Shading and extended photoperiods cause exaggerated stem elongation (ESE) in soybean, reducing high-density planting yields at high latitudes. This study identifies a plant height gene, PH13, encoding a WD40 protein with three haplotypes. A retrotransposon insertion in haplotype 3 (PH13H3) leads to a truncated protein, reduced interaction with GmCOP1s, STF1/2 accumulation, and shorter plants. PH13H3 shows strong selection at high latitudes. Deleting PH13 and its paralog PHP prevents shade-induced ESE, enabling high-density planting. This clarifies shade resistance and offers solutions for breeding high-yielding soybeans for high-latitude regions.

Chao Qin, Ying-hui Li, Delin Li, Xueru Zhang, Lingping Kong, Yonggang Zhou, Xiangguang Lyu, Ronghuan Ji, Xiuzhi Wei, Qican Cheng, Zhiwei Jia, Xiaojiao Li, Qiang Wang, Yueqiang Wang, Wen Huang, Chunyan Yang, Like Liu, Xing Wang, Guangnan Xing, Guoyu Hu, Zhihui Shan, Ruizhen Wang, Haiyan Li, Hongyu Li, Tao Zhao, Jun Liu, Yuping Lu, Xiping Hu, Fanjiang Kong, Li-juan Qiu, Bin Liu