Haplotype Analysis of the Wx and SSIIa Genes and Their Association with Starch Physicochemical Properties in Diverse Rice Germplasm

Starch physicochemical properties are key determinants of rice (Oryza sativa L.) grain quality, influencing cooking performance, texture, nutritional value, and industrial functionality. Among the genes regulating starch biosynthesis, Wx (encoding granule-bound starch synthase I, GBSSI) and SSIIa (starch synthase IIa) are major-effect loci controlling amylose content and amylopectin chain length distribution, respectively. Although classical studies identified major functional polymorphisms within these genes, recent genomic analyses reveal extensive haplotypic diversity that better explains quantitative variation in starch traits across diverse rice germplasm. This review synthesizes current knowledge on the molecular structure, regulation, and allelic diversity of Wx and SSIIa, highlighting the importance of haplotype-based approaches for interpreting starch physicochemical behavior. Wx haplotypes primarily modulate amylose accumulation and associated properties such as gel consistency, pasting characteristics, and resistant starch formation, whereas SSIIa haplotypes largely determine gelatinization temperature and amylopectin structural organization. Evidence from association mapping and population genomic studies further demonstrates that combined Wx–SSIIa haplotypes exert additive and epistatic effects on starch thermal properties, pasting profiles, and eating quality traits. Environmental factors, particularly temperature during grain filling, also influence gene expression and starch structure, generating important genotype × environment interactions. Integration of haplotype information into molecular breeding, genomic prediction, and genome editing strategies provides powerful opportunities to develop rice varieties with tailored starch functionality and improved quality under changing climatic conditions.