A MITE-mediated Cis-regulatory module regulates PsiGCN2 expression for high-intensity light acclimation in Populus...

The genetic basis of long-term photoprotection under sustained high-light exposure in perennial trees remains poorly understood. Here, we report that a miniature inverted-repeat transposable element (MITE) located 1.2 kb upstream of PsiGCN2 reduces promoter activity by approximately 26% (P < 0.01) in transient heterologous reporter assays, consistent with a potential cis-regulatory contribution in Populus simonii. Genome-wide association study of 334 accessions identified PsiGCN2 (Chr07:14786025) as significantly associated with electron transport rate (ETR, P < 1 × 10-7) and non-photochemical quenching (NPQ, P < 3.72 × 10-7) under high-intensity light stress. Loss-of-function paggcn2 mutants demonstrated enhanced photoprotection during prolonged high-intensity light exposure, including 19% higher maximum PSII efficiency, 46% increased NPQ, and 10 to 20% ETR following 8-d exposure compared to wild-type plants. Transcriptomic profiling revealed 432 differentially expressed genes, with photosynthetic antenna proteins significantly upregulated (NES = 1.86, P < 0.001) and reduced enrichment of mitogen-activated protein kinase signaling components (NES = -1.56, P = 0.0078) in mutants. Nuclear-localized PsiGCN2 is positioned as an integrative regulatory hub, coordinating 514 protein interactions spanning proteostasis, photosynthesis, and RNA metabolism pathways. Genome-wide annotation identified 27,395 MITEs with 42.6% of genes harboring insertions near transcriptional boundaries. Phylogenetic analysis revealed episodic MITE amplification at 16.7 million years ago, coinciding with Mid-Miocene climatic shifts. These findings support a MITE-PsiGCN2-phenotype regulatory axis that influences the balance between photoprotection and photosynthetic efficiency under sustained high-light conditions. They also shed light on how promoter-proximal transposable element insertions contribute to transcriptional modulation of light acclimation in woody species.