Integrated Transcriptomic and Phenotypic Analyses Reveal Tissue-Specific Nitrogen Responses and Candidate Genes for Low-Nitrogen Tolerance in Sorghum

Abstract

Sorghum (Sorghum bicolor (L.) Moench) is an important crop with remarkable tolerance to adverse environments, including nitrogen deficiency. To investigate the mechanisms underlying sorghum tolerance to low-nitrogen (LN) stress, we integrated phenotypic evaluation, transcriptome profiling, weighted gene co-expression network analysis (WGCNA), and haplotype analysis. Two accessions, the LN-tolerant ‘Liaonian B-1’ and the LN-sensitive ‘Yikeerli’, were examined under hydroponic and field conditions. Under LN conditions, Liaonian B-1 showed increases of 32% in root length, 4.3-fold in root fresh weight, and 91% in root dry weight, whereas the LN-sensitive accession showed severe reductions in shoot biomass and a decrease in root fresh weight, with root dry weight remaining relatively stable. Transcriptomic analysis revealed more shared differentially expressed genes and stronger enrichment of N metabolism pathways in shoots, whereas roots showed enrichment of ATP-binding cassette (ABC) transporter and fatty acid elongation pathways. WGCNA identified 500 hub genes in roots and shoots. Five genes in the glutamine synthetase/glutamate synthase (GS-GOGAT) pathway were significantly associated with nitrogen-related traits. SORBI_3001G116400, which encodes glutamate synthase, showed the strongest haplotype effect in 232 sorghum accessions. The A allele (Hap1) was significantly associated with increased plant height, SPAD value, grain number, nitrogen accumulation, and biomass under LN stress, suggesting that SORBI_3001G116400 as a candidate gene requiring functional validation and testing in additional genetic backgrounds.