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.

遮荫与延长光周期相结合会导致大豆茎伸长（ESE）过大，在高纬度地区高密度种植时会导致倒伏和产量降低。然而，植物高度适应这些地区的遗传基础仍不清楚。在这里，通过全基因组关联研究，我们在自然群体中鉴定了13号染色体（ PH13 ）上编码WD40蛋白的植物高度调节基因，具有三种主要单倍型。我们发现，在单倍型 3 中插入​​ Ty1/Copia样逆转录转座子会导致 PH13 ^H3截短，与 GmCOP1 的相互作用减少，从而导致 STF1/2 的积累，并降低植物高度。此外， PH13 ^H3等位基因已被强烈选择用于高纬度地区的遗传改良。删除PH13及其旁系同源物PHP可以防止遮荫诱导的 ESE 并允许高密度种植。该研究揭示了耐荫性的机制，并为高纬度地区选育高产大豆品种提供了潜在的解决方案。