PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retro-transposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar 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