{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T05:47:05Z","timestamp":1782798425018,"version":"3.54.5"},"reference-count":210,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010825","name":"China Tobacco Yunnan Industrial Corp","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>Dissecting complex quantitative traits is constrained by limited genetic diversity in biparental populations and population structure confounding in genome-wide association studies. Multi-parent Advanced Generation Inter-Cross (MAGIC) populations address these limitations by intercrossing multiple diverse founders followed by selfing to generate immortalized recombinant inbred lines exhibiting extensive recombination and balanced allele frequencies. MAGIC populations synergistically combine high mapping resolution with broad genetic diversity, enabling detection of small-effect QTLs, epistatic interactions, and genotype-by-environment effects. Despite their immense potential and successful deployment across diverse crops, several critical challenges remain regarding founder selection strategies, computational efficiency of haplotype reconstruction, and seamless integration into existing breeding pipeline. In this review, we synthesize current knowledge of MAGIC construction principles, crossing designs, and inbreeding strategies, and critically evaluate genotyping technologies and statistical frameworks including hidden Markov models, identity-by-descent mapping, and multi-locus mixed models. Furthermore, we explored how integrating with high-throughput phenotyping enhances multi-environment trait characterization, with applications across diverse crops revealing common bottlenecks and successful strategies. We also outlined transformative opportunities through joint linkage-association analysis for causal variant identification, integrating MAGIC Populations with AI-driven genomic selection for accelerated genetic gain, and multi-omics approaches for mechanistic trait dissection. This synthesis provides actionable frameworks for optimizing MAGIC population development and exploitation, advancing precision crop improvement in the face of climate change and resource constraints.<\/jats:p>","DOI":"10.3389\/fpls.2026.1867756","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T05:40:29Z","timestamp":1782798029000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["MAGIC populations: a next-generation framework for dissecting complex quantitative traits and accelerating molecular breeding in crops"],"prefix":"10.3389","volume":"17","author":[{"given":"Asad","family":"Ullah","sequence":"first","affiliation":[{"name":"Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences","place":["Kunming, China"]},{"name":"Institute of Crop Science and Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhijun","family":"Tong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Kamran","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"family":"Umaira","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuejun","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiming","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingguang","family":"Xiao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1534\/genetics.114.167577","article-title":"Characterizing uncertainty in high-density maps from multiparental populations","volume":"198","author":"Ahfock","year":"2014","journal-title":"Genetics"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.70096","article-title":"A chickpea MAGIC population to dissect the genetics of complex traits","volume":"18","author":"Akinlade","year":"2025","journal-title":"Plant Genome"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1186\/s40246-025-00718-9","article-title":"Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues","volume":"19","author":"Alemu","year":"2025","journal-title":"Hum. 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