Proteomic reprogramming during amaranth seed germination reveals a domestication signature associated with stress versus growth strategies

Introduction: Amaranth is a nutrient-rich underutilised crop with potential to enhance food security, yet the molecular effects of domestication on seed germination remain poorly understood. Elucidating how domestication has reshaped the germination proteome can guide breeding towards faster and more stress-resilient varieties.

Methods: We performed label-free quantitative shotgun proteomics on seeds of cultivated (Amaranthus hypochondriacus cv Cristalina) and wild (A. hybridus) amaranth species. Seeds were germinated at 25 °C in darkness, and five morphological phases were collected according to germination curves, each with three biological replicates. Proteins were retained if quantified in at least two replicates in late stages (PIII or Post germ). After median imputation, differential expression (limma, |log₂FC| > 1, adj.P < 0.05), WGCNA, STRING networks, and GO enrichment were applied to 614 filtered proteins.

Results: A 15-protein domestication signature was identified: chaperones (ClpB, HSP17.4), annexin D2, and antioxidant enzymes were consistently more abundant in the wild, whereas proteasome subunits, ribosomal proteins, and glycolytic enzymes were higher in the cultivated line – a pattern suggesting a trade-off between stress preparedness and rapid growth. WGCNA confirmed a stress-related module strongly upregulated in wild (r = 0.966, p = 5×10⁻¹⁸) and an energy module conserved across phases. The proportion of differentially abundant proteins peaked at PII (120/614, 19.5 %), highlighting this phase as the major divergence point. Oleosin and ribokinase were identified as stable markers of species identity and early germination vigour, respectively.

Conclusions: Domestication appears to have shifted the amaranth proteome from constitutive stress defense toward accelerated energy production and translation. This work provides candidate markers for breeding and contributes to the valorization of underutilized crops for sustainable food systems.