The genome-wide association analysis was performed to identify SNP loci significantly associated with nitrogen use efficiency (NUE) traits in Brassica juncea at seedling stage and to predict the relevant candidate genes, providing a theoretical basis for revealing the molecular mechanism of nitrogen use efficiency in rapeseed and creating nitrogen-efficient germplasm.

The population of 153 Brassica juncea resources was used as the analysis population. Two treatments, low N and normal N, were established using three replicates for each treatment, and two replicated nutrient culture trials were conducted over a two-year period (2021 and 2022). The relative values of root-shoot ratio and shoot nitrogen concentration (low/normal N) were calculated and utilized as NUE traits for a genome-wide association study (GWAS) aimed at exploring candidate genes for NUE.

NUE traits of Brassica juncea resources exhibited abundant variation, ranging from 0.21-2.44 with coefficients of variation of 22.92%-26.19%. The GWAS identified 45 significant SNP loci, among which 16 overlapped between the first relative root-shoot ratio (RRSR1) and the second relative root-shoot ratio (RRSR2), accounting for a phenotype variance range of 10.69%-15.39%. Additionally, 29 significant SNP loci were shared between the first relative shoot nitrogen concentration (RSNC1) and the second relative shoot nitrogen concentration (RSNC2), explaining a phenotype variance range of 13.22%-23.96%. 15 candidate genes for NUE were identified within 200 kb upstream and downstream regions of significant SNP loci, including 5 genes related to nitrate transport (BjuNPF5.8, BjuNRT2.7, BjuNPF2.3, BjuCLCb and BjuNRT1.3), 3 genes associated with nitrogen metabolism (BjuASN3, BjuGLU2 and BjuADCS), 4 genes involved in plant growth and development (BjuCOBL8, BjuPYL6, BjuSAUR72 and BjuUP3) and 3 genes participated in stress response (BjuNTP7, BjuJUB1 and BjuPYL6).

45 SNP loci were detected significantly associated with NUE traits and 15 candidate genes for NUE were identified in this study.