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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


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.


Cotton Drought Oligonucleotide microarray Gene expression 


G. arboreum

Gossypium arboreum

G. hirsutum

Gossypium hirsutum


Expression sequence tags


Alcohol dehydrogenases


pyruvate dehydrogenase


Abscisic acid


Gene Ontology



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.


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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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