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

The accessions were evaluated under four nitrogen application rates, labeled N0, N150, N210 and N270, across two growing environments. Phenotypic responses differed among the traits measured. Spike number per square metre, grain number per spike and plant height reached their highest values at N210. In contrast, thousand-grain weight declined as nitrogen application increased, while grain protein content increased with additional nitrogen. The study therefore found trait-specific responses to nitrogen supply rather than a single pattern across all yield and quality characteristics.

To assess performance across nitrogen conditions, the researchers constructed an Adaptability Score based on thousand-grain weight, spike number and grain number per spike, together with a separate Low Nitrogen Tolerance Index. These measures were used to classify the accessions into four performance groups. Forty-one accessions, representing 21.5% of the panel, were identified as having both high yield stability and strong low-nitrogen tolerance. The group-based analysis also provided a basis for comparing expression patterns in tolerant and sensitive genotypes.

Genome-wide association analyses identified 85 significant quantitative trait loci that were supported across the tested environments and statistical models, including multiple co-localized loci associated with more than one trait. The researchers used linkage-disequilibrium-based locus consolidation to refine candidate regions. GWAS supplied statistical associations between genetic regions and adaptability traits or nitrogen-response indices, while RNA-seq and co-expression network analyses helped prioritize genes whose expression patterns were consistent with those associations. TraesCS7A02G040900 was prioritized as the most plausible candidate underlying a locus associated with thousand-grain weight.

The candidate gene encodes a sucrose synthase, placing it within a carbohydrate-metabolism pathway linked in the study to carbon partitioning between nitrogen status and yield performance. Its expression consistently diverged between low-nitrogen-tolerant and low-nitrogen-sensitive groups under both N0 and N210 conditions. This expression difference suggests that variation in the gene’s regulation may be associated with how plants allocate carbon when nitrogen supply changes. It does not, by itself, establish the mechanism or demonstrate that the gene causes greater tolerance. The study was limited to a panel of 191 accessions and two environments, so the loci and expression patterns will require evaluation in additional populations and field conditions. The authors characterized the sucrose-synthase gene and carbohydrate metabolism as promising targets for subsequent functional work.

Subject of Research: Genomic and transcriptomic analysis of wheat yield traits under low nitrogen

Article Title: Integrative GWAS and RNA-seq analysis identifies carbohydrate metabolism genes associated with yield traits under low nitrogen

Article References: Cui, Y., Ren, K., Yang, T., Liu, W., Zhang, W., Meng, X., Xie, X., Ni, J., Yang, F., Xu, J., Reynolds, M. P., Li, F., Zhao, C., Xu, X., Li, J., Ma, W., & Xu, D. (2026). Integrative GWAS and RNA-seq analysis identifies carbohydrate metabolism genes associated with yield traits under low nitrogen. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09883-y

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09883-y

Keywords: wheat, low nitrogen, nitrogen use efficiency, yield traits, GWAS, RNA sequencing, carbohydrate metabolism, sucrose synthase, quantitative trait loci, grain protein, Integrative, RNA-seq