{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T18:01:40Z","timestamp":1790359300199,"version":"4.1.0"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1134248"],"award-info":[{"award-number":["OPP1134248"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Early-maturing maize is vital for strengthening food security across the drought-prone agro-ecologies of Sub-Saharan Africa (SSA). Advancing genetic gain in these environments requires a clear understanding of genetic diversity and population structure patterns to support parental selection and future genomic-assisted breeding efforts. The study aimed at assessing genetic diversity and population structure of a panel of early-maturing yellow and orange kernel maize inbred lines, classify the inbred lines into putative heterotic groups, and identify a core set of elite, genetically divergent lines suitable for use in hybrid breeding and long-term genetic improvement. A panel of 376 elite early-maturing yellow and orange maize inbred lines from four source populations were genotyped using the DArTag SNP markers. After quality filtering, 1,954 high-quality SNP markers retained exhibited moderate diversity with an average polymorphic information content (PIC) of 0.38 and minor allele frequency (MAF) of 0.28. Linkage disequilibrium analysis showed a mean r\n                    <jats:sup>2<\/jats:sup>\n                    of 0.046, with rapid LD decay across the genome, indicating substantial historical recombination and suggesting potential utility of the panel for future association studies. The Admixture analysis and discriminant analysis of principal components (DAPC) consistently resolved the panel into two major subpopulations with overlapping membership. Phylogenetic clustering also resolved the panel into two broad molecular clusters corresponding to putative heterotic groups. Analysis of molecular variance (AMOVA) revealed that most genetic variation occurred within groups (86%), with moderate differentiation among groups (14%). A core set representing 20% of the collection was identified using an allelic-richness\u2013based greedy algorithm, offering valuable insights to accelerate breakthrough hybrid development for SSA farming systems. The study provides a comprehensive genomic characterization of early-maturing maize germplasm, providing genomic insights that may support future hybrid development and germplasm management efforts for SSA maize breeding programs.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0358751","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T17:44:39Z","timestamp":1790358279000},"page":"e0358751","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic diversity and population structure of early-maturing yellow and orange maize inbred lines for improved breeding applications"],"prefix":"10.1371","volume":"21","author":[{"given":"Neo Jeremiah","family":"Mahula","sequence":"first","affiliation":[{"name":"Program of Plant Breeding, Pan African University Life and Earth Sciences Institute (including Health and Agriculture), PAULESI","place":["Nigeria"]},{"name":"Maize Improvement Program, (MIP), International Institute of Tropical Agriculture (IITA)","place":["Ibadan, Nigeria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6533-0612","authenticated-orcid":true,"given":"Idris Ishola","family":"Adejumobi","sequence":"additional","affiliation":[{"name":"Maize Improvement Program, (MIP), International Institute of Tropical Agriculture (IITA)","place":["Ibadan, Nigeria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julius Akinyemi","family":"Fagbayide","sequence":"additional","affiliation":[{"name":"Program of Plant Breeding, Pan African University Life and Earth Sciences Institute (including Health and Agriculture), PAULESI","place":["Nigeria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baffour","family":"Badu-Apraku","sequence":"additional","affiliation":[{"name":"Maize Improvement Program, (MIP), International Institute of Tropical Agriculture (IITA)","place":["Ibadan, Nigeria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Derera","sequence":"additional","affiliation":[{"name":"Maize Improvement Program, (MIP), International Institute of Tropical Agriculture (IITA)","place":["Ibadan, Nigeria"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"issue":"1","key":"pone.0358751.ref001","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1186\/s12864-016-3041-3","article-title":"Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers","volume":"17","author":"X Zhang","year":"2016","journal-title":"BMC Genomics"},{"issue":"7","key":"pone.0358751.ref002","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.3390\/agronomy11071371","article-title":"Gene action, heterotic patterns, and inter-trait relationships of early maturing pro-vitamin a maize inbred lines and performance of testcrosses under contrasting environments","volume":"11","author":"B Badu-Apraku","year":"2021","journal-title":"Agronomy"},{"key":"pone.0358751.ref003","doi-asserted-by":"crossref","first-page":"1463924","DOI":"10.3389\/fpls.2024.1463924","article-title":"Genetic analysis of grain yield and related traits of extra-early orange maize inbred lines and their hybrids under drought and rain-fed conditions","volume":"15","author":"TO Bonkoungou","year":"2024","journal-title":"Front Plant Sci"},{"key":"pone.0358751.ref004","doi-asserted-by":"crossref","DOI":"10.1016\/j.fcr.2013.10.015","article-title":"Heterotic grouping of tropical early-maturing maize inbred lines based on combining ability in Striga-infested and Striga-free environments and the use of SSR markers for genotyping,","volume":"156","author":"RO Akinwale","year":"2014","journal-title":"F. 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Evol"},{"issue":"1","key":"pone.0358751.ref020","article-title":"FactoMineR: An R package for multivariate analysis","volume":"25","author":"S L\u00ea","year":"2008","journal-title":"J. Stat. Softw"},{"key":"pone.0358751.ref021","author":"A Kassambara","year":"2020"},{"issue":"11","key":"pone.0358751.ref022","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btn129","article-title":"Adegenet: A R package for the multivariate analysis of genetic markers","volume":"24","author":"T Jombart","year":"2008","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0358751.ref023","article-title":"A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides","volume":"10","author":"ZL Chen","year":"2019","journal-title":"Nat. Commun"},{"issue":"4","key":"pone.0358751.ref024","doi-asserted-by":"crossref","DOI":"10.1016\/j.gpb.2021.08.005","article-title":"GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction,","volume":"19","author":"J Wang","year":"2021","journal-title":"Genomics, Proteomics Bioinforma"},{"key":"pone.0358751.ref025","author":"RC. Team","year":"2017"},{"issue":"3","key":"pone.0358751.ref026","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"S Purcell","year":"2007","journal-title":"Am J Hum Genet"},{"issue":"19","key":"pone.0358751.ref027","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: software for association mapping of complex traits in diverse samples","volume":"23","author":"PJ Bradbury","year":"2007","journal-title":"Bioinformatics"},{"key":"pone.0358751.ref028","first-page":"160","article-title":"ggplot2 - Elegant Graphics for Data Analysis (2nd Edition),","author":"V G\u00f3mez-Rubio","year":"2017","journal-title":"J. Stat. Softw"},{"issue":"20","key":"pone.0358751.ref029","doi-asserted-by":"crossref","first-page":"11479","DOI":"10.1073\/pnas.201394398","article-title":"Structure of linkage disequilibrium and phenotypic associations in the maize genome","volume":"98","author":"DL Remington","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pone.0358751.ref030","article-title":"Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers,","volume":"4","author":"J Yan","year":"2009","journal-title":"PLoS One"},{"key":"pone.0358751.ref031","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2156-11-94","article-title":"Discriminant analysis of principal components: a new method for the analysis of genetically structured populations","volume":"11","author":"T Jombart","year":"2010","journal-title":"BMC Genet"},{"key":"pone.0358751.ref032","article-title":"Ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R,","author":"E Paradis","year":"2019","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0358751.ref033","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data,","volume":"8","author":"G Yu","year":"2017","journal-title":"Methods Ecol. Evol"},{"issue":"28","key":"pone.0358751.ref034","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/bts460","article-title":"GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update.","author":"R Peakall","year":"2012","journal-title":"Bioinformatics"},{"key":"pone.0358751.ref035","author":"H De Beukelaer","year":"2018"},{"key":"pone.0358751.ref036","article-title":"Core collections: A practical approach to genetic resources management,\u201d in Genome","author":"AHD Brown","year":"1989"},{"issue":"8","key":"pone.0358751.ref037","doi-asserted-by":"crossref","DOI":"10.1007\/s00122-001-0556-y","article-title":"A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement","volume":"102","author":"HD Upadhyaya","year":"2001","journal-title":"Theor Appl Genet"},{"key":"pone.0358751.ref038","article-title":"R Core Team 2023 R: A language and environment for statistical computing. R foundation for statistical computing","author":"R. C. Team","year":"2023","journal-title":"R Found Stat Comput"},{"key":"pone.0358751.ref039","author":"Y Beyene","year":"2015"},{"key":"pone.0358751.ref040","author":"J Crossa","year":"2017"},{"issue":"4","key":"pone.0358751.ref041","article-title":"Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs","volume":"129","author":"Y Wu","year":"2016","journal-title":"Theor Appl Genet"},{"key":"pone.0358751.ref042","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2164-13-113","article-title":"Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers","volume":"13","author":"K Semagn","year":"2012","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0358751.ref043","doi-asserted-by":"crossref","DOI":"10.1186\/s12870-017-1058-7","article-title":"Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu,","volume":"17","author":"X Wang","year":"2017","journal-title":"BMC Plant Biol"},{"issue":"1906","key":"pone.0358751.ref044","first-page":"20190486","article-title":"Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize","volume":"286","author":"JA Aguirre-Liguori","year":"2019","journal-title":"Proc Biol Sci"},{"key":"pone.0358751.ref045","article-title":"Genetic analysis of early white quality protein maize inbreds and derived hybrids under low\u2010nitrogen and combined drought and heat stress environments,","author":"OA Bhadmus","year":"2021","journal-title":"Plants"},{"issue":"1","key":"pone.0358751.ref046","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s00122-009-1162-7","article-title":"Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms","volume":"120","author":"Y Lu","year":"2009","journal-title":"Theor Appl Genet"},{"key":"pone.0358751.ref047","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1186\/1471-2105-10-243","article-title":"Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures","volume":"10","author":"C Thachuk","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"pone.0358751.ref048","author":"TL Odong","year":"2013"},{"issue":"1","key":"pone.0358751.ref049","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/s00122-014-2418-4","article-title":"Training set optimization under population structure in genomic selection","volume":"128","author":"J Isidro","year":"2015","journal-title":"Theor Appl Genet"},{"issue":"1","key":"pone.0358751.ref050","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s12711-015-0116-6","article-title":"Optimization of genomic selection training populations with a genetic algorithm","volume":"47","author":"D Akdemir","year":"2015","journal-title":"Genet Sel Evol"},{"key":"pone.0358751.ref051","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2016.00210","article-title":"Efficient breeding by genomic mating","volume":"7","author":"D Akdemir","year":"2016","journal-title":"Front Genet"},{"issue":"1","key":"pone.0358751.ref052","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/jhered\/92.1.93","article-title":"MSTRAT: an algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness","volume":"92","author":"B Gouesnard","year":"2001","journal-title":"J Hered"},{"key":"pone.0358751.ref053","author":"M B\u00e4nziger","year":"2000"},{"key":"pone.0358751.ref054","author":"JE Cairns","year":"2013"},{"key":"pone.0358751.ref055","author":"BM Prasanna","year":"2021"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0358751","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T17:44:52Z","timestamp":1790358292000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0358751"}},"subtitle":[],"editor":[{"given":"Vikas","family":"Sharma","sequence":"first","affiliation":[{"name":"Sant Baba Bhag Singh University","place":["INDIA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,25]]},"references-count":55,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0358751","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,25]]}}}