Maize ZmCK1-8 loss associated with enhanced roots under low nitrogen

Loss of the maize gene ZmCK1-8 was associated with enhanced root growth and changes in nitrogen-related physiological traits when plants were cultivated hydroponically under low-nitrogen conditions. The result emerged from a genome-wide and functional study that identified 20 members of the maize casein kinase 1 family and selected ZmCK1-8, a nitrate-responsive gene, for detailed analysis. Two mutant lines, ck1-8-1 and ck1-8-2, showed stronger root growth than the B73 reference background. The experiments link loss of ZmCK1-8 function with changes in root architecture under nitrogen limitation, while also showing that the precise molecular pathway connecting the gene to those changes remains unresolved.

The researchers characterized the 20-member ZmCK1 family through phylogenetic analysis, prediction of conserved motifs and protein domains, analysis of gene structure, annotation of promoter cis-regulatory elements, and nitrate-responsive transcriptome profiling. They then compared the B73 background and the two ZmCK1-8 mutant lines in low-nitrogen hydroponic cultures. Root architecture was evaluated together with traits related to nitrogen metabolism, including glutamine synthetase, glutamate synthase and nitrate reductase, along with protein and nitrogen contents. This controlled experimental design allowed the researchers to assess the association between ZmCK1-8 function, root development and nitrate-responsive physiology in maize seedlings.

The mutant comparisons indicated that loss of ZmCK1-8 function was associated with enhanced root growth under low nitrogen and with altered nitrogen-related physiological traits. The researchers also found that loss of the gene was associated with upregulation of ZmGS1-5, a glutamine synthetase gene. These observations identify ZmGS1-5 as a candidate downstream responder associated with the mutant phenotype, rather than establishing a complete route from ZmCK1-8 to root development. Transcriptome analysis also showed that the two mutants did not respond to nitrate in exactly the same way: the study identified 256 genotype-dependent nitrate-responsive genes in ck1-8-1 and 660 in ck1-8-2.

The genes that differed between the two genetic backgrounds were enriched in hormone signaling, responses to stimuli and transmembrane transporter activity. Other nitrate-responsive genes, including ZmPTR12, ZmNPF25 and ZmNPF34, also displayed distinct expression patterns in the two mutant backgrounds. These findings show that two lines carrying changes in the same targeted locus can produce different transcriptomic responses to nitrate. The variation in affected gene sets, together with the common association with enhanced root growth, complicates the interpretation of ZmCK1-8 as part of a single, uniform nitrate-response pathway.

Molecular assays supplied further evidence for a possible regulatory connection. Yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that ZmCK1-8 physically interacts with ZmCHB101, which the study identifies as a chromatin remodeler. Reverse-transcription quantitative PCR analysis of a ZmCHB101 RNA-interference line further suggested that ZmCHB101 and ZmCK1-8 share several downstream targets, including ZmGS1-5, GOGAT and ZmPTR11. That shared target pattern is consistent with a functional connection, but the researchers state that the mechanistic link between the ZmCK1-8–ZmCHB101 interaction and regulation of these genes has not been established.

Overall, the study provides experimental evidence that ZmCK1-8 is associated with nitrate-induced root growth and low-nitrogen physiological responses in maize. Its strongest results come from comparisons among B73 and two mutant lines in controlled hydroponic culture, and the reported findings do not establish the full causal network governing the phenotype. The physical interaction with ZmCHB101 and the candidate status of ZmGS1-5 provide specific molecular leads, but the study leaves unresolved how the interaction affects target-gene regulation and root architecture. The authors nevertheless identify ZmCK1-8 as a new component of a candidate maize nitrogen-signaling network and a gene relevant to further functional investigation of low-nitrogen adaptation.

Subject of Research: Functional characterization of maize ZmCK1-8 in root architecture and low-nitrogen responses

Article Title: Genome‑wide analysis of the maize CK1 family and functional characterization of ZmCK1-8 in modulating root architecture and nitrate‑responsive physiological traits under low‑nitrogen conditions

Article References: Xue, R., Zhu, Z., Yu, X., Qi, H., & Meng, X. (2026). Genome‑wide analysis of the maize CK1 family and functional characterization of ZmCK1-8 in modulating root architecture and nitrate‑responsive physiological traits under low‑nitrogen conditions. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09833-8

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09833-8

Keywords: maize, ZmCK1-8, casein kinase 1, low nitrogen, nitrate response, root architecture, nitrogen metabolism, ZmGS1-5, ZmCHB101, transcriptomics, Genome, wide