Deciphering the genetic determinants of calcium, iron, magnesium and zinc accumulation in grain amaranth (Amaranthus hypochondriacus) through a multi environment GWAS approach

Micronutrient malnutrition poses a global challenge, highlighting the need for biofortified crops with enhanced mineral density. Grain amaranth (Amaranthus hypochondriacus), a nutrient-rich pseudocereal, offers high levels of essential minerals, yet its genetic basis for mineral accumulation remains poorly understood. We evaluated 192 diverse accessions across two contrasting environments for calcium (Ca), iron (Fe), magnesium (Mg), and zinc (Zn) content, which varied from 90.5 to 249.7 mg/100 g (1.8-fold) for Ca, 6.8-35.7 mg/100 g (5.2-fold) for Fe, 182.2-471.7 mg/100 g (2.6-fold) for Mg, and 2.6-9.2 mg/100 g (3.6-fold) for Zn. High broad-sense heritability (H² ≥ 0.87) and substantial genetic advance confirmed strong genetic control and scope for selection. A multi-locus genome-wide association study using 41,931 SNPs identified 368 significant associations, of which 25 environmentally stable marker trait associations (MTAs) were detected across traits. Candidate gene analysis revealed 92 putative genes related to mineral homeostasis, and expression profiling validated functional relevance of key candidates. This study provides a comprehensive genomic framework for marker-assisted breeding of biofortified amaranth cultivars with enhanced mineral density.