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Groundnut, a nutrient rich legume, contains several essential nutrients, high protein, essential amino-acids and vitamins required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) and protein content (PC), along with whole genome re-sequencing (WGRS) data from a mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in Fe (7.6 \u2013 42.8\u00a0ppm), Zn (10.9 \u2013 62.4\u00a0ppm) and PC (12.7 \u2013 33.6%). GWAS analysis identified a total of 15 marker-trait associations (MTAs) and 28 candidate genes for pooled season data, and 44 MTAs and 62 candidate genes for individual seasons. Key candidate genes like\n                    <jats:italic>MYB transcription factor<\/jats:italic>\n                    (\n                    <jats:italic>Arahy.QI0PHV<\/jats:italic>\n                    ,\n                    <jats:italic>Arahy.1I6ZSS<\/jats:italic>\n                    ),\n                    <jats:italic>Zn finger MYM type protein<\/jats:italic>\n                    ,\n                    <jats:italic>RING finger MYM type protein<\/jats:italic>\n                    (\n                    <jats:italic>Arahy.7P97F6<\/jats:italic>\n                    ,\n                    <jats:italic>Arahy.9R964H<\/jats:italic>\n                    ,\n                    <jats:italic>Arahy.I3B88T<\/jats:italic>\n                    ) and\n                    <jats:italic>NAC domain protein<\/jats:italic>\n                    (\n                    <jats:italic>Arahy.LV3APC<\/jats:italic>\n                    ), were found to be associated with the Fe and Zn homeostasis pathway. In addition, genes related to protein homeostasis, such as\n                    <jats:italic>Protein kinase family protein<\/jats:italic>\n                    (\n                    <jats:italic>Arahy.4D7KBI<\/jats:italic>\n                    ), and\n                    <jats:italic>E3 ubiquitin-protein ligase<\/jats:italic>\n                    (\n                    <jats:italic>Arahy.PE3CF6<\/jats:italic>\n                    ), were identified within significant MTA regions. These findings provide basis for the detection and characterization of potential candidate genes associated with nutritional quality traits. Haplo-pheno analysis revealed that accessions with superior haplotypes for kernel Fe and Zn content were predominantly found in the Spanish Bunch\/Valencia Bunch types, whereas the accessions with inferior haplotypes were more common in the Virginia Bunch\/Virginia Runner types. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 MTAs were designed and validated for Fe and Zn. Among these, three markers (snpAH00636 and snpAH00641 for Fe, and snpAH00644 for Zn) showed polymorphism, and could be utilized in genomics-assisted breeding to develop nutrient-rich groundnut varieties.\n                  <\/jats:p>","DOI":"10.1038\/s41598-026-57575-2","type":"journal-article","created":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T14:35:16Z","timestamp":1781361316000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut"],"prefix":"10.1038","volume":"16","author":[{"given":"U. 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