The excessive application of nitrogen fertilizers has led to ecological pollution and waste of agricultural resources. Developing nitrogen-efficient wheat varieties and improving nitrogen use efficiency are effective approaches for achieving sustainable agricultural development and environmental protection. Screening low-nitrogen-tolerant germplasm resources and identifying genetic loci and candidate genes associated with low-nitrogen tolerance can provide materials and theoretical foundations for breeding nitrogen-efficient wheat varieties.

A natural population consisting of 389 wheat varieties was cultivated under high-nitrogen (HN) and low-nitrogen (LN) treatments in 10 field environments. Grain yield per plant (GYP) was measured to calculate the stress tolerance index (STI), thereby enabling the classification of varieties with differential low-nitrogen tolerance. Genome-wide association studies (GWAS) were conducted using 660K SNP array genotyping data to identify stable genetic loci associated with low-nitrogen tolerance. Candidate genes were prioritized through haplotype analysis, expression profiling, and functional annotation.

Twelve wheat varieties with strong low-nitrogen tolerance were identified, including Zhongluo 08-1, Jimai 15, Jinghua 2, Kehong 1, Mianyang 19, Jimai 22, Zhenmai 4, Yumai 35, Fengkang 7, Mianyang 11, Jinmai 31, and Lumai 5. Fourteen loci significantly associated with STI were detected, among which four (qSTI1A.1, qSTI3B, qSTI6A, and qSTI7A.2) overlapped with previously reported low-nitrogen tolerance or yield-related QTLs. Notably, qSTI3B-replicated across three environments-was identified as a key locus governing low-nitrogen tolerance. Functional annotation revealed that its candidate gene, TraesCS3B02G042400, encodes an AP2/EREBP (APETALA2/ethylene-responsive element-binding protein) transcription factor. Haplotype analysis showed significant STI divergence among varieties carrying distinct haplotypes, while expression levels of TraesCS3B02G042400 exhibited nitrogen dose-responsive upregulation.

Twelve wheat varieties with strong low-nitrogen tolerance were screened. A stable genetic locus, qSTI3B, and a candidate gene, TraesCS3B02G042400, associated with low-nitrogen tolerance were identified.