Functional annotation of differentially expressed genes under salt stress in Dichanthium annulatum

  • Anita MannEmail author
  • Naresh Kumar
  • Charu Lata
  • Ashwani Kumar
  • Arvind Kumar
  • B. L. Meena
Original Article


Soil salinity is one of the important abiotic stresses affecting plant growth and development. Halophytes can be one of the options to explore the salt tolerance potential and to identify the potential gene(s) which can be used in crop improvement programs. In view of this, the present experiment was conducted on grass halophyte, Dichanthium annulatum, which can tolerate soil salinity up to EC 30 dS/m (~ 300 mM NaCl) to identify the gene(s) for salt tolerance. The de novo assembly generated 267,196 transcripts and these assembled transcripts were further clustered into 188,353 transcripts. An average of 64.47% of the transcripts was functionally annotated against the viridiplantae databases since no genomic reference is available for Dichanthium. Gene ontology and pathways analysis using KAAS database identified that 48.13% transcripts were involved in molecular function, 37.21% in cellular component and 14.66% in biological processes. The annotation of these genes provides a pathway analysis for their putative functions under salt stress conditions.


Salt stress Halophytes Dichanthium Gene Salt tolerance 



The authors are highly thankful to the Director, ICAR-CSSRI, Karnal for providing necessary facilities to carry out the research work. The first author also sincerely acknowledges the ICAR-National Agricultural Science Fund (NASF), New Delhi for funding this work.


  1. Acosta-Motos, J. R., Ortuño, M. F., Bernal-Vicente, A., Diaz-Vivancos, P., Sanchez-Blanco, M. J., & Hernandez, J. A. (2017). Plant responses to salt stress: Adaptive mechanisms. Agronomy, 7(1), 18.CrossRefGoogle Scholar
  2. Agarwal, P. K., Shukla, P. S., Gupta, K., & Jha, B. (2013). Bioengineering for salinity tolerance in plants: State of the art. Molecular Biotechnology, 54(1), 102–123.CrossRefGoogle Scholar
  3. Assaha, D. V. M., Ueda, A., Saneoka, H., Al-Yahyai, R., & Yaish, M. W. (2017). The role of Na+ and K+ transporters in salt stress adaptation in glycophytes. Frontiers in Physiology. Scholar
  4. Barrett-Lennard, E. G., & Setter, T. L. (2010). Developing saline agriculture: Moving from traits and genes to systems. Functional Plant Biology, 37(7), iii–iv.CrossRefGoogle Scholar
  5. Colmer, T. D., Munns, R., & Flowers, T. J. (2006). Improving salt tolerance of wheat and barley: Future prospects. Australian Journal of Experimental Agriculture, 45(11), 1425–1443.CrossRefGoogle Scholar
  6. Das, K., & Roychoudhury, A. (2014). Reactive oxygen species (ROS) and response of antioxidants as ROS-scavengers during environmental stress in plants. Frontiers in Environmental Science. Scholar
  7. de Barajas-Lopez, J. D., Moreno, J. R., Gamez-Arjona, F. M., Pardo, J. M., Punkkinen, M., Zhu, J.-K., et al. (2018). Upstream kinases of plant SnRKs are involved in salt stress tolerance. The Plant Journal, 93(1), 107–118. Scholar
  8. Délano-Frier, J. P., Avilés-Arnaut, H., Casarrubias-Castillo, K., Casique-Arroyo, G., Castrillón-Arbeláez, P. A., Herrera-Estrella, L., et al. (2011). Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: Comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress. BMC Genomics, 12(1), 363.CrossRefGoogle Scholar
  9. De Vos, S., Van Stappen, G., Sorgeloos, P., Vuylsteke, M., Rombauts, S., & Bossier, P. (2019). Identification of salt stress response genes using the Artemia transcriptome. Aquaculture, 500, 305–314. Scholar
  10. Deng, Y., Srivastava, R., & Howell, S. (2013). Endoplasmic reticulum (ER) stress response and its physiological roles in plants. International Journal of Molecular Sciences, 14(4), 8188–8212.CrossRefGoogle Scholar
  11. Dugas, D. V., Monaco, M. K., Olson, A., Klein, R. R., Kumari, S., Ware, D., et al. (2011). Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics, 12(1), 514. Scholar
  12. Ferreira de Carvalho, J., Poulain, J., Da Silva, C., Wincker, P., Michon-Coudouel, S., Dheilly, A., et al. (2013). Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Heredity, 110(2), 181–193.CrossRefGoogle Scholar
  13. Flowers, T. J., & Colmer, T. D. (2008). Salinity tolerance in halophytes. New Phytologist, 179(4), 945–963.CrossRefGoogle Scholar
  14. Flowers, T. J., Munns, R., & Colmer, T. D. (2014). Sodium chloride toxicity and the cellular basis of salt tolerance in halophytes. Annals of Botany, 115(3), 419–431.CrossRefGoogle Scholar
  15. Garg, R., Patel, R. K., Tyagi, A. K., & Jain, M. (2011). De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Research, 18(1), 53–63.CrossRefGoogle Scholar
  16. Gedye, K., Gonzalez-Hernandez, J., Ban, Y., Ge, X., Thimmapuram, J., Sun, F., et al. (2010). Investigation of the transcriptome of prairie cord grass, a new cellulosic biomass crop. The Plant Genome Journal, 3(2), 69.CrossRefGoogle Scholar
  17. Glenn, E. P., Brown, J. J., & Blumwald, E. (1999). Salt tolerance and crop potential of halophytes. Critical Reviews in Plant Sciences, 18(2), 227–255.CrossRefGoogle Scholar
  18. Himabindu, Y., Chakradhar, T., Reddy, M. C., Kanygin, A., Redding, K. E., & Chandrasekhar, T. (2016). Salt-tolerant genes from halophytes are potential key players of salt tolerance in glycophytes. Environmental and Experimental Botany, 124, 39–63.CrossRefGoogle Scholar
  19. Hu, L., Li, H., Chen, L., Lou, Y., Amombo, E., & Fu, J. (2015). RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. BMC Genomics, 16(1), 575.CrossRefGoogle Scholar
  20. Kasuga, M., Liu, Q., Miura, S., Yamaguchi-Shinozaki, K., & Shinozaki, K. (1999). Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nature Biotechnology, 17(3), 287.CrossRefGoogle Scholar
  21. Kumar, A., Kumar, A., Lata, C., Kumar, S., Mangalassery, S., Singh, J. P., et al. (2018). Effect of salinity and alkalinity on response of halophytic grasses Sporobolus marginatus and Urochondra setulosaIndian Journal of Agricultural Sciences, 88(8), 149–157.Google Scholar
  22. Liu, J., Qiao, Q., Cheng, X., Du, G., Deng, G., Zhao, M., et al. (2016). Transcriptome differences between fiber-type and seed-type Cannabis sativa variety exposed to salinity. Physiology and Molecular Biology of Plants, 22(4), 429–443.CrossRefGoogle Scholar
  23. Lv, X., Jin, Y., & Wang, Y. (2018). De novo transcriptome assembly and identification of salt-responsive genes in sugar beet M14. Computational Biology and Chemistry, 75, 1–10.CrossRefGoogle Scholar
  24. Naika, M., Shameer, K., & Sowdhamini, R. (2013). Comparative analyses of stress-responsive genes in Arabidopsis thaliana: Insight from genomic data mining, functional enrichment, pathway analysis and phenomics. Molecular BioSystems, 9(7), 1888–1908.CrossRefGoogle Scholar
  25. Palavalasa, H. K., Narasu, L. N., Varshney, R. K., & KaviKishor, P. B. (2017). Genome wide analysis of sodium transporters and expression of Na+/H+-antiporter-like protein (SbNHXLP) gene in tomato for salt tolerance. In: InterDrought-V, Hyderabad, India, February 21–25.Google Scholar
  26. Pang, Q., Chen, S., Dai, S., Chen, Y., Wang, Y., & Yan, X. (2010). Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila. Journal of Proteome Research, 9(5), 2584–2599.CrossRefGoogle Scholar
  27. Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010). Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. BMC Genomics, 11(1), 180.CrossRefGoogle Scholar
  28. Shabala, S. (2013). Learning from halophytes: Physiological basis and strategies to improve abiotic stress tolerance in crops. Annals of Botany, 112(7), 1209–1221.CrossRefGoogle Scholar
  29. Shinde, H., Tanaka, K., Dudhate, A., Tsugama, D., Mine, Y., Kamiya, T., et al. (2018). Comparative de novo transcriptomic profiling of the salinity stress responsiveness in contrasting pearl millet lines. Environmental and Experimental Botany, 155, 619–627.CrossRefGoogle Scholar
  30. Sun, C., Li, Y., Wu, Q., Luo, H., Sun, Y., Song, J., et al. (2010). De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics, 11(1), 262.CrossRefGoogle Scholar
  31. Tiwari, B., Kalim, S., Tyagi, N., Kumari, R., Bangar, P., Barman, P., et al. (2018). Identification of genes associated with stress tolerance in moth bean [Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop. Physiology and Molecular Biology of Plants, 24(4), 551–561.CrossRefGoogle Scholar
  32. Tuteja, N. (2007). Mechanisms of high salinity tolerance in plants. Methods in Enzymology, 428, 419–438.CrossRefGoogle Scholar
  33. Wang, X., Chang, L., Wang, B., Wang, D., Li, P., Wang, L., et al. (2013). Comparative proteomics of Thellungiella halophila leaves from plants subjected to salinity reveals the importance of chloroplastic starch and soluble sugars in halophyte salt tolerance. Molecular and Cellular Proteomics, 12(8), 2174–2195.CrossRefGoogle Scholar
  34. Yao, L., Wang, J., Li, B., Meng, Y., Ma, X., Si, E., et al. (2018). Transcriptome sequencing and comparative analysis of differentially-expressed isoforms in the roots of Halogeton glomeratus under salt stress. Gene, 646, 159–168.CrossRefGoogle Scholar
  35. Yoshida, T., Mogami, J., & Yamaguchi-Shinozaki, K. (2014). ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Current Opinion in Plant Biology, 21, 133–139.CrossRefGoogle Scholar
  36. Zhang, M., Mu, H., Zhang, R., Liu, S., & Lee, I. (2018). Genome-wide pathway analysis of microarray data identifies risk pathways related to salt stress in Arabidopsis thaliana. Interdisciplinary Sciences: Computational Life Sciences, 10(3), 566–571.Google Scholar

Copyright information

© Indian Society for Plant Physiology 2019

Authors and Affiliations

  1. 1.ICAR-Central Soil Salinity Research InstituteKarnalIndia

Personalised recommendations