Association Mapping of Starch Quality with Starch Biosynthesizing Genes in Waxy Rice (Oryza sativa L.)

Although glutinous rice (or waxy rice) is not suitable for staple food, it is popularly used for traditional food processing, such as brewing, pastry, and other foodstuffs. Therefore, improvement of the quality of glutinous rice becomes more valuable than to increase its yield as compared to non-glutinous rice. In this study, association analysis was carried out between the starch gene markers and starch quality traits to explore the formation mechanism influencing starch quality of glutinous rice. With all 36 gene-specific markers, each produced polymorphic alleles with the polymorphic information content ranging from 0.0348 to 0.5409. Cluster analysis revealed two groups representing indica and japonica rice, indicating that the starch genes in waxy rice genome have already diverged into indica and japonica subspecies. The association analysis showed that eight genes, i.e. AGPsma, GBSSII, SSI, SSII-1, SSII-3 (SSIIa), SBE1, SBE3 and ISA, were significantly associated (P <0.05) with starch quality traits. Among them, SSII-3 and SSI have a greater impact on starch quality than the others. Gelatinization temperature and retrogradation were mainly controlled by SSII-3 and SSI. Many genes were associated with rapid visco analyzer viscosities, indicating that the genetic mechanism of viscosity parameters were quite complex. Some starch property parameters were also controlled by a wide range of genetic interactions.