Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.).

Waxy (glutinous) rice is widely used in traditional foods, and understanding the genetic bases of its diverse physicochemical properties will contribute to breeding of new waxy rice with unique qualities. The objective of this study was to investigate the genetic relationship between the starch biosynthesis related genes and the physicochemical properties of waxy rice using association mapping. A total of 36 molecular markers representing 18 genes were used to genotype 50 waxy rice accessions for which starch properties were previously available. Most of the starch properties differed between high and low gelatinization temperature (GT) groups, whereas most traits were similar between the low-GT indica rice and low-GT japonica rice, suggesting GT was the main determinant of the starch quality of waxy rice. Association mapping indicated that the starch properties of waxy rice were mainly controlled by starch synthase IIa (SSIIa or SSII-3, a major gene responsible for the gelatinization temperature) and SSI. It was found that gene-gene interactions were also important for the genetic control of starch properties of waxy rice. This study suggests that application of the functional SNPs of SSIIa in molecular breeding may facilitate quality improvement of waxy rice.