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Biologia

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Transcriptomic analysis of root specific drought mediated response of G. arboreum and G. hirsutum

  • Zarnab Ahmad
  • Sajjad Sadique
  • Muhammad B. Sarwar
  • Bushra RashidEmail author
  • Sameera Hassan
  • Sultana Rasheed
  • Khurram Bashir
  • Motoaki Seki
  • Tayyab Husnain
Original Article
  • 17 Downloads

Abstract

Gossypium hirsutum is a model species for domestication and genetic-engineering. Gossypium arboreum acts as a reference species for understanding G. hirsutum genome. Drought causes losses in crop productivity and requires its mitigation strategies. Microarray technology has been used in this study to identify the potential transcripts in G. hirsutum and G. arboreum under drought stress. G. arboreum and G. hirsutum plants were grown under drought stress and their drought specific genetic response was subsequently analyzed in the root samples. Customized 500 drought specific oligonucleotides were designed by cross species analysis of the Expression Sequence Tags (ESTs) of G. arboreum, G. hirsutum with Arabidopsis. An in-house microarray system was developed by printing the 500 drought specific oligonucleotides on glass substrate slides and probes were hybridized with the labeled cDNA of both the cotton species. In order to screen out drought responsive key elements, different bioinformatics tools analyzed and identified the upregulated and down regulated EST’s in both the species. The functional characterization of EST’s shows their association with different biological pathways involved for drought as well as other abiotic stresses. Real-Time PCR analyses showed the expression of the relevant transcripts responsible for different biological functions in root tissues under the drought stress condition. These results provide an insight to the root specific drought responsive differential expression of transcriptome between the two cotton species. Further characterization of upregulated transcripts will indicate the metabolism of these species to conserve energy during drought stress enabling them to survive longer during stress conditions.

Keywords

Cotton Drought Oligonucleotide microarray Gene expression 

Abbreviations

G. arboreum

Gossypium arboreum

G. hirsutum

Gossypium hirsutum

ESTs

Expression sequence tags

ADH

Alcohol dehydrogenases

PDH

pyruvate dehydrogenase

ABA

Abscisic acid

GO

Gene Ontology

Notes

Acknowledgments

This work was supported by HEC (Higher Education Commission) Pakistan.

Author’s contribution

TH and BR conceived the idea and secured the grant as PI and CoPI, SS designed the oligos and prepared the plant materials, ZA printed the array and did real-time PCR analyses, MBS and SR did the bioinformatics analyses, SH drafted the manuscript, KB prepared the data submission file and critically analyzed the data, MS critically reviewed the final version of manuscript. All authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

Authors declare that there is no conflict of interests.

References

  1. Ahmed M, Stockle CO (2016) Quantification of climate variability, adaptation and mitigation for agricultural sustainability. Springer, SwitzerlandGoogle Scholar
  2. Alavilli H, Lee H, Park M, Yun D-J, Lee B-h (2018) Enhanced multiple stress tolerance in Arabidopsis by overexpression of the polar moss peptidyl prolyl isomerase FKBP12 gene. Plant Cell Rep 37:453–465.  https://doi.org/10.1007/s00299-017-2242-9 CrossRefPubMedGoogle Scholar
  3. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676.  https://doi.org/10.1093/bioinformatics/bti610 CrossRefGoogle Scholar
  4. Hossain MA, Wani SH, Bhattacharjee S, Burritt DJ, Tran L-SP (2016) Drought stress tolerance in plants volume 2. Springer, SwitzerlandCrossRefGoogle Scholar
  5. Jaakola L, Pirttilä AM, Halonen M, Hohtola A (2001) Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Mol Biotechol 19:201–203.  https://doi.org/10.1385/MB:19:2:201 CrossRefGoogle Scholar
  6. Koevoets IT, Venema JH, Elzenga JTM, Testerink C (2016) Roots withstanding their environment: exploiting root system architecture responses to abiotic stress to improve crop tolerance. Front Plant Sci 7:1335.  https://doi.org/10.3389/fpls.2016.01335 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Li R, Erpelding JE (2016) Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing. Genetica 144:535–545.  https://doi.org/10.1007/s10709-016-9921-2 CrossRefPubMedGoogle Scholar
  8. Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J (2015) Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530.  https://doi.org/10.1038/nbt.3208 CrossRefGoogle Scholar
  9. Marino D, Froidure S, Canonne J, Khaled SB, Khafif M, Pouzet C, Jauneau A, Roby D, Rivas S (2013) Arabidopsis ubiquitin ligase MIEL1 mediates degradation of the transcription factor MYB30 weakening plant defence. Nat Commun 4:1476.  https://doi.org/10.1038/ncomms2479 CrossRefPubMedGoogle Scholar
  10. Mondragón-Palomino M, Stam R, John-Arputharaj A, Dresselhaus T (2017) Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms. BMC Evol Biol 17:255.  https://doi.org/10.1186/s12862-017-1099-4 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Nasimi R, Khan I, Iqbal M, Khan A (2016) Genetic analysis of drought tolerance with respect to fiber traits in upland cotton. Genet Mol Res 15.  https://doi.org/10.4238/gmr.15048626
  12. Osakabe Y, Osakabe K, Shinozaki K, Tran L-S (2014) Response of plants to water stress. Front Plant Sci 5.  https://doi.org/10.3389/fpls.2014.00086
  13. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nat 492:423–427.  https://doi.org/10.1038/nature11798 CrossRefGoogle Scholar
  14. Purushothaman R, Krishnamurthy L, Upadhyaya HD, Vadez V, Varshney RK (2017) Genotypic variation in soil water use and root distribution and their implications for drought tolerance in chickpea. Funct Plant Biol 44:235–252  https://doi.org/10.1071/FP16154 CrossRefGoogle Scholar
  15. Rasheed S, Bashir K, Matsui A, Tanaka M, Seki M (2016a) Transcriptomic analysis of soil-grown Arabidopsis thaliana roots and shoots in response to a drought stress. Front Plant Sci 7:180.  https://doi.org/10.3389/fpls.2016.00180 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Rasheed S, Bashir K, Nakaminami K, Hanada K, Matsui A, Seki M (2016b) Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots. Plant Signal Behav 11:e1215792.  https://doi.org/10.1080/15592324.2016.1215792 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Rasheed S, Bashir K, Kim J-M, Ando M, Tanaka M, Seki M (2018) The modulation of acetic acid pathway genes in Arabidopsis improves survival under drought stress. Sci Rep 8:7831.  https://doi.org/10.1038/s41598-018-26103-2 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Sengupta D, Naik D, Reddy AR (2015) Plant aldo-keto reductases (AKRs) as multi-tasking soldiers involved in diverse plant metabolic processes and stress defense: a structure-function update. J Plant Physiol 179:40–55.  https://doi.org/10.1016/j.jplph.2015.03.004 CrossRefPubMedGoogle Scholar
  19. Wang S, Callaway RM, Zhou DW, Weiner J (2017) Experience of inundation or drought alters the responses of plants to subsequent water conditions. J Ecol 105:176–187.  https://doi.org/10.1111/1365-2745.12649 CrossRefGoogle Scholar
  20. Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S (2014) SOAP denovo-trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30:1660–1666.  https://doi.org/10.1093/bioinformatics/btu077 CrossRefPubMedGoogle Scholar
  21. Yang P, Smalle J, Lee S, Yan N, Emborg TJ, Vierstra RD (2007) Ubiquitin C-terminal hydrolases 1 and 2 affect shoot architecture in Arabidopsis. The Plant J 51:441–457.  https://doi.org/10.1111/j.1365-313X.2007.03154.x CrossRefPubMedGoogle Scholar
  22. Yao D, Zhang X, Zhao X, Liu C, Wang C, Zhang Z, Zhang C, Wei Q, Wang Q, Yan H (2011) Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). Genomics 98:47–55.  https://doi.org/10.1016/j.ygeno.2011.04.007 CrossRefPubMedGoogle Scholar
  23. Zandalinas SI, Mittler R, Balfagón D, Arbona V, Gómez-Cadenas A (2017) Plant adaptations to the combination of drought and high temperatures. Physiol Plantarum 162:2–12.  https://doi.org/10.1111/ppl.12540 CrossRefGoogle Scholar
  24. Zhang X, Yao D, Wang Q, Xu W, Wei Q, Wang C, Liu C, Zhang C, Yan H, Ling Y (2013) mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. PLoS One 8:e54762.  https://doi.org/10.1371/journal.pone.0054762 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33:531–537.  https://doi.org/10.1038/nbt.3207 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Institute of Molecular Biology, Slovak Academy of Sciences 2019

Authors and Affiliations

  1. 1.Centre of Excellence in Molecular BiologyUniversity of the Punjab LahoreLahorePakistan
  2. 2.Plant Genomic Network Research TeamRIKEN Center for Sustainable Resource SciencesYokohamaJapan

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