Genetic architecture of seed protein composition in grain amaranth (Amaranthus hypochondriacus): a multi-environment genome-wide association study

Introduction Grain amaranth ( Amaranthus hypochondriacus ), a nutrient-rich pseudocereal, holds immense potential for protein biofortification, yet the genetic architecture of its seed protein fraction composition remains uncharacterized. Methods To dissect this complex trait, we conducted a multi-environment genome-wide association study (GWAS) on a diversity panel of 192 accessions for albumin, globulin, glutelin, prolamin, and total protein content. Significant phenotypic variation was observed for all fractions, with high broad-sense heritability (H 2 ≥ 0.91) for albumin and total protein, indicating strong genetic control and high selection potential. A multi-locus GWAS using 41,931 SNPs identified 356 significant marker-trait associations (MTAs). Results Crucially, filtering for cross-environmental stability revealed 17 robust MTAs for total protein (6), albumin (5), glutelin (5), and globulin (1), while prolamin content was governed by environment-specific loci. Strikingly, candidate gene analysis of these stable loci revealed that natural variation is predominantly controlled by trans-regulatory mechanisms rather than by cis-variation in the storage structural genes themselves. Key regulatory hubs were identified, implicating the abscisic acid (ABA) biosynthesis and signaling pathway in glutelin accumulation and endoplasmic reticulum (ER) protein folding capacity in limiting globulin content. Discussion This work establishes the first comprehensive genomic framework for seed protein composition in amaranth, providing environmentally stable markers and validated biological pathways to accelerate the development of nutritionally enhanced cultivars through marker-assisted selection.