Genome-wide association study and transcriptome analysis identify candidate genes associated with low nitrogen-induced root plasticity in Zea mays L.

Abstract Background and Aims The maize (Zea mays L.) root system is crucial for nitrogen (N) acquisition, yet the genetic mechanisms underlying its adaptive response to low N remain poorly understood. This study aims to dissect the genetic basis of low-N-responsive root traits during early growth stage and examine their natural variation across maize subpopulations. Methods We evaluated six root and two shoot traits under normal and low N in 387 maize accessions from four subpopulations. A genome-wide association study (GWAS) was conducted using 1.2 million single nucleotide polymorphisms (SNPs), and integrated with transcriptome data derived from lines exhibiting contrasting responses to low N to elucidate the genetic architecture underlying root adaptation to low-N stress. Key Results Seedling traits showed substantial variation, with broad-sense heritability ranging from 0.27 to 0.46. Under low N, plant height, shoot dry weight, and average root diameter decreased by 12.00%, 13.61%, and 3.62%, respectively, while root length, surface area, and root-to-shoot ratio increased by 14.31%, 10.27%, and 43.46%, respectively. The SS subpopulation exhibited stronger low-N responses in root elongation and diameter reduction compared to the Mixed and NSS groups. GWAS detected 246, 290, and 294 significant SNPs under normal N, low N, and low-N-response datasets, implicating 509, 603, and 855 candidate genes, respectively. Transcriptome profiling of inbred lines with contrasting low-N responses revealed 848 differentially expressed genes (DEGs) in high-response lines and 431 DEGs in low-response lines. Integrated GWAS and transcriptome analysis and WGCNA identified 16 co-localized candidate genes, and narrowed to four core candidates. Haplotype analysis of the four core genes revealed significant phenotypic differences. The favorable haplotypes were enriched in the SS subpopulation and exhibited domestication signals. Conclusions These results uncover key genomic regions and candidate genes governing root plasticity under low-N stress, offering valuable genetic targets for enhancing N-efficiency through molecular breeding.