Identification of miRNAs associated with Aspergillus flavus infection and their targets in groundnut (Arachis hypogaea L.)

    Joshi, Pushpesh and Sharma, V and Pandey, A K and Nayak, S N and Bajaj, P and Sudini, H and Sharma, Shailendra and Varshney, R K and Pandey, M K (2025) Identification of miRNAs associated with Aspergillus flavus infection and their targets in groundnut (Arachis hypogaea L.). BMC Plant Biology (TSI), 25. pp. 1-17. ISSN 1471-2229

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    Abstract

    Background The quality of groundnut produce is adversely impacted due to aflatoxin contamination by the fungus Aspergillus flavus. Although the transcriptomic control is not fully understood, the interaction between long non-coding RNAs and microRNAs in regulating A. flavus and aflatoxin contamination remains unclear. This study was carried out to identify microRNAs (miRNAs) to enhance the understanding of in vitro seed colonization (IVSC) resistance mechanism in groundnut. Result In this study, resistant (J 11) and susceptible (JL 24) varieties of groundnut were treated with toxigenic A. flavus (strain AF-11–4), and total RNA was extracted at 1 day after inoculation (1 DAI), 2 DAI, 3 DAI and 7 DAI. Seeds of JL 24 showed higher mycelial growth than J 11 at successive days after inoculation. A total of 208 known miRNAs belonging to 36 miRNA families, with length varying from 20–24 nucleotides, were identified, along with 27 novel miRNAs, with length varying from 20–22 nucleotides. Using psRNATarget server, 952 targets were identified for all the miRNAs. The targeted genes function as disease resistant proteins encoding, auxin responsive proteins, squamosa promoter binding like proteins, transcription factors, pentatricopeptide repeat-containing proteins and growth regulating factors. Through differential expression analysis, seven miRNAs (aly-miR156d-3p, csi-miR1515a, gma-miR396e, mtr-miR2118, novo-miR-n27, ptc-miR482d-3p and ppe-miR396a) were found common among 1 DAI, 2 DAI, 3 DAI and 7 DAI in J 11, whereas ten miRNAs (csi-miR159a-5p, csi-miR164a-3p, novo-miR-n17, novo-miR-n2, osa-miR162b, mtr-miR2118, ptc-miR482d-3p, ptc-miR167f-3p, stu-miR319-3p and zma-miR396b-3p) were found common among 1 DAI, 2 DAI, 3 DAI and 7 DAI in JL 24. Two miRNAs, ptc-miR482d-3p and mtr-miR2118, showed contrasting expression at different time intervals between J 11 and JL 24. These two miRNAs were found to target those genes with NBS-LRR function, making them potential candidates for marker development in groundnut breeding programs aimed at enhancing resistance against A. flavus infection. Conclusion This study enhances our understanding of the involvement of two miRNAs namely, ptc-miR482d-3p and mtr-miR2118, along with their NBS-LRR targets, in conferring resistance against A. flavus-induced aflatoxin contamination in groundnut under in vitro conditions.

    Item Type: Article
    Divisions: Center of Excellence in Genomics and Systems Biology
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Aspergillus flavus, Differential expression, Genes, Groundnut, MicroRNA
    Subjects: Mandate crops > Groundnut
    Others > Genetics and Genomics
    Others > Plant Virology
    Depositing User: Mr Nagaraju T
    Date Deposited: 09 Jun 2025 05:31
    Last Modified: 09 Jun 2025 05:31
    URI: http://oar.icrisat.org/id/eprint/13131
    Official URL: https://link.springer.com/article/10.1186/s12870-0...
    Projects: Tropical Legumes III project
    Funders: USAID-US University Collaboration Grant, Peanut & Mycotoxin Innovation Lab, Bill & Melinda Gates Foundation
    Acknowledgement: The authors are thankful for partial financial assistance received from the Indian Council of Agricultural Research (ICAR) through ICAR-ICRISAT collaborative project, Department of Biotechnology (DBT), Government of India and MARS-Wrigley and Bill and Melinda Gates Foundation (BMGF), USA. PJ and VS acknowledge Chaudhary Charan Singh University (CCSU), Meerut, for collaborating with ICRISAT and the opportunity given as a student to pursue this investigation at ICRISAT. VS acknowledges the Council of Scientific and Industrial Research (CSIR), Govt. of India for the award of CSIR-SRF Direct fellowship (File No: 09/0800(18433)/2024-EMR-I) for PhD.
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