Integrative GWAS and RNA-seq analysis identifies carbohydrate metabolism genes associated with yield traits under low nitrogen

Nitrogen use efficiency (NUE) is a key determinant of sustainable wheat production, yet its genetic basis remains incompletely understood under variable nitrogen supply. Grain yield and quality traits exhibit distinct responses to different nitrogen dosages, and the genetic loci and core genes governing low-nitrogen adaptability have not been systematically dissected via multi-omics integration. We evaluated 191 wheat accessions under four nitrogen application rates (N0, N150, N210, N270) across two environments and implemented an integrated framework combining multi-model GWAS, LD-based locus consolidation, RNA-seq, and WGCNA analyses to identify candidate genes. Phenotypic analysis revealed strong trait-specific nitrogen responses, with spike number (SN), grain number per spike (GNS), and plant height (PH) peaking at N210, while thousand grain weight (TGW) declined and grain protein content (GPC) increased with increasing nitrogen. Based on TGW, SN, and GNS, adaptability scores and low-nitrogen tolerance indices were constructed to classify genotypes into four performance groups, identifying 41 accessions (21.5%) with both high yield stability and strong low-nitrogen tolerance. GWAS of adaptability traits and nitrogen-response indices identified 85 significant QTLs supported across environments and models, including multiple co-localized multi-trait loci. Integrative analysis incorporating transcriptomics and co-expression networks prioritized TraesCS7A02G040900 , encoding a sucrose synthase, as the most plausible candidate gene underlying a TGW-associated locus. This gene exhibited consistent expression divergence between low nitrogen-tolerant and sensitive groups under both N0 and N210 conditions, indicating genetically determined regulation of carbon partitioning. Our work validates the power of integrating adaptability indices and multi-omics data to unravel the genetic architecture of wheat NUE. Carbon partitioning metabolism is proven to be a critical pathway connecting nitrogen status and yield performance, with TraesCS7A02G040900 represents a promising correlative candidate gene requiring subsequent functional characterization. The germplasm and molecular targets identified here lay a solid foundation for breeding nitrogen-efficient wheat.