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

• Published in: Nature communications 2023-10, Vol.14 (1), p.6813-13, Article 6813
• Main Authors: Qin, Chao, Li, Ying-hui, Li, Delin, Zhang, Xueru, Kong, Lingping, Zhou, Yonggang, Lyu, Xiangguang, Ji, Ronghuan, Wei, Xiuzhi, Cheng, Qican, Jia, Zhiwei, Li, Xiaojiao, Wang, Qiang, Wang, Yueqiang, Huang, Wen, Yang, Chunyan, Liu, Like, Wang, Xing, Xing, Guangnan, Hu, Guoyu, Shan, Zhihui, Wang, Ruizhen, Li, Haiyan, Li, Hongyu, Zhao, Tao, Liu, Jun, Lu, Yuping, Hu, Xiping, Kong, Fanjiang, Qiu, Li-juan, Liu, Bin
• Format: Article
• Language: English
• Subjects: 38/1; 38/23; 38/39; 38/43; 38/44; 38/77; 38/88; 45/41; 631/208/8; 631/449/1870; 631/449/2686; 631/449/711; Chromosome 13; Cultivars; Elongation; Genetic improvement; Genome-wide association studies; Genome-Wide Association Study; Genomes; Glycine max - genetics; Haplotypes; High density; Humanities and Social Sciences; Insertion; Latitude; Lodging; multidisciplinary; Phenotype; Photoperiods; Plant Breeding; Planting; Proteins; Retroelements; Science; Science (multidisciplinary); Shade; Soybeans
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-42608-5

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 retrotransposon in the haplotype 3 leads to a truncated PH13 H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13 H3 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. How plant height is adaptive to high latitudes and high density planting is unclear. Here, the authors report a retrotransposon insertion in a WD40 protein encoding gene PH13 affects its interaction with GmCOP1s and increases the abundance of STF1/2, leading to reduced soybean height and increased shade resistance.