As a staple food for more than half of the world's population, the importance of rice is self-evident.Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identi ed a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two oury outer endosperm mutants ( o19-1 and o19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain lling rate. Through haplotype analysis, we identi ed a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.