Seed Morphogenesis: Genetic Architecture, Regulatory Mechanisms, and Breeding Opportunities

Seed morphogenesis determines seed size, shape, tissue organization, and developmental patterning, which influence crop yield and quality. This review compiles the genetic architecture, regulatory mechanisms, and breeding strategies for seed morphogenesis in major crops. Functionally validated genes and QTLs are cataloged with clear inclusion criteria to distinguish direct evidence for the causal gene from candidate genes identified by GWAS and linkage mapping. Developmental and environmental signals converge through hormonal crosstalk and epigenetic control, including Polycomb repressive complex 2 (PRC2) mediated histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs to shape seed morphogenesis. Six central regulatory modules govern seed morphogenesis: endosperm proliferation and cellularization, seed coat development, embryo patterning, hormonal integration, cell cycle and expansion control, and ncRNAs. Conserved and species-specific pathways are compared across Arabidopsis, cereals, and legumes, demonstrating that embryo patterning (LAFL, WOX, HD-ZIP III) is highly conserved, while endosperm development (MINI3/IKU2, AGL62) and seed coat development (SHP1/SHP2, STK, MYB5) are divergent, highlighting the need for species-specific frameworks. Modern technological advances such as high-throughput phenotyping, multi-omics, and CRISPR/Cas9 enable module-level functional validation. Breeding programs can deploy validated module genes through MAS, GS, and genome editing. Despite these advances, phenotyping, G × E interactions, pleiotropy, and the functional validation gap in underutilized crops remain unresolved. These gaps can be overcome by shifting from single-gene level manipulation to network-level engineering, integrating multi-omics and systems biology to translate module-level discoveries into improved seed morphogenesis.