Wx^lv, the Ancestral Allele of Rice Waxy Gene

In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wx^lv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wx^lv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wx^b, Wx^a, and Wxⁱⁿ) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wx^lv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.