Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 May 21;44(6):124.
doi: 10.1007/s00299-025-03515-9.

Transcriptional response of cultivated peanut (Arachis hypogaea L.) roots to salt stress and the role of DNA methylation

Shree P Pandey  1 , Chen Chen  2 , Shivam Singh  3 , Jalak N Maniar  4 , Avinash Mishra  4 , Suman Bakshi  5 , V K Mishra  3 , Sandeep Sharma  6
Affiliations

Transcriptional response of cultivated peanut (Arachis hypogaea L.) roots to salt stress and the role of DNA methylation

Shree P Pandey et al. Plant Cell Rep. .

Abstract

Our study unravels a complex multi-layered molecular response of peanut roots to salinity, where reprograming of gene-expression is partly executed by changes in methylome via RdDM pathway and exerted through transcription factors. Peanut (Arachis hypogaea L.) is a major oilseed crop of global importance, whose production is severely impacted by salinity. Here, we have explored the transcriptional response of peanut roots to salinity stress using deep sequencing. Further, we have unravelled the salinity-induced changes in peanut root methylome. When peanut seedlings were grown under high-salt conditions for 7 days, their root and shoot growth was significantly impaired. A large-scale transcriptional reprogramming was recorded where 1926 genes were down- and 3260 genes were up-regulated due to salt stress in peanut roots. The molecular response of peanut root comprised several layers of regulators, which included the genes related to ion transport, osmolyte accumulation, signal transduction, and salt stress-responsive genes. Several negative regulators are also differentially expressed in peanut roots, which may contribute to its susceptibility. This response is regulated by a large number of transcription factors (TFs) and epigenetically by changes in DNA methylation. The DNA methylation changes in roots were highly complex and context dependent when exposed to salt stress. An inverse relationship between the changes in gene expression and methylation status was partially observed for several important gene sets and TFs. A treatment with 5'-azacytidine recovered the inhibitory impact of salt stress in peanut roots. Thus, a complex multilayered molecular response to salinity in peanut roots was observed. A part of this response may be modulated by the reprogramming of RNA-directed DNA methylation pathway. This investigation also serves as a resource for future gene-mining and methylation studies for improving peanut resistance to salt stress.

Keywords: Arachis hypogaea; Gene Expression; Methylation; Methylome; Peanut; Salinity.

PubMed Disclaimer

Conflict of interest statement

Declarations. Conflict of interest: The authors declare no conflict of interest.

References

    1. Al-Lawati A, Al-Bahry S, Victor R, Al-Lawati AH, Yaish MW (2016) Salt stress alters DNA methylation levels in alfalfa (Medicago spp). Genet Mol Res 15:15018299 - PubMed - DOI
    1. Arefian M, Vessal S, Malekzadeh-Shafaroudi S, Siddique KHM, Bagheri A (2019) Comparative proteomics and gene expression analyses revealed responsive proteins and mechanisms for salt tolerance in chickpea genotypes. BMC Plant Biol 19:300 - PubMed - PMC - DOI
    1. Awana M, Yadav K, Rani K, Gaikwad K, Praveen S, Kumar S, Singh A (2019) Insights into Salt Stress-Induced Biochemical, Molecular and Epigenetic Regulation of Spatial Responses in Pigeonpea (L). J Plant Growth Regul 38:1545–61 - DOI
    1. Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araujo AC, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimaraes PM, Isobe S, Guo B, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–46 - PubMed - DOI
    1. Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballen-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51:877–84 - PubMed - DOI

MeSH terms

LinkOut - more resources