lam E, Kato N, Lawton M (2001) Programmed cell death, mitochondria and the plant hypersensitive response. Nature 411:848–853. CrossRefPubMedGoogle Scholar
  26. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Markakis MN, Boron AK, Van Loock B, Saini K, Cirera S, Verbelen JP, Vissenberg K (2013) Characterization of a small auxin-up RNA (SAUR)-like gene involved in Arabidopsis thaliana development. PLoS One 8:e82596. CrossRefPubMedPubMedCentralGoogle Scholar
  28. Morot-Gaudry-Talarmain Y, Rockel P, Moureaux T, Quillere I, Leydecker MT, Kaiser WM, Morot-Gaudry JF (2002) Nitrite accumulation and nitric oxide emission in relation to cellular signaling in nitrite reductase antisense tobacco. Planta 215:708–715. CrossRefPubMedGoogle Scholar
  29. Nakazawa M, Yabe N, Ichikawa T, Yamamoto YY, Yoshizumi T, Hasunuma K, Matsui M (2001) DFL1, an auxin-responsive GH3 gene homologue, negatively regulates shoot cell elongation and lateral root formation, and positively regulates the light response of hypocotyl length. Plant J 25:213–221CrossRefGoogle Scholar
  30. Ockerse R, Galston AW (1967) Gibberellin-auxin interaction in pea stem elongation. Plant Physiol 42:47–54CrossRefGoogle Scholar
  31. Peng J et al (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Poveda K, Steffan-Dewenter I, Scheu S, Tscharntke T (2003) Effects of below- and above-ground herbivores on plant growth, flower visitation and seed set. Oecologia 135:601–605. CrossRefPubMedGoogle Scholar
  33. Pratap A, Kumar J (2014) Alien gene transfer in crop plants, vol 2. Spinger, New York, USA. CrossRefGoogle Scholar
  34. Quint M, Gray WM (2006) Auxin signaling. Curr Opin Plant Biol 9:448–453. CrossRefPubMedPubMedCentralGoogle Scholar
  35. Scholthof HB, Scholthof KB, Jackson AO (1995) Identification of tomato bushy stunt virus host-specific symptom determinants by expression of individual genes from a potato virus X vector. Plant Cell 7:1157–1172PubMedPubMedCentralGoogle Scholar
  36. Stincone A et al (2015) The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol Rev Camb Philos Soc 90:927–963. CrossRefPubMedGoogle Scholar
  37. Striker GG (2012) Flooding stress on plants: anatomical, morphological and physiological responses. Botany. CrossRefGoogle Scholar
  38. Suarez-Rodriguez MC et al (2007) MEKK1 is required for flg22-induced MPK4 activation in Arabidopsis plants. Plant Physiol 143:661–669. CrossRefPubMedPubMedCentralGoogle Scholar
  39. Tanimoto E (2012) Tall or short? Slender or thick? A plant strategy for regulating elongation growth of roots by low concentrations of gibberellin. Ann Bot 110:373–381. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Tao Y, Yuan F, Leister RT, Ausubel FM, Katagiri F (2000) Mutational analysis of the Arabidopsis nucleotide binding site-leucine-rich repeat resistance gene RPS2. Plant Cell 12:2541–2554PubMedPubMedCentralGoogle Scholar
  41. Tatrai ZA, Sanoubar R, Pluhar Z, Mancarella S, Orsini F, Gianquinto G (2016) Morphological and physiological plant responses to drought stress in Thymus citriodorus. Int J Agron 20:16. (Artn 4165750) CrossRefGoogle Scholar
  42. ten Hove CA et al (2011) Probing the roles of LRR RLK genes in Arabidopsis thaliana roots using a custom T-DNA insertion set. Plant Mol Biol 76:69–83. CrossRefPubMedPubMedCentralGoogle Scholar
  43. Tenhaken R, Doerks T, Bork P (2005) DCD—a novel plant specific domain in proteins involved in development and programmed cell death. BMC Bioinform 6:169. CrossRefGoogle Scholar
  44. Tian CE, Muto H, Higuchi K, Matamura T, Tatematsu K, Koshiba T, Yamamoto KT (2004) Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition. Plant J 40:333–343. CrossRefPubMedGoogle Scholar
  45. Wang X, Deng Z, Zhang W, Meng Z, Chang X, Lv M (2017) Effect of waterlogging duration at different growth stages on the growth, yield and quality of cotton. PLoS One 12:e0169029. CrossRefPubMedPubMedCentralGoogle Scholar
  46. Wrzaczek M, Brosche M, Kangasjarvi J (2013) ROS signaling loops-production, perception, regulation. Curr Opin Plant Biol 16:575–582. CrossRefPubMedGoogle Scholar
  47. Zhang Y, Turner JG (2008) Wound-induced endogenous jasmonates stunt plant growth by inhibiting mitosis. PLoS One 3:e3699. CrossRefPubMedPubMedCentralGoogle Scholar
  48. Zhang P, Liu X, Tong H, Lu Y, Li J (2014) Association mapping for important agronomic traits in core collection of rice (Oryza sativa L.) with SSR markers. PLoS One 9:e111508. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  • Yong-Wook Ban
    • 1
    • 2
  • Neha Samir Roy
    • 1
    • 3
  • Heejung Yang
    • 4
  • Hong-Kyu Choi
    • 5
  • Jin-Hyun Kim
    • 5
  • Prakash Babu
    • 2
  • Keon-Soo Ha
    • 6
  • Jin-Kwan Ham
    • 6
  • Kyong Cheul Park
    • 1
  • Ik-Young Choi
    • 1
    • 3
    Email author
  1. 1.Department of Agriculture and Life IndustryKangwon National UniversityChuncheonSouth Korea
  2. 2.Department of Forest Environmental SystemKangwon National UniversityChuncheonSouth Korea
  3. 3.Agriculture and Life Sciences Research InstituteKangwon National UniversityChuncheonSouth Korea
  4. 4.Laboratory of Natural Products Chemistry, College of PharmacyKangwon National UniversityChuncheonSouth Korea
  5. 5.Department of Molecular GeneticsDong-A UniversityBusanSouth Korea
  6. 6.Gangwondo Agricultural Research and Extension ServicesChuncheonSouth Korea

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