Exploratory Transcriptomic Profiling of Seed Development in Amaranthus hypochondriacus Prioritizes Candidate Genes for Future Studies on Grain Quality and Seed Maturation

OV was character-ized by transcripts associated with structural organization and early developmental processes, whereas IS showed increased representation of metabolic and biosynthetic functions consistent with active reserve accumulation. MS displayed transcript-abundance patterns associated with stress responses, redox homeostasis, abscisic acid-associated processes, and desiccation-related protection. Selected genes related to gibberellin me-tabolism, reserve regulation, developmental control, and cellular protection showed stage-associated expression patterns.

Across developmental-stage comparisons, 1083 genes showed higher and 2801 lower transcript representation in OV relative to IS, whereas 5692 and 4424 genes, respectively, differed between OV and MS, and 6399 and 4128 between IS and MS. Semi-quantitative RT-PCR and targeted H3K4me3 ChIP-PCR provided complementary evidence for selected loci. Because each developmental stage was represented by a single composite RNA-seq library, the transcriptomic contrasts are interpreted as exploratory and hypothesis-generating rather than as statistically repli-cated developmental effects.

Therefore, this study provides a stage-resolved tran-scriptomic resource for grain amaranth and prioritizes candidate genes and biological processes for future functional, physiological, and breeding-oriented studies of seed maturation and composition.