Integration of GWAS and WGCNA Identifies PUE-Related Gene TaERF112 in Wheat

Phosphorus (P) is a critical element that limits plant growth in agricultural and natural ecosystems, and its deficiency can significantly reduce wheat yield. We systematically evaluated the response of 296 natural wheat populations to low phosphate (Pi) stress at the seedling stage. Using genome-wide association studies with 190 892 single-nucleotide polymorphism markers, we identified 580 marker-trait associations that exhibited a significant association with low-Pi tolerance coefficients for 18 P use efficiency (PUE) related traits. This analysis revealed 44 multi-environment stable quantitative trait loci (QTLs) and 904 candidate genes. By integrating root transcriptome data from low-Pi tolerant and sensitive genotypes under low-Pi treatment for 3 days, 14 days, and post-Pi resupply for 4 days, we performed weighted gene co-expression network analysis (WGCNA) to identify specific modules associated with PUE. Functional annotation and enrichment analysis identified four hub genes (TraesCS2A03G0333400, TraesCS2A03G0335700, TraesCS4B03G0787300 and TraesCS7D03G0752400) linked to PUE, among which TraesCS4B03G0787300 (TaERF112), a candidate gene for the stable QTL qRDW4B.1. Further validation through expression analysis and gene knockout experiments confirmed that TaERF112 positively regulates low-Pi tolerance in wheat seedlings. This study provides novel insights into the genetic and molecular basis of wheat PUE, offering a foundation for breeding P-efficient wheat varieties that enhance agricultural sustainability.