Transcriptome sequencing of garlic reveals key genes related to the heat stress response.
Allium sativum L.
Gene expression
Heat stress
RNA-seq
Transcript profiles
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
10 Jul 2024
10 Jul 2024
Historique:
received:
23
01
2024
accepted:
03
07
2024
medline:
11
7
2024
pubmed:
11
7
2024
entrez:
10
7
2024
Statut:
epublish
Résumé
With global warming, heat stress has become an important factor that seriously affects crop yield and quality. Therefore, understanding plant responses to heat stress is important for agricultural practice, but the molecular mechanism of high-temperature tolerance in garlic remains unclear. In this study, 'Xusuan No. 6' was used as the experimental material. After heat stress for 0 (CK), 2 and 24 h, transcriptome sequencing was used to screen metabolic pathways and differentially expressed genes (DEGs) closely related to heat stress and was further verified by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 86,110 unigenes obtained from the raw transcriptome sequencing data were spliced. After 2 h of heat treatment, the expression levels of 8898 genes increased, and 3829 genes were decreased in leaves. After 24 h, the expression levels of 7167 genes were upregulated, and 3176 genes were downregulated. Gene Ontology enrichment analysis showed that DEGs were mainly enriched in seven categories: cellular processes, metabolic processes, binging, catalytic activity, cellular anatomical entity and protein-containing complex response to stimulus. Kyoto Encyclopedia of Genes and Genomes pathway enrichment showed that DEGs are involved in protein processing in the endoplasmic reticulum, plant hormone signal transduction, phenylpropanoid biosynthesis, and photosynthetic antenna proteins. Six genes were selected and further verified by qRT-PCR. In this study, the full-length transcriptome of garlic was constructed, and the regulatory genes related to the heat resistance of garlic were studied. Taken together, these findings can provide a theoretical basis for the cloning of heat resistance genes in garlic and for the analysis of heat resistance mechanisms.
Identifiants
pubmed: 38987349
doi: 10.1038/s41598-024-66786-4
pii: 10.1038/s41598-024-66786-4
doi:
Substances chimiques
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
15956Subventions
Organisme : China Agriculture Research System
ID : CARS-24-A-07
Organisme : Xuzhou science and technology project
ID : KC22452
Informations de copyright
© 2024. The Author(s).
Références
Ma, K.-H. et al. Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.). Sci. Hortic. 122, 355–361 (2009).
doi: 10.1016/j.scienta.2009.06.010
Martins, N., Petropoulos, S. & Ferreira, I. C. Chemical composition and bioactive compounds of garlic (Allium sativum L.) as affected by pre-and post-harvest conditions: A review. Food Chem. 211, 41–50 (2016).
pubmed: 27283605
doi: 10.1016/j.foodchem.2016.05.029
Bano, C., Amist, N. & Singh, N. Role of polyamines in plants abiotic stress tolerance: Advances and future prospects. In Plant Life Under Changing Environment 481–496 (2020).
Sabina, A. & Sameena, C. Plant growth and stomatal responses of potato cultivars under high temperature stress. Indian J. Agric. Res. 56, 18–21 (2022).
Wahid, A., Gelani, S., Ashraf, M. & Foolad, M. R. Heat tolerance in plants: an overview. Environ. Exp. Bot. 61, 199–223 (2007).
doi: 10.1016/j.envexpbot.2007.05.011
Zhou, J. et al. A non-canonical role of ATG8 in Golgi recovery from heat stress in plants. Nat. Plants 9, 749–765 (2023).
pubmed: 37081290
doi: 10.1038/s41477-023-01398-w
Guo, M. et al. The plant heat stress transcription factors (HSFs): Structure, regulation, and function in response to abiotic stresses. Front. Plant Sci. 7, 114 (2016).
pubmed: 26904076
pmcid: 4746267
doi: 10.3389/fpls.2016.00114
Li, J. Y., Yang, C., Xu, J., Lu, H. P. & Liu, J. X. The hot science in rice research: How rice plants cope with heat stress. Plant Cell Environ. 46, 1087–1103 (2023).
pubmed: 36478590
doi: 10.1111/pce.14509
Lin, S. et al. Integrative analysis of transcriptome and metabolome reveals salt stress orchestrating the accumulation of specialized metabolites in Lycium barbarum L. fruit. Int. J. Mol. Sci. 22, 4414 (2021).
pubmed: 33922536
pmcid: 8122869
doi: 10.3390/ijms22094414
Xu, Z., Song, N., Ma, L. & Wu, J. IRE1-bZIP60 pathway is required for Nicotiana attenuata resistance to fungal pathogen Alternaria alternata. Front. Plant Sci. 10, 263 (2019).
pubmed: 30941151
pmcid: 6434776
doi: 10.3389/fpls.2019.00263
Gao, J., Wang, M.-J., Wang, J.-J., Lu, H.-P. & Liu, J.-X. bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis. Abiotech 1–11 (2022).
Larkindale, J. & Huang, B. Effects of abscisic acid, salicylic acid, ethylene and hydrogen peroxide in thermotolerance and recovery for creeping bentgrass. Plant Growth Regul. 47, 17–28 (2005).
doi: 10.1007/s10725-005-1536-z
Pawar, G. et al. Effect of abiotic stress on plant growth and development, physiological and breeding strategies to overcome stress condition. Int. J. Plant Environ. 8, 1–9 (2022).
doi: 10.18811/ijpen.v8i03.01
Wang, Q., Yu, F. & Xie, Q. Balancing growth and adaptation to stress: Crosstalk between brassinosteroid and abscisic acid signaling. Plant, Cell & Environment 43, 2325–2335 (2020).
doi: 10.1111/pce.13846
Shi, Q., Bao, Z., Zhu, Z., Ying, Q. & Qian, Q. Effects of different treatments of salicylic acid on heat tolerance, chlorophyll fluorescence, and antioxidant enzyme activity in seedlings of Cucumis sativa L. Plant Growth Regul. 48, 127–135 (2006).
doi: 10.1007/s10725-005-5482-6
Tian, X. et al. Heat shock transcription factor A1b regulates heat tolerance in wheat and Arabidopsis through OPR3 and jasmonate signalling pathway. Plant Biotechnol. J. 18, 1109 (2020).
pubmed: 31559685
doi: 10.1111/pbi.13268
Li, H. et al. Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination. Sci. Rep. 11, 19345 (2021).
pubmed: 34588562
pmcid: 8481303
doi: 10.1038/s41598-021-98907-8
Liu, R. et al. Transcriptome analysis reveals key genes involved in the eggplant response to high-temperature stress. Environ. Exp. Bot. 211, 105369 (2023).
doi: 10.1016/j.envexpbot.2023.105369
Zhao, N. et al. Transcriptome and co-expression network analyses reveal differential gene expression and pathways in response to severe drought stress in peanut (Arachis hypogaea L.). Front. Genet. 12, 672884 (2021).
pubmed: 33995498
pmcid: 8120245
doi: 10.3389/fgene.2021.672884
Wang, G.-L. et al. Transcript profiling reveals an important role of cell wall remodeling and hormone signaling under salt stress in garlic. Plant Physiol. Biochem. 135, 87–98 (2019).
pubmed: 30529171
doi: 10.1016/j.plaphy.2018.11.033
Zhou, Y. et al. TCP transcription factors associate with PHYTOCHROME INTERACTING FACTOR 4 and CRYPTOCHROME 1 to regulate thermomorphogenesis in Arabidopsis thaliana. Iscience 15, 600–610 (2019).
pubmed: 31078553
pmcid: 6547012
doi: 10.1016/j.isci.2019.04.002
Chen, Y. et al. Integrative analysis of transcriptome and yeast screening system identified heat stress-responding genes in ryegrass. Environ. Exp. Bot. 210, 105333 (2023).
doi: 10.1016/j.envexpbot.2023.105333
Zhang, Y., Li, Y., Han, B., Liu, A. & Xu, W. Integrated lipidomic and transcriptomic analysis reveals triacylglycerol accumulation in castor bean seedlings under heat stress. Ind. Crops Prod. 180, 114702 (2022).
doi: 10.1016/j.indcrop.2022.114702
Cheng, B. et al. A Trifolium repens flavodoxin-like quinone reductase 1 (TrFQR1) improves plant adaptability to high temperature associated with oxidative h/stasis and lipids remodeling. Plant J. 115, 369–385 (2023).
pubmed: 37009644
doi: 10.1111/tpj.16230
Terrón-Camero, L. C. et al. Gene network downstream plant stress response modulated by peroxisomal H
pubmed: 36082297
pmcid: 9445673
doi: 10.3389/fpls.2022.930721
Sandhu, J. et al. Endoplasmicreticulum stress pathway mediates the early heat stress response of developing riceseeds. Plant Cell Environ. 8, 2604–2624 (2021).
doi: 10.1111/pce.14103
Lu, D. P. & Christopher, D. A. Light enhances the unfolded protein response as measured by BiP2 gene expression and the secretory GFP-2SC marker in Arabidopsis. Physiol. Plant. 134, 360–368 (2008).
pubmed: 18494858
doi: 10.1111/j.1399-3054.2008.01133.x
Wakasa, Y. et al. Expression of ER quality control-related genes in response to changes in BiP1 levels in developing rice endosperm. Plant J. 65, 675–689 (2011).
pubmed: 21223397
doi: 10.1111/j.1365-313X.2010.04453.x
Sandhu, J. et al. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds. Plant Cell Environ. 44, 2604–2624 (2021).
pubmed: 34036580
doi: 10.1111/pce.14103
Lin, S. et al. Rice HEAT SHOCK PROTEIN60–3B maintains male fertility under high temperature by starch granule biogenesis. Plant Physiol. 192, 2301–2317 (2023).
pubmed: 36861636
pmcid: 10315285
doi: 10.1093/plphys/kiad136
Song, N.-H. & Ahn, Y.-J. DcHsp17. 7, a small heat shock protein in carrot, is tissue-specifically expressed under salt stress and confers tolerance to salinity. New Biotechnol. 28, 698–704 (2011).
doi: 10.1016/j.nbt.2011.04.002
Qin, F., Yu, B. & Li, W. Heat shock protein 101 (HSP101) promotes flowering under nonstress conditions. Plant Physiol. 186, 407–419 (2021).
pubmed: 33561259
pmcid: 8154077
doi: 10.1093/plphys/kiab052
Xie, H. et al. Combined transcriptomic and metabolomic analyses of high temperature stress response of quinoa seedlings. BMC Plant Biol. 23, 1 (2023).
doi: 10.1186/s12870-023-04310-y
Dale, M. The Role of Phytohormones in Controlling Heat Stress Responses During Wheat Anther Development (University of Nottingham, 2021).
He, J.-D., Li, J.-L. & Wu, Q.-S. Effects of Rhizoglomus intraradices on plant growth and root endogenous hormones of trifoliate orange under salt stress. J. Anim. Plant Sci. 29, 245–250 (2019).
Lv, X. et al. The role of calcium-dependent protein kinase in hydrogen peroxide, nitric oxide and ABA-dependent cold acclimation. J. Exp. Bot. 69, 4127–4139 (2018).
pubmed: 29868714
pmcid: 6054180
doi: 10.1093/jxb/ery212
Kim, J. B., Kang, J. Y. & Kim, S. Y. Over-expression of a transcription factor regulating ABA-responsive gene expression confers multiple stress tolerance. Plant Biotechnol. J. 2, 459–466 (2004).
pubmed: 17168892
doi: 10.1111/j.1467-7652.2004.00090.x
Leyser, O. Auxin signaling. Plant Physiol. 176, 465–479 (2018).
pubmed: 28818861
doi: 10.1104/pp.17.00765
Chen, D. et al. Expression and distribution of the auxin response factors in Sorghum bicolor during development and temperature stress. Int. J. Mol. Sci. 20, 4816 (2019).
pubmed: 31569745
pmcid: 6801764
doi: 10.3390/ijms20194816
Yu, B. et al. Heat stress resistance mechanisms of two cucumber varieties from different regions. Int. J. Mol. Sci. 23, 1817 (2022).
pubmed: 35163740
pmcid: 8837171
doi: 10.3390/ijms23031817
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
pubmed: 30423086
pmcid: 6129281
doi: 10.1093/bioinformatics/bty560
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
doi: 10.1186/s13059-014-0550-8
Ashburner, M. et al. Gene ontology: Tool for the unification of Biology. Nature Genet. 25, 25–29 (2000).
pubmed: 10802651
doi: 10.1038/75556
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
pubmed: 10592173
pmcid: 102409
doi: 10.1093/nar/28.1.27
Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45–e45 (2001).
pubmed: 11328886
pmcid: 55695
doi: 10.1093/nar/29.9.e45