Co-expression network analysis for identification of candidate genes regulating phosphorus use efficiency in wheat (Triticum aestivum L.)
DOI:
https://doi.org/10.14719/pst.3328Keywords:
Phosphorus, wheat, phosphorus use efficiency, cytoscape, hub genes, KEGGAbstract
Phosphorus (P) is a crucial nutrient for plants, but its deficiency can significantly reduce crop yields, especially in wheat. To understand the genetic basis of Phosphorus Use Efficiency (PUE) in wheat, we analyzed the gene expression patterns of plants under phosphorus stress. We identified and analyzed 1194 differentially expressed genes, constructing a network of these genes through cytoscape. We have extracted 26 hub genes from this network, which are key players in PUE. These hub genes are involved in various biological processes related to phosphorus uptake, transport and utilization, as revealed by KEGG pathway analysis. Our findings provide valuable insights into the genetic mechanisms underlying PUE in wheat and may contribute to the development of strategies for improving crop yields in phosphorus-deficient environments.
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Sharma I, Tyagi BS, Singh G, Venkatesh K, Gupta OP. Enhancing wheat production - A global perspective. Indian Journal of Agricultural Science. 2015;85(1):pp. 3-13. https://doi.org/10.56093/ijas.v85i1.45935
Venske E, Dos Santos RS, Busanello C, Gustafson P, de Oliveira AC. Bread wheat: A role model for plant domestication and breeding. Hereditas. 2019;156:pp. 1-11. https://doi.org/10.1186/s41065-019-0093-9
Abbas H, et al. Role of wheat phosphorus starvation tolerance 1 genes in phosphorus acquisition and root architecture. Genes. 2022;13:p. 487. https://doi.org/10.3390/
McDonald G, et al. Responses to phosphorus among wheat genotypes. Crop and Pasture Science. 2015;66:pp. 430-44. https://doi.org/10.1071/CP14191
Reddy VRP, et al. Genetic dissection of phosphorous uptake and utilization efficiency traits using GWAS in Mungbean. Agronomy. 2011;11: p. 1401. https://doi.org/10.3390/agronomy11071401
Su J, et al. Mapping QTLs for phosphorus-deficiency tolerance at wheat seedling stage. Plant and Soil. 2006;281:pp. 25-36. https://doi.org/10.1007/s11104-005-3771-5
Van de Wiel, CCM, et al. Improving Phosphorus Use Efficiency in agriculture: opportunities for breeding. Euphytica. 2016;207: pp. 1-22. https://doi.org/10.1007/s10681-015-1572-3
Menzies N, Lucia S. The science of phosphorus nutrition: Forms in the soil, plant uptake and plant response. https://grdc.com.au/resources-and-publications/grdc-update-papers/tab-content/grdc-update-papers/2009/02/thescience-of-phosphorus-nutrition-forms-in-the-soil-plant-uptake-and-plant-response
Zhang D, et al. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet. 2014;10:p. e1004061. https://doi.org/10.1371/journal.pgen.1004061
Desnos T. Root branching responses to phosphate and nitrate. Current Opinion in Plant Biology. 2008;11:pp. 82-87. https://doi.org/10.1016/j.pbi.2007.10.003
Soumya PR, et al. Response of diverse bread wheat genotypes in terms of root architectural traits at seedling stage in response to low phosphorus stress. Plant Physiology Reports. 2021;26:pp. 152-61. https://doi.org/10.1007/s40502-020-00540-6
Uygur V, Mustafa S. The effect of phosphorus application on nutrient uptake and translocation in wheat cultivars. International Journal of Agricultural, Forestry and Life Sciences. 2018;2:pp. 171-79.
Wang J, et al. Transcriptome analysis in roots and leaves of wheat seedlings in response to low-phosphorus stress. Scientific Reports. 2019;9(1):p. 19802. https://doi.org/10.1038/s41598-019-56451-6
Bhadouria J, Giri J. Purple acid phosphatases: Roles in phosphate utilization and new emerging functions. Plant Cell Reports. 2022;41(1):pp. 33-51. https://doi.org/10.1007/s00299-021-02773-7
Zhang X, et al. Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat. Research Square. 2020. https://doi.org/10.21203/rs.3.rs-45684/v1
Ferrol Nuria, et al. Review: Arbuscular mycorrhizas as key players in sustainable plant phosphorus acquisition: An overview on the mechanisms involved. Plant Science. 2018;172:pp. S0168945218307258. https://doi.org/10.1016/j.plantsci.2018.11.011
Kumar A, et al. Functional and structural insights into candidate genes associated with nitrogen and phosphorus nutrition in wheat (Triticum aestivum L.). International Journal of Biological Macromolecules. 2018;118: pp. 76-91. https://doi.org/10.1016/j.ijbiomac.2018.06.009
Fukushima A, et al. Integrated omics approaches in plant systems biology. Current Opinion in Chemical Biology. 2009;13(5–6):pp. 532-38. https://doi.org/10.1016/j.cbpa.2009.09.022
Carter H, et al. Genotype to phenotype via network analysis. Current Opinion in Genetics and Development. 2013;23(6):pp. 611-21. https://doi.org/10.1016/j.gde.2013.10.003
Aya K, et al. Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser micro dissection and 143 spatiotemporal microarrays. PLoS One. https://doi.org/10.1371/journal.pone.0026162
Suratanee A, et al. Two-state co-expression network analysis to identify genes related to salt tolerance in Thai rice. Genes. 2018;9(12):p. 594. https://doi.org/10.3390/genes9120594
Plaimas K, et al. Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Systems Biology. 2010;vol. 4(1):56. https:// doi.org/ 10. 1186/ 1752- 0509-4- 56
Dam SV, et al. Gene co-expression analysis for functional classification and gene–disease predictions. Briefings in Bioinformatics. 2018;19(4):pp. 575-92. https://doi.org/10.1093/bib/bbw139
Kaur G, et al. Physiological and molecular responses to combinatorial iron and phosphate deficiencies in hexaploid wheat seedlings. Genomics. 2021;113(6):pp. 3935-50. https://doi.org/10.1016/j.ygeno.2021.09.019
Ray P, et al. Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation. Applied Microbiology International. 2020;23(4): pp. 1876-88. https://doi.org/10.1111/1462-2920.15242
Sultana N, et al. Transcriptomic study for identification of major nitrogen stress responsive genes in Australian bread wheat cultivars. Frontiers in Genetics. vol. 11: https://doi.org/10.3389/fgene.2020.583785
Zhang X, et al. Transcriptome analysis reveals different responsive patterns to nitrogen deficiency in two wheat near-isogenic lines contrasting for nitrogen use efficiency. Biology. 2021;10: p. 1126. https://doi.org/10.3390/biology10111126
Szklarczyk D, et al. STRING v10: Protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Research. 2015;43(1): pp. 447-52. https://doi.org/10.1093/nar/gku1003
Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003;13(11): pp. 2498-504. https://doi.org/10.1101/gr.1239303
Chen J, et al. Identification of QTLs for phosphorus utilization efficiency in maize (Zea mays L.) across P levels. Euphytica. 2009;167: pp. 245-52. https://doi.org/10.1007/s10681-009-9883-x
Shomali A, et al. Diverse physiological roles of flavonoids in plant environmental stress responses and tolerance. Plants. 2021; 11: p. 3158. https://doi.org/10.3390/plants11223158
Bassett VJ, et al. A meta-analysis of phosphatase activity in agricultural settings in response to phosphorus deficiency. Soil Biology and Biochemistry. 2022; vol. 165. https://doi.org/10.1016/j.soilbio.2021.108537
Gholizadeh F, et al. Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response. PLoS ONE. 2020;15(8). https://doi.org/10.1371/journal.pone.0236226
Murphy KM, Zerbe P. Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity. Phytochemistry. 2020;172: https://doi.org/10.1016/j.phytochem.2020.112289
Rasool F, et al. Phenylalanine ammonia-lyase (PAL) genes family in wheat (Triticum aestivum L.): Genome-wide characterization and expression profiling. Agronomy. 2021;11: p. 2511. https://doi.org/10.3390/agronomy11122511
Pontigo S, et al. Phosphorus efficiency modulates phenol metabolism in wheat genotypes. Journal of Soil Science and Plant Nutrition. https://10.4067/S0718-95162018005002603
Goyal RK, et al. Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species. BMC Genomics. 2018;19: p. 178. https://doi.org/10.1186/s12864-018-4545-9
Said K, Wissal E, Mohamed L, Ammar I, Meryem H, Rachid G, et al. Phosphate solubilizing bacteria can significantly contribute to enhance P availability from polyphosphates and their use efficiency in wheat. Microbiological Research. 2022;262: p. 127094. https://doi.org/10.1016/j.micres.2022.127094
Kumar M, Mehra R, Yogi R, Singh N, Salar RK, Saxena G, Rustagi S. A novel tannase from Klebsiella pneumoniae KP715242 reduces haze and improves the quality of fruit juice and beverages through de-tannification. Frontiers in Sustainable Food Systems. 2023 Jun 2;7:1173611. https://doi.org/10.3389/fsufs.2023.1173611
Srivastava RP, Kumar S, Singh L, Madhukar M, Singh N, Saxena G, et al. Major phenolic compounds, antioxidant, antimicrobial and cytotoxic activities of Selinum carvifolia (L.) collected from different altitudes in India. Frontiers in Nutrition. 2023 Jul 13;10:1180225. https://doi.org/10.3389/fnut.2023.1180225
Rajak BK, Rani P, Singh N, Singh DV. Sequence and structural similarities of ACCase protein of Phalaris minor and wheat: An insight to explain herbicide selectivity. Frontiers in Plant Science. 2023 Jan 4;13:1056474. https://doi.org/10.3389/fpls.2022.1056474
Singh N, Jiwani G, Rocha LS, Mazaheri R. Bioagents and volatile organic compounds: An emerging control measures for rice bacterial diseases. In: Bacterial Diseases of Rice and Their Management. Apple Academic Press; 2023 May 5. pp. 255-74. https://doi.org/10.1201/9781003331629
Rajak BK, Rani P, Mandal P, Chhokar RS, Singh N, Singh DV. Emerging possibilities in the advancement of herbicides to com-bat acetyl-CoA carboxylase inhibitor resistance. Frontiers in Agronomy. 2023 Jul 20;5:1218824. https://doi.org/10.3389/fagro.2023.1218824
Malik C, Dwivedi S, Rabuma T, Kumar R, Singh N, Kumar A, et al. De novo sequencing, assembly and characterization of Aspara-gus racemosus transcriptome and analysis of expression profile of genes involved in the flavonoid biosynthesis pathway. Frontiers in Genetics. 2023 Sep 7;14:1236517. https://doi.org/10.3389/fgene.2023.1236517
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Copyright (c) 2024 Nikhil Chand, Rekha Dixit, Pankaj Kumar, Kuldeep Tyagi, Neelesh Kapoor, Nitesh Singh, Prashant Vikram, Sumira Malik
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