A distal regulatory element regulates Wx gene expression and the amylose content in rice

Granule-bound starch synthase I (GBSSI) is encoded by the <i>Waxy</i> (<i>Wx</i>) gene, which is responsible for amylose biosynthesis and is an important factor determining rice cooking and eating quality in rice grains. Although some studies have edited the promoter of <i>Wx</i> to fine-tuning gene expression level and amylose content, few studies have focused on the distal allelic variations of <i>Wx</i>. In this study, we identified and confirmed one distal cis-regulatory element (CRE) related to the <i>Wx</i> gene. Furthermore, the <i>cre</i> mutants were generated in the Nipponbare background carrying the <i>Wx^b</i> or <i>Wx^a</i> allele. The amylose content of <i>Wx^b-cre</i> mutant decreased by 21.43%-31.51% compared with that of wild-type rice with the <i>Wx^b</i> allele. However, no significant difference in amylose content was observed between wild-type plants and <i>Wx^a-cre</i> mutants which carried the <i>Wx^a</i> allele. The altered mature mRNA transcript and protein level of <i>Wx</i> gene caused by CRE showed a high consistency with their amylose content. Meanwhile, lower gelatinization temperature and final viscosity were found in the <i>Wx^b-cre</i> mutants, whereas the grain shape and chalkiness and major agronomic traits were not affected. Possibly, the <i>cre</i> mutant causes the transcriptional reprogramming of starch metabolism. Overall, we identified a distal CRE to finely regulate the <i>Wx</i> gene expression and amylose content, which provided a potentially useful allele for quality improvement in rice breeding.