ترنسکریپتومیکس: رویکردی با کارایی بالا در مطالعه واکنش گیاهان به تنش‌های غیر زیستی

Agarwal, P., Arora, R., Ray, S., Singh, A. K., Singh, V. P., Takatsuji, H., Kapoor, S., & Tyagi, A. K. 2007. Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Molecular Biology, 65(4): 467–485. https://doi.org//10.1007/s11103-007-9199-y

Aguayo, P., Lagos, C., Conejera, D., Medina, D., Fernandez, M., & Valenzuela, S. 2019. Transcriptome-wide identification of WRKY family genes and their expression under cold acclimation in Eucalyptus globulus. Trees (Berl), 33(10): 1313–1327. https://doi: 10.1007/s00468-019-01860-3

Akbudak, M., Filiz, E., & Kontbay, K. 2018. DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum (Sorghum bicolor): Genome-wide identification, characterization and expression profiles under cadmium and salt stresses. 3 Biotech, 8: 426. https://doi:  10.1007/s13205-018-1454-1

Anderson, J. T., & Mitchell-Olds, T. 2011. Ecological genetics and genomics of plant defenses: Evidence and approaches. Functional Ecology, 25(2): 312–324. https://doi.org/10.1111/j.1365-2435.2010.01785.x

Andrási, N., Pettkó-Szandtner, A., & Szabados, L. 2021. Diversity of plant heat shock factors: Regulation, interactions, and functions. Journal of Experimental Botany, 72(5): 1558–1575. https://doi.org/10.1093/jxb/eraa576

Ankit, A., Singh, A., Kumar, S., & Singh, A. 2023. Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K+) deficiency response in two contrasting chickpea cultivars. Frontiers in Plant Science, 13: 1054821. https://doi.org/10.3389/fpls.2022.1054821

Arora, R., Agarwal, D., Singh, A. K., Singh, V. P., Tyagi, A. K., & Kapoor, S. 2007. MADS-box gene family in rice: Genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics, 8(1): 242. https://doi.org/10.1186/1471-2164-8-242

Athanasopoulou, K., Boti, M. A., Adamopoulos, P. G., Skourou, P. C., & Scorilas, A. 2021. Third-generation sequencing: The spearhead towards the radical transformation of modern genomics. Life, 12: 30. https://doi.org/10.3390/life12010030

Bayer, P.E., Golicz, A.A., Scheben, A., Batley, J. and Edwards, D. 2020. Plant pan-genomes are the new reference. Nature Plants, 6(8): 914-920. https://doi.org/10.1038/s41477-020-0733-0

Bi, C., Yu, Y., Dong, C., Yang, Y., Zhai, Y., Du, F., Xia, C., Ni, Z., Kong, X., & Zhang, L. 2021. The bZIP transcription factor TabZIP15 improves salt stress tolerance in wheat. Plant Biotechnology Journal, 19(2): 209. https://doi.org/10.1111/pbi.13453

Carrera, F. P., Noceda, C., Maridueña-Zavala, M. G., & Cevallos-Cevallos, J. M. 2021. Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress. Agronomy, 11(5): 824. https://doi.org/10.3390/agronomy11050824

Challam, C., Nandhakumar, N., & Kardile, H. B. 2019. Advances in crop improvement: Use of miRNA technologies for crop improvement. OMICS-Based Approaches in Plant Biotechnology, 55–74. https://doi.org/10.3389/fpls.2015.00208

Chandran, A. K. N., Kim, J. W., Yoo, Y. H., Park, H. Y., Kim, Y. J., Cho, M. H., & Jung, K. H. 2019. Transcriptome analysis of rice-seedling roots under soil-salt stress using RNA-Seq method. Plant Biotechnology Reports, 13(6): 567–578. https://doi.org/10.10077/s11816-019-00550-3

Chauhan, H., Khurana, N., Agarwal, P., & Khurana, P. 2011. Heat shock factors in rice (Oryza sativa L.): Genome-wide expression analysis during reproductive development and abiotic stress. Molecular Genetics and Genomics, 286(2): 171–187. https://doi.org/10.1007/s00438-011-0638-8

Chen, K., Song, M., Guo, Y., Liu, L., Xuo, H., Dai, H., & Zhang, Z. 2019. MdMYB46 could enhance salt and osmotic stress tolerance in apple by directly activating stress-responsive signals. Plant Biotechnology Journal, 17(12): 2341–2355. https://doi.org/10.1111/pbi.13151

Chen, Y., Li, C., Zhang, B., Yi, J., Yang, Y., Kong, C., Lei, C., & Gong, M. 2019. The role of the late embryogenesis-abundant (LEA) protein family in development and the abiotic stress response: A comprehensive expression analysis of potato (Solanum Tuberosum). Genes, 10(2): 148. https://doi.org/10.3390/genes10020148

Cheng, Z., Lei, N., Li, S., Liao, W., Shen, J., & Peng, M. 2019. The regulatory effects of MeTCP4 on cold stress tolerance in Arabidopsis thaliana: a transcriptome analysis. Plant Physiology Biochemistry, 138: 9–16. https://doi.org/10.1016/j.plaphy.2019.02.015

Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., & Mortazavi, A. 2016. A survey of best practices for RNA-seq data analysis. Genome biology, 17, 13. https://doi.org/10.1186/s13059-016-0881-8

 Dai, X., Zhuang, Z., Boschiero, C., Dong, Y., & Zhao, P. X. 2021. Legume IP V3: From models to crops—An integrative gene discovery platform for translational genomics in legumes. Nucleic Acids Research, 49: D1472–D1479. https://doi.org/10.1093/nar/gkaa976

Dash, S., Van Hemert, J., Hong, L., Wise, R. P. & Dickerson, J. A. 2012. PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Research, 40: D1194–D1201. https://doi.org/10.1093/nar/gkr938

de Abreu, A.R., Ibrahim, J., Lemonidis, V. et al. 2025. Comparison of current methods for genome-wide DNA methylation profiling. Epigenetics & Chromatin, 18: 57. https://doi.org/10.1186/s13072-025-00616-3

Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. 2012. Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant cell, 24(3): 893–914. https://doi.org/10.1105/tpc.112.096180

El-Esawi, M. A., Al-Ghamdi, A. A., Ali, H. M., & Ahmad, M. 2019. Overexpression of AtWRKY30 transcription factor enhances heat and drought stress tolerance in wheat (Triticum aestivum L.). Genes, 10(2): 163. https://doi.org/10.3390/genes10020163

FAO. 2022. The future of food and agriculture – Drivers and triggers for transformation. The Future of Food and Agriculture, no. 3. Rome. https://doi.org/10.4060/cc0959en

Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Z., Catala, C., Giovannoni, J. J., Rose, J. K. C., & Mueller, L. A. 2017. The tomato expression atlas. Bioinformatics, 33(15): 2397–2398. https://doi.org/10.1093/bioinformatics/btx190

Fu, X., Lu, Z., Wei, H., Zhang, J., Yang, X., Wu, A., Ma, L., Kang, M., Lu, J., & Wang, H. 2020. Genome-wide identification and expression analysis of the NHX (sodium/hydrogen antiporter) gene family in cotton. Frontiers in Genetics, 18(11): 964. https://doi.org/10.3389/fgene.2020.00964

García-Ruiz, S., Gil-Martínez, A. L., Cisterna, A., Jurado-Ruiz, F., Reynolds, R. H., Cookson, M. R., Hardy, J., Ryten, M., & Botía, J. A. 2021. CoExp: A web tool for the exploitation of co-expression networks. Frontiers in Genetics, 12: 630187. https://doi.org/10.3389/fgene.2021.630187

Grant, D., Nelson, R. T., Cannon, S. B., & Shoemaker, R. C. 2009. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research, 38: D843–D846. https://doi.org/10.1093/nar/gkp798

Guo, H., Mao, M., Deng, Y., Sun, L., Chen, R., Cao, P., Lai, J., Zhang, Y., Wang, C., Li, C., Li, Y., Bai, Q., Ta, T., Yang, J., & Wang, S. 2022. Multi-omics analysis reveals that SlERF.D6 synergistically regulates SGAs and fruit development. Frontiers in Plant Science, 13: 860577. https://doi.org/10.3389/fpls.2022.860577

Guo, Z. H., Liu, C. X., Xiao, W., Wang, R., Zhang, L., Guan, S., Zhang, S., Cai, L., Liu, H., Huang, X., Guo, J., Zhou, X., Du, X., Pan, G., & Chen, Z. 2019. Comparative transcriptome profile analysis of anther development in reproductive stage of rice in cold region under cold stress. Plant Molecular Biology Reporter, 37(03): 129–145. https://doi.org/10.1007/s11105-019-01137-6

Gupta, A., & Shaw, B. P. 2020. Biochemical and molecular characterisations of salt tolerance components in rice varieties tolerant and sensitive to NaCl: The relevance of Na+ exclusion in salt tolerance in the species. Functional Plant Biology, 48(1): 72–87. https://doi.org/10.1071/FP20089

Hamada, K., Hongo, K., Suwabe, K., Shimizu, A., Nagayama, T., Abe, R., Kikuchi, S., Yamamoto, N., Fujii, T., Yokoyama, K., Tsuchida, H., Sano, K., Matsuoka, M., Kurata, N., & Yano, K. 2011. Oryza Express: An integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiology, 52(2): 220–229. https://doi.org/10.1093/pcp/pcq195

Hrdlickova, R., Toloue, M., & Tian, B. 2017. RNA-Seq methods for transcriptome analysis. WIREs RNA, 8: e1364. https://doi.org/10.1002/wrna.1364

Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W., & Zimmermann, P. 2008. Genevestigator V3: A reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics, 2008: 420747. https://doi.org/10.1155/2008/420747

Hu, J., Zhou, J., Peng, X., Xu, H., Liu, C., Du, B., Yuan, H., Zhu, L., & He, G. 2011. The Bphi008a gene interacts with the ethylene pathway and transcriptionally regulates MAPK genes in the response of rice to brown planthopper feeding. Plant Physiology, 156: 856–872. https://doi.org/10.1104/pp.111.174334

Huang, L., Kuang, L., Li, X., Wu, L., Wu, D., & Zhang, G. 2018. Metabolomic and transcriptomic analyses reveal the reasons why Hordeum marinum has higher salt tolerance than Hordeum vulgare. Environmental and Experimental Botany, 156: 48–61. https://doi.org/10.1016/j.envexpbot.2018.08.019

Huang, Y., Chen, H., Reinfelder, J. R., Liang, X., Sun, C., Liu, C., Li, F., & Yi, J. A. 2019. Transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root. The Science of The Total Environment, 666: 445–460. https://doi.org/10.1016/j.scitotenv.2019.02.281

Hwang, J. E., Kim, Y. J., Jeong, D. Y., & Park, H. C. 2019. Transcriptome analysis of Korean fir (Abies koreana) in response to elevated carbon dioxide and high temperature. Plant Biotechnology Reports, 13(6): 603–612. https://doi.org/10.1007/s11816-019-00553-0

Jain, M., Ghanashyam, C., & Bhattacharjee, A. 2010. Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics, 11: 73. https://doi.org/10.1186/1471-2164-11-73

Jiang, Q. T., Liu, T., Ma, J., Wei, Y. M., Lu, Z. X., Lan, X. J., Dai, S. F., & Zheng, Y. L. 2011. Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress. Genetica, 139(10): 1283–1292. https://doi.org/10.1007/s10709-012-9630-4

Kamali, S.,  & Singh, A. 2023. Genomic and Transcriptomic Approaches to Developing Abiotic Stress-Resilient Crops. Agronomy, 13(12): 2903. https://doi.org/10.3390/agronomy13122903

Kaur, B., Sandhu, K. S., Kamal, R., Kaur, K., Singh, J., Röder, M. S., & Muqaddasi, Q. H. 2021. Omics for the improvement of abiotic, biotic, and agronomic traits in major cereal crops: Applications, challenges, and prospects. Plants, 10(10): 1989. https://doi.org/10.3390/plants10101989

Khan, M. K. R., Ditta, A., Wang, B., Fang, L., Anwar, Z., Ijaz, A., Ahmed, S. R., & Khan, S. M. 2023. The intervention of multi-omics approaches for developing abiotic stress resistance in cotton crop under climate change. In: Sustainable Agriculture in the Era of the OMICs Revolution; Prakash CS, Fiaz S, Nadeem MA, Baloch FS, Qayyum A (Eds), Springer: Cham, Switzerland: 37–82. https://doi.org/10.1007/978-3-031-15568-0_3

Kim, S. H., Kim, D. Y., Yacoubi, I., & Seo, Y. W. 2021. Development of single-nucleotide polymorphism markers of salinity tolerance for Tunisian durum wheat using RNA sequencing. Acta Agriculturae Scandinavica, Section B—Soil  Plant Science, 71(1): 28–44. https://doi.org/10.1080/09064710.2020.1843701

Kinaret, P.A.S., Serra, A., Federico, A., Kohonen, P., Nymark, P., Liampa, I., Ha, M.K., Choi, J.S., Jagiello, K., Sanabria, N. & Melagraki, G. 2020. Transcriptomics in toxicogenomics, part I: experimental design, technologies, publicly available data, and regulatory aspects. Nanomaterials, 10(4), p.750.

Klay, I., Gouia, S., Liu, M., Mila, I., Khoudi, H., Bernadac, A., Bouzayen, M., & Pirrello, J. 2018. Ethylene Response Factors (ERF) are differentially regulated by different abiotic stress types in tomato plants. Plant Science, 274: 137–145. https://doi.org/10.1016/j.plantsci.2018.05.023

Kokkanti, R. R., Vemuri, H., Gaddameedi, A., & Rayalacheruvu, U. 2022. Variability in drought stress-induced physiological, biochemical responses and expression of DREB2A, NAC4 and HSP70 genes in groundnut (Arachis hypogaea L.). South African Journal of Botany, 144: 448–457. https://doi.org/10.1016/j.sajb.2021.09.025

Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y. A., Williams, E., Dylag, M., Kurbatova, N., Brandizi, M., Burdett, T., Megy, K., Pilicheva, E., Rustici, G., Tikhonov, A., Parkinson, H., Petryszak, R., Sarkans, U., & Brazma, A. 2015. ArrayExpress update—Simplifying data submissions. Nucleic Acids Research, 43: D1113–D1116. https://doi.org/10.1093/nar/gku1057

Kumar, J., Gunapati, S., Kianian, S. F., & Singh, S. P. 2018. Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of drought tolerance. Protoplasma, 255: 1487–1504. https://doi.org/10.1007/s00709-018-1237-x

Kumar, M., Chauhan, A. S., Yusuf, M. A., Sanyal, I., & Chauhan, P. 2019. Transcriptome sequencing of Chickpea (Cicer arietinum L.) genotypes for identification of drought-responsive genes under drought stress condition. Plant Molecular Biology Reporter, 37: 186–203. https://doi.org/10.1007/s11105-019-01147-4

Kumar, R., Das, S.P., Choudhury, B.U., Kumar, A., Prakash, N.R., Verma, R., Chakraborti, M., Devi, A.G., Bhattacharjee, B., Das, R. & Das, B. 2024. Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing. Biological Research, 57(1): 80. https://doi.org/10.1186/s40659-024-00562-6

Kusunoki, K., Kobayashi, Y., & Koyama, H. 2018. Comparative characterization of aluminum responsive transcriptome in Arabidopsis roots: comparison with other rhizotoxic ions at different stress intensities. Soil Science and Plant Nutrition, 64: 1–13. https://doi.org/10.1080/00380768.2018.1454253

Lee, S. S., Jung, W. Y., Park, H. J., Lee, A., Kwon, S. Y., Kim, H. S., & Cho, H. S. 2018. Genome-wide analysis of alternative splicing in an inbred cabbage (Brassica oleracea L.) line ‘HO’ in response to heat stress. Current Genomics, 19: 12–20. https://doi.org/10.2174/1389202918666170705151901

Li, J., Gao, Z., Zhou, L., Li, L., Zhang, J., Liu, Y., & Chen, H. 2019. Comparative transcriptome analysis reveals K+ transporter gene contributing to salt tolerance in eggplant. BMC Plant Biology, 19: 67–85. https://doi.org/10.1186/s12870-019-1663-8

Li, P. F., Cai, J., Luo, X., Chang, T., Li, J., Zhao, Y., & Xu, Y. 2018. Transformation of wheat Triticum aestivum with the HvBADH1 transgene from hulless barley improves salinity-stress tolerance. Acta Physiology Plant, 41: 155–169. https://doi.org/10.1007/s11738-019-2940-8

Li, S., Han, X., Lu, Z., Qiu, W., Yu, M., Li, H., He, Z., & Zhuo, R. 2022. MAPK cascades and transcriptional factors: Regulation of heavy metal tolerance in plants. International Journal of Molecular Sciences, 23: 4463. https://doi.org/10.3390/ijms23084463

 Li, W., Sun, Y., Wang, B., Xie, H., Wang, J., & Nan, Z. 2020. Transcriptome analysis of two soybean cultivars identifies an aluminum responsive antioxidant enzyme GmCAT1. Bioscience, Biotechnology and Biochemistry, 84: 1394–1400. https://doi.org/10.1080/09168451.2020.1740970

Liu, X., Zhang, Q., Yang, G., Zhang, C., Dong, H., Liu, Y., Yin, R., & Lin, L. 2020. Pivotal roles of tomato photoreceptor SlUVR8 in seedling development and UV-B stress tolerance. Biochemical and Biophysical Research Communications, 522: 177–183. https://doi.org/10.1016/j.bbrc.2019.11.073

Liu, Y., Beyer, A., & Aebersold, R. 2016. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell, 165(3): 535–550. https://doi.org/10.1016/j.cell.2016.03.014

Liu, Y., Chen, J., Yin, C., Wang, Z., Wu, H., Shen, K., Zhang, Z., Kang, L., Xu, S., Bi, A. & Zhao, X., 2023. A high-resolution genotype–phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biology, 24(1): 196. https://doi.org/10.1186/s13059-023-03044-2

Lu, J. X., Bi, H. T., Zhang, A. H., Guo, T., Li, Y., &  Li, Y. 2018. Comparative transcriptome analysis by RNA-Seq of the regulation of low temperature responses in Dendranthema morifolium. Horticulture Environment and Biotechnology, 59(03): 383–395. https://doi.org/10.1007/s13580-018-0042-y

Maheendran, R., Chilakala, A. R., Shankar, C., Yasodha, P.,  Abida, & P. S. 2022. transcriptomics and its role in crop improvement. Advances in Agriculture: Recent Perspectives, 179–194. https://www.researchgate.net/publication/362931207

Mahmood, U., Li, X., Fan, Y., Chang, W., Niu, Y., Li, J, Qu, C., & Lu, K. 2022. Multi-omics revolution to promote plant breeding efficiency. Front. Plant Sci., 13: 1062952. https://doi.org/10.3389/fpls.2022.1062952

Meena, R. P., Ghosh, G., Vishwakarma, H., & Padaria, J. C. 2022. Expression of a Pennisetum glaucum gene DREB2A confers enhanced heat, drought and salinity tolerance in transgenic Arabidopsis. Molecular Biology Reports, 49(12): 7347–7358. https://doi.org/10.1007/s11033-022-07527-6

Mian, A., Oomen, R. J. F. J., Isayenkov, S., Sentenac, H., Maathuis, F. J. M., & Véry, A. A. 2011. Over-expression of an Na+- and K+-permeable HKT transporter in barley improves salt tolerance. Plant Journal, 68(3): 468–479. https://doi.org/10.1111/j.1365-313X.2011.04701.x

Morozova, O., Hirst, M., & Marra, M. A. 2009. Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics, 10(1): 135–151. https://doi.org/10.1146/annurev-genom-082908-145957

Moustakas, M. 2025. Molecular Mechanisms of Plant Abiotic Stress Tolerance. International Journal of Molecular Sciences, 26(6), 2731. https://doi.org/10.3390/ijms26062731

Munir, S., Liu, H., Xing, Y., Hussain, S., Ouyang, B., Zhang, Y., & Li, H.,  Ye, Z. 2016. Overexpression of calmodulin-like (ShCML44) stress-responsive gene from Solanum habrochaites enhances tolerance to multiple abiotic stresses. Scientific Reports, 6: 31772. https://doi.org/10.1038/srep31772

Muthusamy, S. K., Lenka, S. K., Katiyar, A., Chinnusamy, V., Singh, A. K., & Bansal, K. C. 2018. Genome-Wide identification and analysis of biotic and abiotic stress regulation of C4 photosynthetic pathway genes in rice. Applied Biochemistry and Biotechnology, 187(1): 221–238. https://doi.org/10.1007/s12010-018-2809-0

Nair, J.R., & Pandey, K.M., 2024. Role of Molecular Markers in Crop Breeding: A Review. Agricultural Reviews. 45(1): 52-59. doi: 10.18805/ag.R-2322

Navabpour, S., Najafi, H., Gharakhani, M., & Navabpour, R. 2024. Assessment of Differential Gene Expression and Biochemical Traits in Bread Wheat Cultivars in Response to Silver Nitrate Stress. Cereal Biotechnology and Biochemistry, 3(4), 479–497 (In Persian) https://doi.org/10.22126/cbb.2025.4151.1094

Nawaz, G., & Kang, H. 2019. Rice OsRH58, a chloroplast DEAD-box RNA helicase, improves salt or drought stress tolerance in Arabidopsis by affecting chloroplast translation. BMC Plant Biology, 19(01): 17–28. https://doi.org/10.1186/s12870-018-1623-8

Nejat, N., Ramalingam, A., & Mantri, N. 2018. Advances in transcriptomics of plants. Plant Genetics and Molecular Biology, 161–185. https://doi.org/10.1007/10201752

Parida, S. K., Mondal, N., Yadav, R., Vishwakarma, H., & Rana, J. C. 2023. Mining legume germplasm for genetic gains: An Indian perspective. Frontiers Genetics, 14: 996828. https://doi.org/10.3389/fgene.2023.996828

Park, S. C., Kim, H. S., Lee, H. U., Kim, Y. H., & Kwak, S. S. 2019. Overexpression of Arabidopsis YUCCA6 enhances environment stress tolerance and inhibits storage root formation in sweetpotato. Plant Biotechnology Reports, 13: 345–352. https://doi.org/10.1007/s11816-019-00537-0

Piétu, G., Mariage-Samson, R., Fayein, N. A., Matingou, C., Eveno, E., Houlgatte, R., Decraene, C., Vandenbrouck, Y., Tahi, F., Devignes, M. D., Wirkner, U., Ansorge, W., Cox, D., Nagase, T., Nomura, N., & Auffray, C. 1999. The genexpress IMAGE knowledge base of the human brain transcriptome: A prototype integrated resource for functional and computational genomics. Genome Research, 9: 195–209. https://doi.org/10.1101/gr.9.2.195

Portwood, J. L. II, Woodhouse, M. R., Cannon, E. K., Gardiner, J. M., Harper, L. C., Schaeffer, M. L., Walsh, J. R., Sen, T. Z., Cho, K. T., Schott, D. A., Braun, B. L., Dietze, M., Dunfee, B., Elsik, C. G., Manchanda, N., Coe, E., Sachs, M., Stinard, P., Tolbert, J., Zimmerman, S., & Andorf, C. M. 2018. MaizeGDB 2018: The maize multi-genome genetics and genomics database. Nucleic Acids Research, 47: D1146–D1154. https://doi.org/10.1093/nar/gky1046

Ramírez-González, R., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., van Ex, F., Pasha, A., Khedikar, Y., Robinson, S. J., Cory, A. T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., Ridout, C. J., Chalhoub, B., Mayer, K. F. X., Benhamed, M., Latrasse, D., &  Bendahmane, A. 2018. The transcriptional landscape of hexaploid wheat across tissues and cultivar. Science, 361: 3083–3109. https://doi.org/10.1126/science.aar6089

Ray, S., Agarwal, P., Arora, R., Kapoor, S., & Tyagi, A. K. 2007. Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Molecular Genetics and Genomics, 278(5): 493–505. https://doi.org/10.1007/s00438-007-0267-4

Rich-Griffin, C., Stechemesser, A., Finch, J., Lucas, E., Ott, S., Schäfer, P. 2020. Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics. Trends Plant Sci., 25(2):186-197. doi: 10.1016/j.tplants.2019.10.008.

Roychowdhury, R., Das, S. P., Gupta, A., Parihar, P., Chandrasekhar, K., Sarker, U., Kumar, A., Ramrao, D. P., & Sudhakar, C. 2023. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses. Genes, 14(6): 1281. https://doi.org/10.3390/genes14061281

Saeed, F., Chaudhry, U.K., Bakhsh, A., Raza, A., Saeed, Y., Bohra, A. & Varshney, R.K. 2022. Moving beyond DNA sequence to improve plant stress responses. Frontiers in Genetics, 13: 874648. https://doi.org/10.3389/fgene.2022.874648

Samtani, H., Sharma, A., & Khurana, P. 2022. Overexpression of HVA1 enhances drought and heat stress tolerance in Triticum aestivum doubled haploid plants. Cells, 11(5): 912. https://doi.org/10.3390/cells11050912

Sangwan, R. S., Tripathi, S., Singh, J., Narnoliya, L. K., & Sangwan, N. S. 2013. De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene, 525(1): 58–76. https://doi.org/10.1016/j.gene.2013.04.057

Sato, Y., Takehisa, H., Kamatsuki, K., Minami, H., Namiki, N., Ikawa, H., Ohyanagi, H., Sugimoto, K., Antonio, B.A., & Nagamura, Y. 2012. RiceXPro Version 3.0: Expanding the informatics resource for rice transcriptome. Nucleic Acids Research, 41: D1206–D1213. https://doi.org/10.1093/nar/gks1125

Schaarschmidt, S., Fischer, A., Lawas, L.M.F., Alam, R., Septiningsih, E.M., Bailey-Serres, J., Jagadish, S.V.K., Huettel, B., Hincha, D.K., & Zuther, E. 2020. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. International Journal of Molecular Science, 21, 8148. https://doi.org/10.3390/ijms21218148

Seong, S. Y., Shim, J. S., Bang, S. W., & Kim, J. K. 2020. Overexpression of OsC3H10, a CCCH-zinc finger, improves drought tolerance in rice by regulating stress-related genes. Plants, 9(10): 1298. https://doi.org/10.3390/plants9101298

Shen, L., Gong, J., Caldo, R. A., Nettleton, D., Cook, D., Cook, R. P., & Dickerson, J. 2005. BarleyBase--an expression profiling database for plant genomics. Nucleic Acids Research, 33: D614–D618. https://doi.org/10.1093/nar/gki123

Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., & Schloss, J. A. 2017. DNA Sequencing at 40: past, present and future. Nature, 550: 345–353.

Shi L., Campbell, G., Jones, W.D., Campagne, F., Wen, Z., Walker., S.J., Su, Z., Chu, T.M., Goodsaid, F.M., Pusztai, L., et al. 2010. The MicroArray Quality Control (MAQC)- II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol., 28(8): 827–38. https://doi.org/10.1038/nbt.1665

Shi, F., Dong, Y., Wang, M., & Qiu, D. 2020. Transcriptomics analyses reveal that OsMIOX improves rice drought tolerance by regulating the expression of plant hormone and sugar related genes. Plant Biotechnology Reports, 14(3): 339–349. https://doi.org/10.1007/s11816-020-00608-7

Simorghi, S., Tahmasebi, Z., Mohammadi, R., & Etminan, A. 2025. Expression Analysis of Key Genes in Durum Wheat under Mild and Severe Drought Stress. Cereal Biotechnology and Biochemistry, 4(2), 164–179 (In Persian). https://doi.org/10.22126/cbb.2025.7987.1120

Singh, A., Giri, J., Kapoor, S., Tyagi, A. K., & Pandey, G. K. 2010. Protein phosphatase complement in rice: Genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC Genomics, 11: 435. https://doi.org/10.1186/1471-2164-11-435

Singh, A., Kanwar, P., Yadav, A. K., Mishra, M., Jha, S. K., Baranwal, V., Pandey, A., Kapoor, S., Tyagi, A. K., & Pandey, G. K. 2014. Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice. FEBS Journal, 281: 894–915. https://doi.org/10.1111/febs.12656

Singh, B. A., Pandey, A., Baranwal, V., Kapoor, S., & Pandey, G. K. 2012. Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development. Plant Signaling Behavior, 7(7): 847–855. https://doi.org/10.4161/psb.20385

Singh, D., Chaudhary, P., Taunk, J., Kumar Singh, C., Sharma, S., Singh, V.J., Singh, D., Chinnusamy, V., Yadav, R., & Pal, M. 2021. Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives. J Exp Bot. 72(20): 6836-6855. https://doi.org/10.1093/jxb/erab337

Singh, N., Ujinwal, M. and Singh, A. 2022. Advances in agricultural bioinformatics: an outlook of multi “omics” approaches. In Bioinformatics in Agriculture (pp. 3-21). Academic Press. https://doi.org/10.1016/B978-0-323-89778-5.00001-5

Singh, R. B., Singh, B., & Singh, R. K. 2019. Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses. Industrial Crops and Products, 128: 38–47. https://doi.org/10.1016/j.indcrop.2018.10.071

Song, Y., Lv, J., Ma, Z., & Dong, W. 2019. The mechanism of alfalfa (Medicago sativa L.) response to abiotic stress. Plant Growth Regulation, 89: 239–249. https://doi.org/10.1007/s10725-019-00530-1

Springer, N. M., & Schmitz, R. J. 2017. Exploiting induced and natural epigenetic variation for crop improvement. Nature reviews. Genetics, 18(9): 563–575. https://doi.org/10.1038/nrg.2017.45

Stark, R., Grzelak, M., Hadfield, J. 2019. RNA sequencing: the teenage years. Nat Rev Genet. 20(11):631-656. https://doi.org/10.1038/s41576-019-0150-2

Sun, J. Q., Jiang, H. L., Xu, Y. X., Li, H. M., Wu, X. Y., Xie, Q., & Li, C. Y. 2007. The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant Cell Physiology, 48(8): 1148–1158. https://doi.org/10.1093/pcp/pcm088

Tahmasebi, A., Ashrafi-Dehkordi, E., Shahriari, A. G., Mazloomi, S. M., & Ebrahimie, E. 2019. Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton. Progress in Biophysics and Molecular Biology, 146: 112–122. https://doi.org/10.1016/j.pbiomolbio.2019.02.005

Thakur, S., Choudhary, S., & Bhardwaj, P. 2019. Comparative transcriptome profiling under Cadmium stress reveals the uptake and tolerance mechanism in Brassica juncea. Journal of Plant Growth Regulation, 38(08): 1141–1152. https://doi.org/10.1007/s00344-019-09919-8

Tian, T., You, Q., Zhang, L., Yi, X., Yan, H., Xu, W., &  Su, Z. 2016. SorghumFDB: Sorghum functional genomics database with multidimensional network analysis. Database 2016: baw099. https://doi.org/10.1093/database/baw099

Varoquaux, N., Cole, B., Gao, C., Pierroz, G., Baker, C.R., Patel, D., Madera, M., Jeffers, T., Hollingsworth, J., Sievert, J. & Yoshinaga, Y. 2019. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences, 116(52): 27124-27132. https://doi.org/10.1073/pnas.1907500116

Vennapusa, A. R., Nimmakayala, P., Zaman-Allah, M. A., & Ratnakumar, P. 2023. Physiological, molecular, and genetic perspectives of environmental stress response in plants. Frontiers in Plant Science, 14: 1213762. https://doi.org/10.3389/fpls.2023.1213762

Vogel, C., Marcotte, E. 2012. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 13: 227–232. https://doi.org/10.1038/nrg3185

von Braun, J., Afsana, K., Fresco, L.O., Hassan, M.H.A. & Torero, M. 2023. Food system concepts and definitions for science and political action. Science and Innovations for Food Systems Transformation, pp.11-17. https://doi.org/10.1038/

Wang, A. D., Lu, X., Chen, X., Wang, S., Wang, J., Guo, L., Yin, Z., Chen, Q., & Ye, W. 2020. Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum. BMC Genomics, 21: 838. https://doi.org/10.1186/s12864-020-07260-z

Wang, B. X., Li, N., Li, W., Gao, X., Cha, M., Qin, L., & Liu, L. 2020. Advances in transcriptomics in the response to stress in plants. Global Medical Genetics, 7(2): 30–34. https://doi.org/10.1055/s-0040-1714414

Wang, M., Wang, Y., Zhang, Y., Li, C., Gong, S., Yan, S., Li, G., Hu, G., Ren, H., Yang, J., Yu, T.,  & Yang, K. 2019. Comparative transcriptome analysis of salt-sensitive and salt-tolerant maize reveals potential mechanisms to enhance salt resistance. Genes Genomics, 41(07): 781–801. https://doi.org/10.1007/s13258-019-00793-y

Wang, M., Zhang, X., Li, Q., Chen, X., & Li, X. 2019. Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (Camellia sinensis) treated with exogenous calcium. Planta, 249(03): 775–786. https://doi.org/10.1007/s00425-018-3039-y

Wang, P., Su, L., Gao, H., Jiang, X., Wu, X., Li, Y., & Zhang, Q. 2018. Genome-wide characterization of bHLH genes in grape and analysis of their potential relevance to abiotic stress tolerance and secondary metabolite biosynthesis. Frontiers in Plant Science, 9: 64. https://doi.org/10.3389/fpls.2018.00064

Wang, Z., Gerstein, M., & Snyder, M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1): 57–63. https://doi.org/10.1038/nrg2484

Wang, Z., Gerstein, M., & Snyder, M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1): 5763. http://dx.doi.org/10.1038/nrg2484

Wei, Q., Chen, R., Wei, X., Liu, Y., Zhao, S., Yin, X., & Xie, T. 2020. Genome-wide identification of R2R3-MYB family in wheat and functional characteristics of the abiotic stress responsive gene TaMYB344. BMC Genomics, 21(1): 792. https://doi.org/10.1186/s12864-020-07175-9

Xu, Z., Wang, F., Ma, Y., Dang, H., & Hu, X. 2022. Transcription factor SlAREB1 is involved in the antioxidant regulation under saline–alkaline stress in tomato. Antioxidants, 11(9): 1673. https://doi.org/10.3390/antiox11091673

Yadav, P.K. ed. 2018. Crop improvement for sustainability. New Delhi: Daya Publishing House..

Yan, L., Baoxiang, W., Jingfang, L., Zhiguang, S., Ming, C., Yungao, X., Bo, X., Bo, Y., Jian, L., Jinbo, L., Tinmu, C., Zhaowei, F., Baiguan, L., Dayong, X., & Bello, B. K. 2021. A novel SAPK10-WRKY87-ABF1 biological pathway synergistically enhances abiotic stress tolerance in transgenic rice (Oryza sativa). Plant Physiology and Biochemistry, 168: 252–262. https://doi.org/10.1016/j.plaphy.2021.10.006

Yan, S., Bhawal, R., Yin, Z., Thannhauser, T.W. and Zhang, S., 2022. Recent advances in proteomics and metabolomics in plants. Molecular Horticulture, 2(1): 17. https://doi.org/10.1186/s43897-022-00038-9

Yang, J., Lv, W., Shao, L., Fu, Y., Liu, H., Yang, C., Chen, A., Xie, X., Wang, Z., & Li, C. 2021. PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species. Frontiers in Plant Science, 12: 737004. https://doi.org/10.3389/fpls.2021.737004

Yang, R., Hong, Y., Ren, Z., Tang, K., Zhang, H., Zhu, J. K., & Zhao, C. 2019. A role for PICKLE in the regulation of cold and salt stress tolerance in Arabidopsis. Frontiers in Plant Science, 10: 900. https://doi.org/10.3389/fpls.2019.00900

Yang, S., Zhou, J., Li, Y., Wu, J., Ma, C., Chen, Y., Sun, X., Wu, L., Liang, X., Fu, Q., Xu, Z., Li, L., Huang, Z., Zhu, J., Jia, X., Ye, X., & Chen, R. 2023. AP2/EREBP Pathway Plays an Important Role in Chaling Wild Rice Tolerance to Cold Stress. International Journal of Molecular Sciences, 24: 14441. https://doi.org/10.3390/ijms241914441

Yang, Y., Wang, Y., Jia, L., Yan, G., Xu, X., Zhai, H., He, S., Li, J., Dai, X., Qin, N., Zhu, C., & Liu, Q. 2018. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweet potato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One, 13(2), e0193193. https://doi.org/10.1371/journal.pone.0193193

Yun, S.D., Kim, M.H., Oh, S.A., Soh, M.S., & Park, S.K. 2022. Overexpression of C-Repeat Binding Factor1 (CBF1) gene enhances heat stress tolerance in Arabidopsis. Journal of Plant Biology, 65: 253–260. https://doi.org/10.1007/s12374-022-09350-9

Zhang, H., Lang, Z., & Zhu, J. K. 2018. Dynamics and function of DNA methylation in plants. Nature reviews. Molecular cell biology. 19(8): 489–506. https://doi.org/10.1038/s41580-018-0016-z

Zhao, H., Li, Z., Wang, Y., Wang, J., Xiao, M., Liu, H., Quan, R., Zhang, H., Huang, R., Zhu, L., & Zhang, Z. 2022. Cellulose synthase-like protein OsCSLD4 plays an important role in the response of rice to salt stress by mediating abscisic acid biosynthesis to regulate osmotic stress tolerance. Plant Biotechnology Journal, 20: 468–484. https://doi.org/10.1111/pbi.13729

Zhao, J., He, Y., Li, X., Weng, X., Feng, D., Ying, J., & Wang, Z. 2020. An integrated RNA-Seq and physiological study reveals gene responses involving in the initial imbibition of seed germination in rice. Plant Growth Regulation, 90: 249–263. https://doi.org/10.1007/s10725-019-00567-2

Zhong, R., Wang, Y., Gai, R., Xi, D., Mao, C., & Ming, F. 2020. Rice SnRK protein kinase OsSAPK8 acts as a positive regulator in abiotic stress responses. Plant Science, 292: 110373. https://doi.org/10.1016/j.plantsci.2019.110373

Zhou, J., Huang, J., Tian, X.Y., Zheng, J., & He, X. 2020. Transcriptome analysis reveals dynamic changes in the salt stress response in Salix. Journal of Forestry Research, 31(5): 1851–1862. https://doi.org/10.1007/s11676-019-00941-w

Zhu, M., Meng, X., Cai, J., Li, G., Dong, T., & Li, Z. 2018. Basic leucine zipper transcription factor SlbZIP1 mediates salt and drought stress tolerance in tomato. BMC Plant Biology, 18(01): 83–97. https://doi.org/10.1186/s12870–018–1299–0

Zou, C., Tan, H., Huang, K., Zhai, R., Yang, M., Huang, A., Wei, X., Mo, R., Xiong, & F. 2024. Physiological Characteristic Changes and Transcriptome Analysis of Maize (Zea mays L.) Roots under Drought Stress. Int J Genomics, 17: 5681174. https://doi.org/10.1155/2024/5681174