{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T21:24:39Z","timestamp":1780089879491,"version":"3.54.0"},"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Potato (<jats:italic><jats:italic>Solanum tuberosum<\/jats:italic><\/jats:italic>) is a staple food crop that supports global food security, ranking as the world\u2019s third most important food crop after rice and wheat in terms of human consumption, and it is threatened by Potato virus Y (PVY), which causes severe yield losses. This study integrates bioinformatics analysis and experimental approaches to elucidate molecular defense mechanisms against PVY infection. Using transcriptomic data from PVY-infected potato plants, we constructed protein-protein interaction (PPI) networks and identified hub genes central to defense responses. The qPCR validation showed that three hub genes (<jats:italic>NAD1<\/jats:italic>, <jats:italic>NAD2<\/jats:italic>, <jats:italic>NAD3<\/jats:italic>) were upregulated in resistant Sante plants but downregulated in susceptible Agria. Among these, <jats:italic>NAD2<\/jats:italic> showed a striking 5.58-fold increase in Sante, highlighting its critical role in stress signaling and antiviral defense. Network analysis revealed interactions with microRNAs (miRNAs), including stu-miR8015-5p and stu-miR396-5p, suggesting complex regulatory networks. Codon usage bias analysis highlighted adaptive codon preferences optimized for translational efficiency, supporting potential strategies like codon deoptimization to impair viral fitness. Promoter motif analysis identified stress-responsive <jats:italic><jats:italic>cis<\/jats:italic><\/jats:italic>-regulatory elements linked to abscisic acid signaling, critical for antiviral responses. This comprehensive study establishes a framework for targeting hub genes and miRNAs to engineer PVY-resistant cultivars, thereby offering a sustainable solution.<\/jats:p>","DOI":"10.1371\/journal.pone.0329747","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T19:46:39Z","timestamp":1755200799000},"page":"e0329747","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Integrated gene network analysis and experimental validation identify key hub genes in potato response to Potato Virus Y infection"],"prefix":"10.1371","volume":"20","author":[{"given":"Roya","family":"Karimipour","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5863-2591","authenticated-orcid":true,"given":"Davoud","family":"Koolivand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2183-0033","authenticated-orcid":true,"given":"Abozar","family":"Ghorbani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6661-2590","authenticated-orcid":true,"given":"Masoud","family":"Naderpour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahsa","family":"Rostami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,8,14]]},"reference":[{"issue":"4","key":"pone.0329747.ref001","doi-asserted-by":"crossref","first-page":"858","DOI":"10.3844\/ojbsci.2024.858.876","article-title":"The Impact of Climate Factors on the Epidemiology and Management of Potato virus Y","volume":"24","author":"M Mostafa","year":"2024","journal-title":"OnLine Journal of Biological Sciences"},{"issue":"1","key":"pone.0329747.ref002","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1186\/s12864-015-1666-2","article-title":"RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection","volume":"16","author":"A Goyer","year":"2015","journal-title":"BMC Genomics"},{"issue":"5","key":"pone.0329747.ref003","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0303783","article-title":"Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars","volume":"19","author":"Z Hajibarat","year":"2024","journal-title":"PLoS One"},{"issue":"2","key":"pone.0329747.ref004","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1111\/tpj.14940","article-title":"Network-based approaches for understanding gene regulation and function in plants","volume":"104","author":"DK Ko","year":"2020","journal-title":"Plant J"},{"key":"pone.0329747.ref005","unstructured":"Darvishi B, Naderpour M, Mohammadi H, Hasani F, Alipour D, Pargal F. Dispersion of potato leafroll virus and potato Y virus in potato seed production fields of Hamedan province. 2021."},{"key":"pone.0329747.ref006","volume-title":"Potato Virus Y (PVY) on pepper in Serbia. 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Kehr","year":"2022","journal-title":"Annu Rev Plant Biol"},{"key":"pone.0329747.ref029","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12864-016-2394-y","article-title":"Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection","volume":"17","author":"F Mart\u00ednez","year":"2016","journal-title":"BMC Genomics"},{"key":"pone.0329747.ref030","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/bs.aivir.2020.04.002","article-title":"Hijacking of host cellular components as proviral factors by plant-infecting viruses","volume":"107","author":"K Hyodo","year":"2020","journal-title":"Adv Virus Res"},{"key":"pone.0329747.ref031","doi-asserted-by":"crossref","first-page":"109046","DOI":"10.1016\/j.plaphy.2024.109046","article-title":"Abscisic acid: An emerging player in plant-virus interactions","volume":"215","author":"R Kumar","year":"2024","journal-title":"Plant Physiol 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