Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1–2 mm young panicle stage. This study investigated the transcriptome of 1–2 mm young panicles from 275 rice varieties, identifying thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. Alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. A new method integrating cis- and trans-expression components with traits identified 36 putative causal genes of SPP, including *SDT* (*MIR156j*) and *OsMADS17*, with *OsMADS17* regulating *SDT* expression (experimentally validated). The study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.

Luchang Ming, Debao Fu, Zhaona Wu, Hu Zhao, Xingbing Xu, Tingting Xu, Xiaohu Xiong, Mu Li, Yi Zheng, Ge Li, Ling Yang, Chunjiao Xia, Rongfang Zhou, Keyan Liao, Qian Yu, Wenqi Chai, Sijia Li, Yinmeng Liu, Xiaokun Wu, Jianquan Mao, Julong Wei, Xu Li, Lei Wang, Changyin Wu, Weibo Xie