Genome‐Wide Association Study Reveals Candidate Genes Controlling Tillering and Effective Panicle Number in Rice (Oryza sativa L.)

Tiller number and effective panicle number are important factors affecting rice yield. In this study, the sequencing data of 331 rice varieties were used to carry out genome‐wide association study (GWAS) of these two factors. A total of 58 candidate genes related to tiller number were identified, and their functions involved energy metabolism and cytoplasmic membrane metabolism pathways. There were 19 candidate genes related to effective panicle number, whose functions involved energy metabolism, cytoplasmic membrane metabolism and signal transduction pathways. A new QTL ‘qTNP12’, which controls both tiller number and effective panicle number, was identified on chromosome 12. There was specific variation in the 275th amino acid in the coding frame of the candidate gene. Indica rice with multiple tillers had histidine variation, while japonica rice with few tillers and Oryza rufipogon had arginine variation. Evolutionary analysis showed that the multi‐tiller trait of indica rice was developed through artificial selection and domestication. The results of this study provide a foundation for further clarifying the molecular mechanism of qTPN12 regulating tiller and effective panicle, as well as improving rice architecture through molecular marker‐assisted selection.