Watkins Wheat Landraces Decode Nitrogen-Driven Biomass Trade-offs: GWAS Exposes Root-Shoot Dialectics and Elite Landraces for Resilient Agriculture

Abdul WaheedMuhammad Shahid IqbalZareen SarfrazJunliang HouYanping WeiYunfeng XuBo Song^*Shifeng Cheng^*

• Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China

Nitrogen limitation is a critical abiotic stressor that disrupts plant-environment equilibrium, imposing biomass allocation trade-offs that threaten crop productivity and food security. While modern breeding prioritizes shoot performance, the genetic mechanisms coordinating root-shoot responses under nitrogen stress remain unresolved. To address this gap, we leverage the novel use of 308 genetically diverse Watkins landraces, a reservoir of untapped adaptive alleles to dissect the molecular and physiological foundations of nitrogen-driven resilience in wheat. Phenotyping under low (LN) and normal nitrogen (NN) conditions revealed stark contrasts in root-shoot allocation strategies. Genome-wide association studies (GWAS) identified 130 candidate genes governing nitrogen-responsive traits, including root-specific RALF33 and shoot-prioritizing TaNAR1. Functional annotation and transcriptomic validation exposed antagonistic gene networks (TAF6, TaAPY6) balancing root meristem activity and stress adaptation, with allelic haplotypes mirroring geographic adaptation patterns. European landraces harboring RALF33 adaptive alleles optimized root proliferation under LN, while Eurasian lines leveraged TaNAR1 variants for shoot-root coordination under NN. Multivariate analysis classified landraces into four biomass allocation strategies, highlighting elite genotypes with resilience to nitrogen limitation. By integrating genomics, phenomics, and haplotype mapping, this study bridges molecular mechanisms of nutrient stress with ecophysiological adaptation. Our findings provide actionable targets the RALF33 and TaAPY6 genes for marker-assisted breeding to engineer nitrogen-efficient wheat, advancing sustainable agriculture in low-input environments. This work underscores the potential of evolutionary-informed genetics anchored in Watkins landraces to decode stress resilience, offering a roadmap for crop design in the face of global nutrient scarcity.