Wheat study links carbohydrate metabolism genes to yield under low nitrogen

A multi-omics study of 191 wheat accessions identified carbohydrate-metabolism genes associated with yield traits and low-nitrogen tolerance. Researchers combined genome-wide association studies, RNA sequencing and weighted gene co-expression network analysis to examine how genetic variation may connect nitrogen supply with grain performance. The strongest candidate was TraesCS7A02G040900, a gene encoding a sucrose synthase. The findings are associative: the study did not show that manipulating the gene improves yields, and the authors said further functional characterization is required.

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