Genetic Determinants and Breeding Strategies for Rice Cooking and Eating Quality: A Comprehensive Review

Abstract

Rice cooking and eating quality (CEQ), a core agronomic trait tied to consumer preference and market value, is regulated by endosperm starch, protein, and lipid metabolism; this review synthesizes advances in its molecular mechanisms, focusing on genetic determinants and regulatory networks of storage substances. Starch is key: the Wx gene (central hub) has ≥ 9 allelic variants (e.g., Wxᵃ, Wxᵇ and Wxela), modulating amylose content (AC) via GBSSI activity, Wx gene expression levels, splicing efficiency, etc., and exerting pleiotropic effects on protein/lipid metabolism, grain transparency, and taste; storage proteins (80% glutelin) harm CEQ by inhibiting starch gelatinisation, regulated by relevant gene families and vesicular pathways (e.g., Rab5a-VPS9a); lipids (0.3%–3% of endosperm) affect Rapid Visco Analyzer (RVA) profiles and aroma via genes like OsFAD, PDCT, FGC3; modules (e.g., OsNF-Ys, OsbZIP60, Ghd7-OsNAC42) balance starch-protein accumulation. Breeding strategies include marker-assisted selection, CRISPR/Cas9 editing of Wx elements or glutelin genes, gene pyramiding (Wx, ALK, GS3), and artificial intelligence (AI)-integrated intelligent breeding to boost efficiency; the review first proposes a framework: ‘Wx genotype determination – amylopectin/glutelin regulation – CEQ improvement’, and the establishment of this framework is rooted in the core role of the Wx gene in determining rice eating quality, which is achieved through its pleiotropic regulation of starch, protein, and lipid metabolism in the endosperm. Future directions: use Wx allelic diversity, decipher multi-omics modules (e.g., RNA methylation in starch metabolism), and integrate aroma, Nitrogen Use Efficiency (NUE), grain shape, chalkiness, sugar transport genes to balance yield and CEQ for rice breeding.