{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:15:29Z","timestamp":1793319329081,"version":"4.5.0"},"reference-count":19,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T00:00:00Z","timestamp":1768435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>Plant molecular marker technologies have reshaped crop genetics and breeding by making it possible to analyse genome-wide variation with a precision that phenotype-based selection, even in experienced programmes, cannot reach in routine practice. This review summarises recent progress in marker platforms from classical RFLP and SSR systems to high-throughput SNP genotyping, with emphasis on KASP, multiple nucleotide polymorphism and multi-gene panel technologies, and on sequencing-based methods such as GBS, GBTS and Hyper-seq that often serve as an upstream discovery layer for targeted assays and databases. These platforms are increasingly integrated into practical workflows for marker-assisted and genomic selection, DNA fingerprinting, germplasm characterisation and plant variety protection, and multi-locus markers have become a central tool for high-resolution DUS testing and EDV determination that adds an independent layer of evidence to morphology-based assessments. Key challenges now include cross-platform standardisation, design of marker panels that balance cost with information content, interoperability of databases across institutions and countries, and the definition of molecular distance thresholds that are acceptable both biologically and in legal and regulatory settings. The review also considers the rapid integration of molecular marker data with artificial intelligence, including AI-driven marker discovery and panel optimisation, genomic prediction in multi-environment trials and the concept of an intelligent seed-industry operating system that links genotypic, phenotypic and environmental information in a coherent data framework. These developments collectively point to a shift from isolated marker assays towards platform-level, AI-supported infrastructures that can accelerate variety innovation and contribute to the modernisation and quality improvement of the seed industry.<\/jats:p>","DOI":"10.3389\/fpls.2025.1757949","type":"journal-article","created":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T17:01:44Z","timestamp":1768496504000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["Advances and challenges in plant molecular marker technologies and their applications in the artificial intelligence empowered era"],"prefix":"10.3389","volume":"16","author":[{"given":"Xiaoxu","family":"Li","sequence":"first","affiliation":[{"name":"Technology Center, China Tobacco Hunan Industrial Co., Ltd.","place":["Changsha, China"]},{"name":"Beijing Life Science Academy","place":["Beijing, China"]},{"name":"Tobacco Research Institute, Chinese Academy of Agricultural Sciences","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengrong","family":"Hu","sequence":"additional","affiliation":[{"name":"Hunan Tobacco Science Research Institute","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Yu","sequence":"additional","affiliation":[{"name":"Institute of Tobacco Science, Fujian Provincial Tobacco Company","place":["Fuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Xie","sequence":"additional","affiliation":[{"name":"Yunnan Academy of Tobacco Agricultural Sciences","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuebo","family":"Wang","sequence":"additional","affiliation":[{"name":"Tobacco Science Research Institute of Guangdong Province","place":["Shaoguan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pingjun","family":"Huang","sequence":"additional","affiliation":[{"name":"Technology Center, China Tobacco Hunan Industrial Co., Ltd.","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Technology Center, China Tobacco Hunan Industrial Co., Ltd.","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiashuo","family":"Yang","sequence":"additional","affiliation":[{"name":"Hunan Tobacco Science Research Institute","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangyang","family":"Li","sequence":"additional","affiliation":[{"name":"Hunan Tobacco Science Research Institute","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weicai","family":"Zhao","sequence":"additional","affiliation":[{"name":"Tobacco Science Research Institute of Guangdong Province","place":["Shaoguan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaonian","family":"Yang","sequence":"additional","affiliation":[{"name":"Technology Center, China Tobacco Hunan Industrial Co., Ltd.","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenchen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Crops Research Institute, Guangdong Academy of Agricultural Sciences","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxuan","family":"Pu","sequence":"additional","affiliation":[{"name":"Technology Center, China Tobacco Hunan Industrial Co., Ltd.","place":["Changsha, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyuan","family":"Li","sequence":"additional","affiliation":[{"name":"Tobacco Research Institute, Chinese Academy of Agricultural Sciences","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,15]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e20556","DOI":"10.1002\/tpg2.20556","article-title":"Molecular markers enhance substantially the distinctness of alfalfa varieties for registration and protection","volume":"18","author":"Annicchiarico","year":"2025","journal-title":"Plant Genome"},{"key":"B2","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1177\/00307270221124008","article-title":"Because error has a price: A systematic review of the applications of DNA fingerprinting for crop varietal identification","volume":"51","author":"Euler","year":"2022","journal-title":"Outlook Agric."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1101\/2021.03.09.434561","article-title":"Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations","volume":"10","author":"Fang","year":"2021","journal-title":"bioRxiv"},{"key":"B4","doi-asserted-by":"publisher","first-page":"565","DOI":"10.3390\/applbiosci2040036","article-title":"Agrigenomic diversity unleashed: Current single nucleotide polymorphism genotyping methods for the agricultural sciences","volume":"2","author":"Lawrie","year":"2023","journal-title":"Appl. Biosci."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1016\/j.scienta.2023.112642","article-title":"Establishment and application of a multiple nucleotide polymorphism molecular identification system for grape cultivars","volume":"325","author":"Liu","year":"2024","journal-title":"Sci. Hortic."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3390\/jof9030330","article-title":"). Development of multiple nucleotide polymorphism molecular markers for Flammulina filiformis cultivars identification","volume":"9","author":"Liu","year":"2023","journal-title":"J. Fungi"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.3390\/horticulturae10080845","article-title":"Availability evaluation and application of MNP (multiple nucleotide polymorphism) markers in variety identification of chrysanthemum","volume":"10","author":"Liu","year":"2024","journal-title":"Horticulturae"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cpb.2024.100412","article-title":"Using next-generation sequencing approach for discovery and characterization of plant molecular markers","volume":"40","author":"Panahi","year":"2024","journal-title":"Curr. Plant Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s44372-025-00262-9","article-title":"PCR-based single nucleotide polymorphism (SNP) genotyping for crop improvement-current status and future prospects","volume":"2","author":"Sahoo","year":"2025","journal-title":"Discov. Plants"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11032-013-9917-x","article-title":"). Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): Overview of the technology and its application in crop improvement","volume":"33","author":"Semagn","year":"2014","journal-title":"Mol. Breed."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1460603","article-title":"Development of KASP markers, SNP fingerprinting, and population genetic analysis of Cymbidium ensifolium germplasm resources in China","volume":"15","author":"Shen","year":"2025","journal-title":"Front. Plant Sci."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.655254","article-title":"Development of GBTS and KASP panels for genetic diversity, population structure and fingerprinting of a large collection of broccoli in China","volume":"12","author":"Shen","year":"2021","journal-title":"Front. Plant Sci."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/plants13192676","article-title":"Modern plant breeding techniques in crop improvement and genetic diversity: From molecular markers and gene editing to artificial intelligence-A critical review","volume":"13","author":"Sun","year":"2024","journal-title":"Plants"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1016\/j.molp.2022.09.001","article-title":"Smart breeding driven by big data, artificial intelligence, and integrated genomic\u2013enviromic prediction","volume":"15","author":"Xu","year":"2022","journal-title":"Mol. Plant"},{"key":"B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-024-11139-8","article-title":"SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.)","volume":"25","author":"Yang","year":"2024","journal-title":"BMC Genomics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/genes12081127","article-title":"Plant variety protection: Current practices and insights","volume":"12","author":"Yu","year":"2021","journal-title":"Genes"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-022-04562-9","article-title":"Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice","volume":"23","author":"Yuan","year":"2022","journal-title":"BMC Bioinform."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1603210","article-title":"Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis","volume":"16","author":"Zhang","year":"2025","journal-title":"Front. Plant Sci."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/ffunb.2025.1647126","article-title":"Novel and advanced MNP molecular markers accurately identify the genetic similarity of Hypsizygus marmoreus strains: A comparative evaluation with ISSR and antagonistic methods","volume":"6","author":"Zhao","year":"2025","journal-title":"Front. Fungal Biol."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2025.1757949\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T17:01:44Z","timestamp":1768496504000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2025.1757949\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,15]]},"references-count":19,"alternative-id":["10.3389\/fpls.2025.1757949"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2025.1757949","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,15]]},"article-number":"1757949"}}