Genome-Wide Analysis of Phaseolus vulgaris L. miR172 Gene Family Members Under Heavy Metal Stress

Genome-Wide Analysis of Phaseolus vulgaris L. miR172 Gene Family Members Under Heavy Metal Stress | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genome-Wide Analysis of Phaseolus vulgaris L. miR172 Gene Family Members Under Heavy Metal Stress Burak Muhammed Öner, Ahmed Sidar Aygören, Ayşe Gül Kasapoğlu, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6189246/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 06 Jan, 2026 Read the published version in BMC Genomics → Version 1 posted 23 You are reading this latest preprint version Abstract Background: Phaseolus vulgaris L. are a vital source of protein, vitamins, and minerals, significantly addressing nutritional deficiencies. P. vulgaris, like other plant species, demonstrate considerable susceptibility to heavy metal stress, a significant environmental challenge. miRNAs and their target genes play a crucial role in enabling plant responses to stress. In this study, the role of miR172 gene family, which is essential for growth and development and is among the first miRNAs identified in plants, under heavy metal stress in bean plants was investigated. By employing both bioinformatics and experimental methods, we sought to gain insights into its regulatory mechanisms and possible roles in enhancing stress tolerance. Results: Bioinformatics analysis identified 6 miR172 genes located on 5 different chromosomes in the P. vulgaris genome. The precursor sequences of Pvul-miR172 exhibited a characteristic root-loop structure, and the 19 nucleotide mature sequences were conserved across various species, categorizing them into three distinct phylogenetic classes. Elements responsive to stress were identified in the promoter regions of Pvul-miR172. GO analysis revealed that eight target genes associated with Pvul-miR172 are involved in carrier activity and binding, crucial for stress response. Measured parameters included root and shoot length, cell membrane integrity, relative water content, and chlorophyll levels in two bean genotypes. Exposure to heavy metal stress increased antioxidant enzyme activity and elevated proline, H2O2, and MDA levels. The analysis of expression profiles for Pvul-miR172s and their target genes under heavy metal stress revealed diverse regulatory patterns. PCA highlighted both positive and negative associations between Pvul-miR172s and their target genes. The findings suggest that Pvul-miR172s contribute to increased tolerance to heavy metal stress, with effects differing by genotype. Conclusions: The findings of this study demonstrate that Pvul-miR172s play a vital role in regulating common beans responses to heavy metal stress through interactions with target genes. The conserved features of miR172, coupled with its stress-related cis-acting elements and regulatory effects on target genes, highlight its potential in enhancing stress tolerance. This study elucidates the molecular mechanisms underlying heavy metal stress tolerance, offering potential strategies for developing resilient crop varieties. Antioxidant enzyme gene expression qRT-PCR step-loop target genes Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 06 Jan, 2026 Read the published version in BMC Genomics → Version 1 posted Editorial decision: Revision requested 11 Apr, 2025 Reviews received at journal 09 Apr, 2025 Reviews received at journal 09 Apr, 2025 Reviews received at journal 03 Apr, 2025 Reviews received at journal 02 Apr, 2025 Reviewers agreed at journal 27 Mar, 2025 Reviewers agreed at journal 26 Mar, 2025 Reviewers agreed at journal 26 Mar, 2025 Reviewers agreed at journal 25 Mar, 2025 Reviewers agreed at journal 25 Mar, 2025 Reviews received at journal 25 Mar, 2025 Reviewers agreed at journal 25 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers invited by journal 24 Mar, 2025 Editor assigned by journal 24 Mar, 2025 Editor invited by journal 24 Mar, 2025 Submission checks completed at journal 24 Mar, 2025 First submitted to journal 24 Mar, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6189246","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":433890161,"identity":"9b13154d-7878-4065-af18-5c4e465d5b77","order_by":0,"name":"Burak Muhammed Öner","email":"","orcid":"","institution":"Erzurum Technical University","correspondingAuthor":false,"prefix":"","firstName":"Burak","middleName":"Muhammed","lastName":"Öner","suffix":""},{"id":433890162,"identity":"1e553a92-7f2e-453d-aa90-b0aadd2103bc","order_by":1,"name":"Ahmed Sidar Aygören","email":"","orcid":"","institution":"Erzurum Technical 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P. vulgaris, like other plant species, demonstrate considerable susceptibility to heavy metal stress, a significant environmental challenge. miRNAs and their target genes play a crucial role in enabling plant responses to stress. In this study, the role of miR172 gene family, which is essential for growth and development and is among the first miRNAs identified in plants, under heavy metal stress in bean plants was investigated. By employing both bioinformatics and experimental methods, we sought to gain insights into its regulatory mechanisms and possible roles in enhancing stress tolerance.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eResults: Bioinformatics analysis identified 6 miR172 genes located on 5 different chromosomes in the P. vulgaris genome. The precursor sequences of Pvul-miR172 exhibited a characteristic root-loop structure, and the 19 nucleotide mature sequences were conserved across various species, categorizing them into three distinct phylogenetic classes. Elements responsive to stress were identified in the promoter regions of Pvul-miR172. GO analysis revealed that eight target genes associated with Pvul-miR172 are involved in carrier activity and binding, crucial for stress response. Measured parameters included root and shoot length, cell membrane integrity, relative water content, and chlorophyll levels in two bean genotypes. Exposure to heavy metal stress increased antioxidant enzyme activity and elevated proline, H2O2, and MDA levels. The analysis of expression profiles for Pvul-miR172s and their target genes under heavy metal stress revealed diverse regulatory patterns. PCA highlighted both positive and negative associations between Pvul-miR172s and their target genes. The findings suggest that Pvul-miR172s contribute to increased tolerance to heavy metal stress, with effects differing by genotype.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eConclusions: The findings of this study demonstrate that Pvul-miR172s play a vital role in regulating common beans responses to heavy metal stress through interactions with target genes. The conserved features of miR172, coupled with its stress-related cis-acting elements and regulatory effects on target genes, highlight its potential in enhancing stress tolerance. This study elucidates the molecular mechanisms underlying heavy metal stress tolerance, offering potential strategies for developing resilient crop varieties.\u003c/p\u003e","manuscriptTitle":"Genome-Wide Analysis of Phaseolus vulgaris L. miR172 Gene Family Members Under Heavy Metal Stress","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-26 06:09:28","doi":"10.21203/rs.3.rs-6189246/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-04-11T05:21:10+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-09T14:00:57+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-09T10:09:27+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-03T13:55:28+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-02T15:09:34+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"144035870697067196552001950493718356242","date":"2025-03-27T12:47:33+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"12310349637945849146575430991859284474","date":"2025-03-26T06:08:19+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36708974491720740252919274445982893631","date":"2025-03-26T04:00:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"303540618357673565695064285563853215973","date":"2025-03-25T23:56:20+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"102409938384536505614050725601773685357","date":"2025-03-25T16:39:46+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-03-25T16:10:52+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"55511146401682045258903861883771352739","date":"2025-03-25T04:22:35+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"287159905373492215112734877185492597480","date":"2025-03-25T03:58:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"308334617420857243554930477844471794956","date":"2025-03-25T03:00:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"199311488892703918334607738043263753257","date":"2025-03-24T18:26:01+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"45127758534340042552109895206138532094","date":"2025-03-24T15:55:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"137431691287991195788927498544426077618","date":"2025-03-24T14:01:38+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"259870195879985336397489903253281534398","date":"2025-03-24T13:37:13+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-24T13:26:09+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-03-24T13:16:16+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-03-24T13:04:24+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-03-24T11:34:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-03-24T11:33:38+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"f5186955-b4f0-4b35-b6f6-45b10825a769","owner":[],"postedDate":"March 26th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-01-12T16:05:48+00:00","versionOfRecord":{"articleIdentity":"rs-6189246","link":"https://doi.org/10.1186/s12864-025-12474-0","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2026-01-06 15:58:55","publishedOnDateReadable":"January 6th, 2026"},"versionCreatedAt":"2025-03-26 06:09:28","video":"","vorDoi":"10.1186/s12864-025-12474-0","vorDoiUrl":"https://doi.org/10.1186/s12864-025-12474-0","workflowStages":[]},"version":"v1","identity":"rs-6189246","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6189246","identity":"rs-6189246","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}