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The  Wx  gene encodes a granule-bound starch synthase (GBSS) and plays a key role in determining rice eating and cooking qualities (ECQs). SSIII-2 (SSIIIa), a member of the soluble starch synthases, is responsible for the synthesis of long chains of amylopectin. To investigate the effects of  Wx  and its interaction with  SSIII-2  on grain ECQs, a population from a hybrid combination was established as a research material. The genotypes of  SSIII-2  and the single nucleotide polymorphisms (SNPs) on intron1, exon6, and exon10 of  Wx , and the physicochemical indicators and rapid visco analyzer (RVA) profile characteristics were analyzed. The results revealed various effects of  SSIII-2  on rice quality under different backgrounds of  Wx  alleles. There was no obvious difference between different  SSIII-2  alleles under the same background of  Wx   a  , whereas there was a significant diversity under the same background of  Wx   b  .  Wx   a   had a dominant epistasis to  SSIII-2  because the effect of  SSIII-2  was masked by the massive synthesis of GBSS under  Wx   a  . The apparent amylose content (AAC) was mainly controlled by the In1G/T SNP, and rice gel consistency (GC) was regulated by the Ex10C/T SNP. The combined effects of three SNPs had a significant influence on all ECQs and RVA profile parameters, except for gelatinization temperature. In1T-Ex6A-Ex10C and In1T-Ex6A-Ex10T were classified as being low AAC type. TT-AA-CC and TT-AA-TT had a low AAC and a soft GC. The combined effects of different SNPs of  Wx  are very important for rice quality breeding.

Effects of Wx and Its Interaction With SSIII-2 on Rice Eating and Cooking Qualities