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Here, we performed multi-stage RNA sequencing of tubers from glyphosate-resistant and -susceptible populations across three developmental stages to investigate the transcriptional dynamics underlying resistance. Differential expression analysis revealed extensive stage-specific transcriptional reprogramming, with the strongest divergence at the III developmental stage. Integrating constitutive and stage-dependent expression patterns identified 34 high-confidence candidate resistance-associated genes. Co-expression and regulatory network analyses uncovered coordinated transcriptional modules involving WRKY, NAC, ERF, MYB, bHLH, and ARF transcription factors together with multiple long non-coding RNAs. Notably, all allelic copies of ABCC8 were consistently up-regulated in glyphosate-resistant plants, validated by RT-qPCR, and occupied a central position in the resistance regulatory network, suggesting multilayered regulation of detoxification. These findings demonstrate that glyphosate resistance in C. rotundus is a developmentally coordinated, multilayered non-target-site resistance process.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c09642","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:02:23Z","timestamp":1790643743000},"page":"31217-31228","source":"Crossref","is-referenced-by-count":0,"title":["Multi-Stage Transcriptomics Reveals TF- and lncRNA-Mediated\nRegulatory Networks Governing Glyphosate Resistance in\n                    <i>Cyperus rotundus<\/i>"],"prefix":"10.1021","volume":"74","author":[{"given":"Shiqin","family":"Zhao","sequence":"first","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lamei","family":"Wu","sequence":"additional","affiliation":[{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]},{"name":"Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences , ,","place":["Changsha, China, 410125"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianbo","family":"Liu","sequence":"additional","affiliation":[{"name":"Tobacco Research Institute of Hunan Province , ,","place":["Changsha, China, 410004"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanxuan","family":"Lu","sequence":"additional","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Zhao","sequence":"additional","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailin","family":"Cai","sequence":"additional","affiliation":[{"name":"Changsha Branch of Hunan Tobacco Company , ,","place":["Changsha, China, 410001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Liu","sequence":"additional","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhanghui","family":"Liu","sequence":"additional","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianyang","family":"Bai","sequence":"additional","affiliation":[{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]},{"name":"Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences , ,","place":["Changsha, China, 410125"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi","family":"Luo","sequence":"additional","affiliation":[{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]},{"name":"Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences , ,","place":["Changsha, China, 410125"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8248-2055","authenticated-orcid":true,"given":"Lang","family":"Pan","sequence":"additional","affiliation":[{"name":"Hunan Agricultural University , , ,","place":["Changsha, China, 410128"]},{"name":"Yuelushan Laboratory , ,","place":["Changsha, China, 410128"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"issue":"1","key":"2026100711074394100_cit1","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1017\/S0890037X00029158","article-title":"Worldwide Distribution of Purple and Yellow Nutsedge\n(Cyperus rotundus and C. esculentus)","volume":"1","author":"Bendixen","year":"1987","journal-title":"Weed Technol."},{"issue":"12","key":"2026100711074394100_cit2","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1007\/s11738-017-2574-7","article-title":"Biology,\nagricultural impact, and management of Cyperus rotundus L.: the world\u2019s\nmost tenacious weed","volume":"39","author":"Peerzada","year":"2017","journal-title":"Acta Physiol. Plant."},{"issue":"5","key":"2026100711074394100_cit3","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1017\/S0043174500044489","article-title":"Seed Production\nand Germination in Cyperus esculentus\nand C. rotundus","volume":"27","author":"Thullen","year":"1979","journal-title":"Weed Sci."},{"key":"2026100711074394100_cit4","first-page":"57","article-title":"Effect of different\nherbicides on control of purple nutsedge (Cyperus rotundus L.)","volume":"16","author":"Rahnavard","year":"2010","journal-title":"Pak. J. Weed Sci. Res."},{"key":"2026100711074394100_cit5","doi-asserted-by":"publisher","first-page":"595","DOI":"10.15159\/AR.20.037","article-title":"Weed management in soybean with a special focus on\nthe control of purple nutsedge (Cyperus rotundus)","volume":"18","author":"Travlos","year":"2020","journal-title":"Agron. Res."},{"issue":"5","key":"2026100711074394100_cit6","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1614\/WS-07-188.1","article-title":"Glyphosate\nHinders Purple Nutsedge (Cyperus rotundus) and Yellow Nutsedge (Cyperus\nesculentus) Tuber Production","volume":"56","author":"Webster","year":"2008","journal-title":"Weed Sci."},{"key":"2026100711074394100_cit7","doi-asserted-by":"publisher","first-page":"101624","DOI":"10.1016\/j.xplc.2025.101624","article-title":"Chromosome-level genome assembly of triploid\nCyperus rotundus uncovers\nallelic expression patterns and herbicide resistance mechanisms","volume":"7","author":"Wu","year":"2026","journal-title":"Plant Commun."},{"issue":"4","key":"2026100711074394100_cit8","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1007\/s00425-015-2324-2","article-title":"Mutations and amplification\nof EPSPS\ngene confer resistance to glyphosate in goosegrass (Eleusine indica)","volume":"242","author":"Chen","year":"2015","journal-title":"Planta"},{"key":"2026100711074394100_cit9","doi-asserted-by":"publisher","first-page":"1692","DOI":"10.3390\/agronomy10111692","article-title":"First Report of Glyphosate-Resistant\nBiotype of Eleusine Indica (L.) 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