Abstract
This study investigates the material foundations underpinning the variations in appearance quality among different types of japonica rice and within different grain positions, thereby providing a theoretical basis for enhancing the quality of soft rice varieties. The experimental results indicate that relative to non-soft rice, soft varieties demonstrate markedly higher levels of chalkiness and reduced transparency in both grain classifications. Structural analyses indicate that soft rice grains, particularly the inferior ones, exhibit lower amylose content along with higher proportions of small starch granules and Fa chains, alongside enhanced crystallinity and short-range order. These characteristics compromise the crystalline integrity and amplify light scattering. Furthermore, the protein network in soft rice is characterized by increased levels of albumin and glutelin, a reduction in prolamin content, and a transition towards α-helix and random coil structures. These changes suggest a diminished integration of starch and protein and introduce spatial limitations. The compounded defects across multiple scales in starch and protein structures are more accentuated in inferior grains, leading to enhanced porosity and optical heterogeneity within the endosperm. This synergistic degradation of starch and protein architectures emerges as the primary mechanism responsible for the relatively poor appearance quality of soft rice. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-026-00886-9.