Genome-wide Identification and Characterization of Zinc Transporter (ZnT) Gene Family in Amaranthus hypochondriacus: Insights into Molecular Mechanisms of Zinc Homeostasis and Biofortification Potential

Abstract

Amaranthus hypochondriacus, a nutritionally superior C4 pseudocereal, naturally accumulates high zinc concentrations in its tissues, making it a promising candidate for biofortification programs adressing global micronutrient malnutrition. However, the molecular mechanisms underlying this zinc accumulation capacity remain largely unexplored. This study presents the first comprehensive genome-wide characterization of the zinc transporter (ZnT) gene family in A. hypochondriacus through systematic in silico analysis. Using in-silico screening of the complete proteome, we identified nine ZnT genes (AhZnT1-AhZnT9) exhibiting remarkable structural diversity with genomic sizes ranging from 2.5-12.7 kb and coding sequences containing 1-12 exons.  All proteins contained the characteristic. Cation Diffusion Facilitator domain, with 55.6% additionally possessing ZT dimer domains, suggesting evolved regulatory mechanisms. Phylogenetic analysis revealed three major evolutionary clades, indicating ancient duplication events and functional diversification, while chromosomal mapping showed dispersed distribution across seven scaffolds. Tissue-specific expression analysis across seven tissue types revealed distinct functional specializations, with AhZnT5 showing highest expression in reproductive tissues (45.8 TPM in flowers) and AhZnT9 in embryonic tissues (44.9 TPM), indicating critical roles in zinc mobilization during reproduction and seed development. Several genes displayed restricted expression profiles, such as AhZnT4 with preferential expression in seed and cotyledon tissues. This comprehensive characterization provides crucial molecular insights into zinc homeostasis mechanisms in amaranth and identifies key candidate genes for biofortification strategies. The identified ZnT genes, particularly AhZnT5 and AhZnT9, represent promising targets for genetic engineering approaches including transgenic expression, CRISPR/Cas gene editing, and marker-assisted breeding. These genes can potentially be transferred to major staple crops to enhance zinc content, establishing a foundation for developing zinc-enriched varieties to combat global micronutrient deficiencies.