Grain size is one of the most important factors that control rice yield, as it is associated with grain weight (GW). To date, dozens of rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Here, the quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB) and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW. RNA sequencing, gene expression quantification, dual-luciferase reporter assays, chromatin immunoprecipitation-quantitative PCR, and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3. OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter, covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells. Furthermore, we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing. Taken together, our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, providing a potential target for the improvement of rice yield.

籽粒大小是控制水稻产量的最重要因素之一，因为它与粒重 (GW) 相关。迄今为止，已分离出数十种调节谷物大小的水稻基因。然而，GW控制背后的监管机制尚不完全清楚。在此，在9311 和日本晴 (NPB) 的重组自交系中鉴定了粒长 (GL) 和 GW的数量性状基因座qGL5，并精细定位到候选基因OsAUX3。OsAUX3启动子中9311和NPB之间的序列变异和OsAUX3功能丧失导致更高的 GL 和 GW。RNA 测序、基因表达定量、双荧光素酶报告基因分析、染色质免疫沉淀定量 PCR 和酵母单杂交分析表明 OsARF6 是调节OsAUX3表达的上游转录因子。OsARF6 直接与OsAUX3启动子的生长素反应元件结合，覆盖 9311 和 NPB/Dongjin/Hwayoung 之间的单核苷酸多态性位点，从而通过改变颖片细胞中的纵向扩展和生长素分布/含量来控制 GL。此外，我们发现miR167a通过指导OsARF6 mRNA 沉默正向调节 GL 和 GW 。总之，我们的研究表明，一种新的 miR167a-OsARF6-OsAUX3 模块调节水稻中的 GL 和 GW，为提高水稻产量提供了潜在的目标。