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Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii

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Abstract

Background

Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement.

Materials and methods

In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors.

Results

A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance.

Conclusion

The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.

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References

  1. Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78:78004–78008

  2. Magwanga RO, Kirungu JN, Lu P et al (2019) Genome wide identification of the trihelix transcription factors and overexpression of Gh_A05G2067 (GT-2), a novel gene contributing to increased drought and salt stresses tolerance in cotton. Physiol Plant. https://doi.org/10.1111/ppl.12920

    Article  PubMed  PubMed Central  Google Scholar 

  3. Guo W, Cai C, Wang C et al (2008) A preliminary analysis of genome structure and composition in Gossypium hirsutum. BMC Genomics. https://doi.org/10.1186/1471-2164-9-314

    Article  PubMed  PubMed Central  Google Scholar 

  4. Yuan Y, Wang X, Wang L et al (2018) Genome-Wide association study identifies candidate genes related to seed oil composition and protein content in gossypium hirsutum l. Front Plant Sci. https://doi.org/10.3389/fpls.2018.01359

    Article  PubMed  PubMed Central  Google Scholar 

  5. Lipiec J, Doussan C, Nosalewicz A, Kondracka K (2013) Effect of drought and heat stresses on plant growth and yield: a review. Int Agrophys 27:463–477. https://doi.org/10.2478/intag-2013-0017

    Article  Google Scholar 

  6. Azhar MT, Rehman A (2018) Overview on effects of water stress on cotton plants and productivity In: Biochemical, physiological and molecular avenues for combating abiotic stress tolerance in plants. Elsevier, Amsterdam, pp 297–316

    Google Scholar 

  7. Magwanga RO, Lu P, Kirungu JN et al (2018) GBS mapping and analysis of genes conserved between gossypium tomentosum and gossypium hirsutum cotton cultivars that respond to drought stress at the seedling stage of the BC2F2 generation. Int J Mol Sci. https://doi.org/10.3390/ijms19061614

    Article  PubMed  PubMed Central  Google Scholar 

  8. Bourland F, Myers GO (2015) Conventional Cotton Breeding, 2nd edn. Wiley, New York. https://doi.org/10.2134/agronmonogr57.2013.0025

  9. Magwanga RO, Lu P, Kirungu JN et al (2018) Whole genome analysis of cyclin dependent kinase (CDK) gene family in cotton and functional evaluation of the role of CDKF4 gene in drought and salt stress tolerance in plants. Int J Mol Sci. https://doi.org/10.3390/ijms19092625

    Article  PubMed  PubMed Central  Google Scholar 

  10. Anjum S, Xie X, Wang L (2011) Morphological, physiological and biochemical responses of plants to drought stress. African J Agric Res 6:2026–2032. https://doi.org/10.5897/AJAR10.027

    Article  Google Scholar 

  11. Sourour A (2017) A review: morphological, physiological, biochemical and molecular plant responses to water deficit stress. Int J Eng Sci 6:1–4. https://doi.org/10.9790/1813-0601010104

    Article  Google Scholar 

  12. Molina-Bravo R, Zamora-Meléndez A (2016) QTLs for genetic improvement under global climate changes. Adv Plant Breed Strateg: Agron Abiotic Biotic Stress Traits 2:471–513. https://doi.org/10.1007/978-3-319-22518-0_13

    Article  Google Scholar 

  13. Zhao C, Piao S, Wang X et al (2016) Plausible rice yield losses under future climate warming. Nat Plants. https://doi.org/10.1038/nplants.2016.202

    Article  PubMed  Google Scholar 

  14. Ashraf M (2010) Inducing drought tolerance in plants: recent advances. Biotechnol Adv 28:169–183. https://doi.org/10.1016/j.biotechadv.2009.11.005

    Article  CAS  PubMed  Google Scholar 

  15. Amombo E, Li H, Fu J (2017) Research advances on tall fescue salt tolerance: from root signaling to molecular and metabolic adjustment. J Am Soc Hortic Sci 142:337–345. https://doi.org/10.21273/jashs04120-17

    Article  CAS  Google Scholar 

  16. Kahl G (2015) Next-next-next generation sequencing (next 3 generation sequencing, third-generation sequencing). In: The dictionary of genomics, transcriptomics and proteomics, 5th edn. Wiley, New York. https://doi.org/10.1002/9783527678679

  17. Bhau BS, Sharma DK, Bora M et al (2016) Molecular markers and crop improvement. Abiotic Stress Resp Plants 3:381–410

    Article  Google Scholar 

  18. Gill MB, Zeng F, Shabala L et al (2019) Identification of QTL related to ROS formation under hypoxia and their association with waterlogging and salt tolerance in Barley. Int J Mol Sci. https://doi.org/10.3390/ijms20030699

    Article  PubMed  PubMed Central  Google Scholar 

  19. Shim J, Mangat PK, Angeles-shim RB (2018) Natural variation in wild gossypium species as a tool to broaden the genetic base of cultivated cotton. J Plant Sci Curr Res. https://doi.org/10.24966/PSCR-3743/100005

    Article  Google Scholar 

  20. Kirungu JN, Deng Y, Cai X et al (2018) Simple sequence repeat (SSR) genetic linkage map of D genome diploid cotton derived from an interspecific cross between Gossypium davidsonii and Gossypium klotzschianum. Int J Mol Sci. https://doi.org/10.3390/ijms19010204

    Article  PubMed  PubMed Central  Google Scholar 

  21. Iseli C, Jongeneel C V, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings Int Conf Intell Syst Mol Biol 99:138–48

  22. Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. https://doi.org/10.1038/nmeth.1226

    Article  CAS  PubMed  Google Scholar 

  23. Karmirantzou M, Hamodrakas SJ (2002) A Web-based classification system of DNA-binding protein families. Protein Eng Des Sel 14:465–472. https://doi.org/10.1093/protein/14.7.465

    Article  Google Scholar 

  24. Tiirikka T, Siermala M, Vihinen M (2014) Clustering of gene ontology terms in genomes. Gene 550:155–164. https://doi.org/10.1016/j.gene.2014.06.060

    Article  CAS  PubMed  Google Scholar 

  25. Conesa A, Götz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. https://doi.org/10.1155/2008/619832

    Article  PubMed  Google Scholar 

  26. Magwanga RO, Lu P, Kirungu JN et al (2018) Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet. https://doi.org/10.1186/s12863-017-0596-1

    Article  PubMed  PubMed Central  Google Scholar 

  27. Lu P, Magwanga RO, Kirungu JN et al (2019) Overexpression of cotton a DTX/MATE gene enhances drought, salt, and cold stress tolerance in transgenic arabidopsis. Front Plant Sci. https://doi.org/10.3389/fpls.2019.00299

    Article  PubMed  PubMed Central  Google Scholar 

  28. Saed-Moucheshi A, Pakniyat H, Pirasteh-Anosheh H, Azooz MM (2014) Role of ROS as signaling molecules in plants. In: Oxidative damage to plants antioxidant networks and signaling. Elsevier, Amsterdam, pp 585–620. https://doi.org/10.1016/B978-0-12-799963-0.00020-4

    Book  Google Scholar 

  29. Tör M, Yemm A, Holub E (2003) The role of proteolysis in R gene mediated defence in plants. Mol Plant Pathol 4:287–296

    Article  PubMed  Google Scholar 

  30. Dhillon A, Sharma K, Rajulapati V, Goyal A (2016) Proteolytic enzymes. In: Current developments in biotechnology and bioengineering: production, isolation and purification of industrial products. Academic press, pp 149–173

  31. Klimyuk VI, Persello-Cartieaux F, Havaux M et al (2007) A Chromodomain protein encoded by the arabidopsis CAO gene is a plant-specific component of the chloroplast signal recognition particle pathway that is involved in LHCP targeting. Plant Cell 11:87. https://doi.org/10.2307/3870840

    Article  Google Scholar 

  32. Rabbani MA, Kyonoshin M, Hiroshi A, Muhammad AK, Koji K, Yusuke I, Kyoko Y, Motoaki S, Kazuo S, Kazuko YS (2003) Monitoring expression profiles of rice genes under cold, drought and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol. https://doi.org/10.1104/pp.103.025742

    Article  PubMed  PubMed Central  Google Scholar 

  33. Jingxia Z, Pei Z, Xuehan H, Yang G, Yu C, Zhangqiang S, Furong W, Jun Z (2021) Comparative phenotypic and transcriptomic analysis reveals key responses of upland cotton to salinity stress during post germination. Front Plant Sci. https://doi.org/10.3389/fpls.2021.639104

    Article  Google Scholar 

  34. Kundrátová K, Bartas M, Pečinka P, Hejna O, Rychlá A, Čurn V, Červeň J (2021) Transcriptomic and proteomic analysis of drought stress response in opium poppy plants during the first week of germination. Plants 10(9):1878. https://doi.org/10.3390/plants10091878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Lixia Q, Huanyang Z, Jing L, Yonghong Z, Gaili J, Chuangyun W, Shenjie W (2022) Down-regulation of GhADF1 in cotton (Gossypium hirsutum) improves plant drought tolerance and increases fiber yield. Crop J. https://doi.org/10.1016/j.cj.2021.12.012

    Article  Google Scholar 

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Acknowledgements

We wish to thank Sangon Biotech (Shanghai) Co., Ltd. for help in sequencing, analysis support and assembly. Authors are thankful to Shahbaz Khan (Pakistan) for inputs regarding manuscript formatting according the journal pattern.

Funding

This program was financially sponsored by National Key R&D Program of China (2021YFE0101200), “Tianshan” Innovation team program of the Xinjiang Uygur Autonomous Region (2021D14007), Hunan Natural Science Foundation Youth Fund (2020JJ5291), “Huxiang Young Talents Plan” Support Project of Hunan Province (2019RS2048), State Key Laboratory of Cotton Biology Open Fund (CB2021A14).

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Authors and Affiliations

  1. Research Base of Tarium, University of State Key Laboratory of Cotton Biology, Tarium University, Alar, 843300, Xinjiang, China

    Cuilian Xu

  2. Cotton Sciences Research Institute of Hunan/National Hybrid Cotton Research Promotion Center, Changde, 415101, Hunan, China

    Yujun Li, Zhengcheng Kuang & Haodong Chen

  3. State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China

    Muhammad Kashif Ilyas, Richard Odongo Magwanga, Hejun Lu, M Kashif Riaz Khan, Zhongli Zhou, Kunbo Wang, Fang Liu & Haodong Chen

  4. School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya

    Richard Odongo Magwanga

  5. Nuclear Institute for Agriculture & Biology (NIAB), Faisalabad, Pakistan

    M Kashif Riaz Khan

  6. National Agricultural Research Centre, Park Road, Islamabad, Pakistan

    Muhammad Kashif Ilyas, Asif Javaid, Danish Ibrar & Abdul Ghafoor

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  1. Cuilian Xu
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Contributions

HC, CX, MKI, ROM & FL designed the experiments. CX, HC, MKRK & HL conceived the experiments and analyzed the results. CX, HC, HL & MKRK carried out all computational analyses. KW, MKI, CX, ZZ, ZK, YL, FL, participated in part of experiments directly or indirectly contributed reagents/materials/analysis tools. HC, AG, DI, AJ, ROM, HL, MKRK, MKI, YL & FL drafted the manuscript and KW, AG, CX, ROM & FL proofread and ROM, MKI, DI & AG revised the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Cuilian Xu, Abdul Ghafoor or Haodong Chen.

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Conflict of Interest

The authors declare no conflict of interest.

Ethical approval

Authors declare that this study was conducted on wild cotton (Gossypium darwinii) crop, and no experimentations were conducted on human or animal subjects using research material during the current studies.

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Xu, C., Ilyas, M.K., Magwanga, R.O. et al. Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii. Mol Biol Rep 49, 11341–11350 (2022). https://doi.org/10.1007/s11033-022-07774-7

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