Scientific Papers

Utilizing transcriptomics and metabolomics to unravel key genes and metabolites of maize seedlings in response to drought stress | BMC Plant Biology


  • Lobell DB, Roberts MJ, Schlenker W, Braun N, Little BB, Rejesus RM, Hammer GL. Greater sensitivity to drought accompanies maize yield increase in the U.S. Midwest. Science. 2014;344(6183):516–9. https://doi.org/10.1126/science.1251423.

    Article 
    CAS 

    Google Scholar
     

  • Boretti A, Rosa L. Reassessing the projections of the world water development report. NPJ Clean Water. 2019;2(1):15. https://doi.org/10.1038/s41545-019-0039-9.

    Article 

    Google Scholar
     

  • de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science. 2020;368(6488):270–4. https://doi.org/10.1126/science.aaz5192.

    Article 
    CAS 

    Google Scholar
     

  • Zhu D, Chang Y, Pei T, Zhang X, Liu L, Li Y, Zhuang J, Yang H, Qin F, Song C, Ren D. MAPK-like protein 1 positively regulates maize seedling drought sensitivity by suppressing ABA biosynthesis. Plant J. 2020;102(4):747–60. https://doi.org/10.1111/tpj.14660.

    Article 
    CAS 

    Google Scholar
     

  • Liu S, Wang X, Wang H, Xin H, Yang X, Yan J, Li J, Tran LS, Shinozaki K, Yamaguchi-Shinozaki K, Qin F. Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L. PLoS Genet. 2013;9(9):e1003790. https://doi.org/10.1371/journal.pgen.1003790.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Mao H, Wang H, Liu S, Li Z, Yang X, Yan J, Li J, Tran LS, Qin F. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nat Commun. 2015;6(1):8326. https://doi.org/10.1038/ncomms9326.

    Article 
    CAS 

    Google Scholar
     

  • Wang X, Wang H, Liu S, Ferjani A, Li J, Yan J, Yang X, Qin F. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat Genet. 2016;48(10):1233–41. https://doi.org/10.1038/ng.3636.

    Article 
    CAS 

    Google Scholar
     

  • Afonso V, Champy R, Mitrovic D, Collin P, Lomri A. Reactive oxygen species and superoxide dismutases: role in joint Diseases. Jt Bone Spine. 2007;74(4):324–9. https://doi.org/10.1016/j.jbspin.2007.02.002.

    Article 
    CAS 

    Google Scholar
     

  • Gill SS, Tuteja N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem. 2010;48(12):909–30. https://doi.org/10.1016/j.plaphy.2010.08.016.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Zhou J, Tian L, Wang S, Li H, Zhao Y, Zhang M, Wang X, An P, Li C. Ovary abortion induced by combined waterlogging and shading stress at the flowering stage involves amino acids and flavonoid metabolism in maize. Front Plant Sci. 2021;12:778717. https://doi.org/10.3389/fpls.2021.778717.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Miller GA, Suzuki N, Ciftci-Yilmaz SU, Mittler RO. Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ. 2010;33(4):453–67. https://doi.org/10.1016/j.jbspin.2007.02.002.

    Article 
    CAS 

    Google Scholar
     

  • Nephali L, Moodley V, Piater L, Steenkamp P, Buthelezi N, Dubery I, Burgess K, Huyser J, Tugizimana F. A metabolomic landscape of maize plants treated with a microbial biostimulant under well-watered and drought conditions. Front Plant Sci. 2021;12:676632. https://doi.org/10.3389/fpls.2021.676632.

    Article 
    PubMed Central 

    Google Scholar
     

  • Sicher RC, Barnaby JY. Impact of carbon dioxide enrichment on the responses of maize leaf transcripts and metabolites to water stress. Physiol Plant. 2012;144(3):238–53. https://doi.org/10.1111/j.1399-3054.2011.01555.x.

    Article 
    CAS 

    Google Scholar
     

  • Obata T, Witt S, Lisec J, Palacios-Rojas N, Florez-Sarasa I, Yousfi S, Araus JL, Cairns JE, Fernie AR. Metabolite profiles of maize leaves in drought, heat, and combined stress field trials reveal the relationship between metabolism and grain yield. Plant Physiol. 2015;169(4):2665–83. https://doi.org/10.1104/pp.15.01164.

    Article 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Miao Y, Xu L, He X, Zhang L, Shaban M, Zhang X, Zhu L. Suppression of tryptophan synthase activates cotton immunity by triggering cell death via promoting SA synthesis. Plant J. 2019;98(2):329–45. https://doi.org/10.1111/tpj.14222.

    Article 
    CAS 

    Google Scholar
     

  • Dubouzet JG, Matsuda F, Ishihara A, Miyagawa H, Wakasa K. Production of indole alkaloids by metabolic engineering of the tryptophan pathway in rice. Plant Biotechnol J. 2013;11(9):1103–11. https://doi.org/10.1111/pbi.12105.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Stahl E, Bellwon P, Huber S, Schlaeppi K, Bernsdorff F, Vallat-Michel A, Mauch F, Zeier J. Regulatory and functional aspects of indolic metabolism in plant systemic acquired resistance. Mol Plant. 2016;9(5):662–81. https://doi.org/10.1016/j.molp.2016.01.005.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Prasad PV, Pisipati SR, Momčilović I, Ristic Z. Independent and combined effects of hightemperature and drought stress during grain filling on plant yield and chloroplast EF-Tu expression in spring wheat. J Agron Crop Sci. 2011;197(6):430–41. https://doi.org/10.1111/j.1439-037X.2011.00477.x.

    Article 
    CAS 

    Google Scholar
     

  • Guo Q, Li X, Niu L, Jameson PE, Zhou W. Transcription-associated metabolomic adjustments in maize occur during combined drought and cold stress. Plant Physiol. 2021;186(1):677–95. https://doi.org/10.1093/plphys/kiab050.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2023;51(1):587–92. https://doi.org/10.1093/nar/gkac963.

    Article 
    CAS 

    Google Scholar
     

  • Want EJ, Masson P, Michopoulos F, Wilson ID, Theodoridis G, Plumb RS, Shockcor J, Loftus N, Holmes E, Nicholson JK. Global metabolic profiling of animal and human tissues via UPLC-MS. Nat Protoc. 2013;8(1):17–32. https://doi.org/10.1038/nprot.2012.135.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Xu G, Li L, Zhou J, Lyu D, Zhao D, Qin S. Comparison of transcriptome and metabolome analysis revealed differences in cold resistant metabolic pathways in different apple cultivars under low temperature stress. Hortic. Plant J. 2022;12(1):1–11. https://doi.org/10.1016/j.hpj.2022.09.002.

    Article 
    CAS 

    Google Scholar
     

  • Stacklies W, Redestig H, Scholz M, Walther D, Selbig J. pcaMethods-a bioconductor package providing PCA methods for incomplete data. Bioinformatics. 2007;23(9):1164–7. https://doi.org/10.1093/bioinformatics/btm069.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Chen W, Gao Y, Xie W, Gong L, Lu K, Wang W, et al. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet. 2014;46(7):714–21. https://doi.org/10.1038/ng.3007.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Zhang F, Wu J, Sade N, Wu S, Egbaria A, Fernie AR, Yan J, Qin F, Chen W, Brotman Y, Dai M. Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biol. 2021;22(1):1–26. https://doi.org/10.1186/s13059-021-02481-1.

    Article 
    CAS 

    Google Scholar
     

  • Xiang Y, Sun X, Gao S, Qin F, Dai M. Deletion of an endoplasmic reticulum stress response element in a ZmPP2C-A gene facilitates drought tolerance of maize seedlings. Mol Plant. 2017;10(3):456–69. https://doi.org/10.1016/j.molp.2016.1.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Yamada M, Morishita H, Urano K, Shiozaki N, Yamaguchi-Shinozaki K, Shinozaki K, Yoshiba Y. Effects of free proline accumulation in petunias under drought stress. J Exp Bot. 2005;56(417):1975–81. https://doi.org/10.1093/jxb/eri195.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Larrainzar E, Molenaar JA, Wienkoop S, GIL-QUINTANA ER, Alibert B, Limami AM, ARRESE‐IGOR CE, Gonzalez EM. Drought stress provokes the down‐regulation of methionine and ethylene biosynthesis pathways in Medicago truncatula roots and nodules. Plant Cell Environ. 2014;37(9):2051–63. https://doi.org/10.1111/pce.12285.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Ding P, Fang L, Wang G, Li X, Huang S, Gao Y, Zhu J, Xiao L, Tong J, Chen F, Xia G. Wheat methionine sulfoxide reductase A4. 1 interacts with heme oxygenase 1 to enhance seedling tolerance to salinity or drought stress. Plant Mol Biol. 2019;101:203–20. https://doi.org/10.1371/journal.pone.0259585.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Tzin V, Galili G. New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Mol Plant. 2010;3(6):956–72. https://doi.org/10.1093/mp/ssq048.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Filiz E, Cetin D, Akbudak MA. Aromatic amino acids biosynthesis genes identification and expression analysis under salt and drought stresses in Solanum lycopersicum L. Sci Hortic. 2019;250:127–37. https://doi.org/10.1016/j.scienta.2019.02.044.

    Article 
    CAS 

    Google Scholar
     

  • Khakdan F, Alizadeh H, Ranjbar M. Molecular cloning, functional characterization and expression of a drought inducible phenylalanine ammonia-lyase gene (ObPAL) from Ocimum basilicum L. Plant Physiol. Biochem. 2018;130:464–72. https://doi.org/10.1016/j.plaphy.2018.07.026.

    Article 
    CAS 

    Google Scholar
     

  • Yang X, Zhu X, Wei J, Li W, Wang H, Xu Y, Yang Z, Xu C, Li P. Primary root response to combined drought and heat stress is regulated via salicylic acid metabolism in maize. BMC Plant Biol. 2022;22(1):417. https://doi.org/10.1186/s12870-022-03805-4.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Fàbregas N, Fernie AR. The metabolic response to drought. J Exp Bot. 2019;70(4):1077–85. https://doi.org/10.1093/jxb/ery437.

    Article 
    CAS 

    Google Scholar
     

  • Cheol Park H, Cha JY, Yun DJ. Roles of YUCCAs in auxin biosynthesis and drought stress responses in plants. Plant Signal Behav. 2013;8(6):e24495. https://doi.org/10.4161/psb.24495.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Cao X, Yang H, Shang C, Ma S, Liu L, Cheng J. The roles of auxin biosynthesis YUCCA gene family in plants. Int J Mol Sci. 2019;20:6343. https://doi.org/10.3390/ijms20246343.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Zheng Z, Wang B, Zhuo C, Xie Y, Zhang X, Liu Y, Zhang G, Ding H, Zhao B, Tian M, Xu M. Local Auxin Biosynthesis regulates Brace Root Angle and Lodging Resistance in Maize. New Phytol. 2023;238(1):142–54. https://doi.org/10.1111/nph.18733.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Cha JY, Kim WY, Kang SB, Kim JI, Baek D, Jung IJ, Kim MR, Li N, Kim HJ, Nakajima M, Asami T. (2015). A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis. Nat Commun 2015;6(1):1–13. https://doi.org/10.1038/ncomms9041.

  • Fiore A, Murray PJ. Tryptophan and indole metabolism in immune regulation. Curr Opin Immunol. 2021;70:7–14. https://doi.org/10.1016/j.coi.2020.12.001.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Zhou S, Kremling KA, Bandillo N, Richter A, Zhang YK, Ahern KR, Artyukhin AB, Hui JX, Younkin GC, Schroeder FC, Buckler ES. Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites. Plant Cell. 2019;31(5):937–55. https://doi.org/10.1105/tpc.18.00772.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Wen W, Li D, Li X, Gao Y, Li W, Li H, Liu J, Liu H, Chen W, Luo J, Yan J. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun. 2014;5(1):3438. https://doi.org/10.1038/ncomms4438.

    Article 
    CAS 

    Google Scholar
     

  • Zhu G, Wang S, Huang Z, Zhang S, Liao Q, Zhang C, Lin T, Qin M, Peng M, Yang C, Cao X. Rewiring of the fruit metabolome in tomato breeding. Cell. 2018;172(1–2):249–61. https://doi.org/10.1016/j.cell.2017.12.019.

    Article 
    CAS 

    Google Scholar
     

  • Xu Z, Xin T, Bartels D, Li Y, Gu W, Yao H, Liu S, Yu H, Pu X, Zhou J, Xu J, Xi C, Lei H, Song J, Chen S. Genome analysis of the ancient tracheophyte Selaginella tamariscina reveals evolutionary features relevant to the acquisition of desiccation tolerance. Mol Plant. 2018;11:983–94. https://doi.org/10.1016/j.molp.2018.05.003.

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Identification of resurrection genes from the transcriptome of dehydrated and rehydrated. Selaginella tamariscina. Plant Signal Behav. 2021;16(12):e111751. https://doi.org/10.1080/15592324.2021.1973703.

    Article 
    CAS 

    Google Scholar
     

  • VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nat Commun. 2018;9(1):13. https://doi.org/10.1038/s41467-017-02546-5.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Less H, Galili G. Principal transcriptional programs regulating plant amino acid metabolism in response to abiotic stresses. Plant Physiol. 2008;147(1):316–30. https://doi.org/10.1104/pp.108.115733.

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     



  • Source link