Genetic diversity analysis of white maize inbred lines using SNP markers Article Swipe

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Biology Genetic diversity Germplasm Genetics Population Inbred strain Single-nucleotide polymorphism Minor allele frequency Genetic distance Genetic structure Genotype Genetic variation Inbreeding Dendrogram SNP Genetic variability Loss of heterozygosity Genetic marker Genetic analysis Breeding program White (mutation) Allele Allele frequency Evolutionary biology Gene pool Population genetics Biotechnology Fixation index Microsatellite Plant breeding Amplified fragment length polymorphism Genetic association Fixation (population genetics)

Snežana Mladenović Drinić , Ana Nikolić , Nikola Grčić , Natalija Kravić , Marko Mladenović , Jelena Srdić , Viоlеtа Аnđеlkоvić ·

YOU? · · 2025 · Open Access · · OA: W7116587867

White maize (Zea mays L.) represents an important genetic resource with significant nutritional and agronomic value. Understanding its genetic diversity is essential for the conservation of local germplasm and the development of improved cultivars with desirable traits. A set of 63 white maize inbred lines sourced from the Gene Bank of the Maize Research Institute and its breeding programs was analyzed to assess genetic diversity and population structure using a 25K SNP Illumina Infinium Array (TraitGenetics). After quality filtering, 19,172 high-quality Single Nucleotide Polymorphism (SNP) markers were retained for analysis. Genetic diversity parameters were estimated using PLINK 1.9, while genetic distances and a dendrogram were generated in Tassel 5. Minor allele frequency (MAF) ranged from 0.05 to 0.5 (average 0.31), observed heterozygosity (Ho) from 0.015 to 0.1 (average 0.03), and expected heterozygosity (He) from 0.095 to 0.5 (average 0.40), indicating a relatively low level of diversity. Cluster analysis classified the inbreds into three main groups, with Group I comprising the majority of genotypes (39), Group II (19) and Group III containing only five. Principal Coordinate Analysis (PCoA) performed in R software supported these findings. Population structure analysis using STRUCTURE v2.3.4 confirmed the presence of three subpopulations (optimal K = 3), although some discrepancies in genotype grouping between cluster and STRUCTURE analyses were observed. These findings provide a comprehensive overview of the genetic relationships among the examined lines and highlight their potential as a valuable resource for future breeding programs and germplasm conservation strategies.