Integrative meta-QTL and RNA-Seq analysis reveals valine-glutamine (VQ) motif-containing ZmVQ56 as a key regulator of water‑nitrogen interaction in maize (Zea mays L.)

Nitrogen and water interact synergistically to affect plant growth and crop productivity. Despite intensive research, the genetic and regulatory mechanisms of water‑nitrogen interactions remain unclear. In this study, we combined meta-QTL and RNA sequencing (RNA-Seq) to identify 18 candidate genes, with ZmVQ56 selected for functional analysis. The low nitrogen and drought-tolerant genotype 'TY6' and the sensitive genotype 'GEMS9' were used under four water‑nitrogen treatments: well-watered and normal nitrogen, water stress and normal nitrogen, well-watered and low nitrogen, and water stress and low nitrogen. We identified 3430 differentially expressed genes (DEGs) in roots and 7703 DEGs in leaves. Integrating meta-QTL, gene expression, and functional annotation identified ZmVQ56 as a candidate gene involved in water‑nitrogen interactions. Since the maize transgenic material has not yet been obtained, Arabidopsis thaliana was used for functional analysis. Functional analysis in Arabidopsis showed that overexpression of ZmVQ56 reduced primary root length, fresh weight, and shoot nitrate content under low nitrogen and drought conditions, while the atsib1 mutant (homologous of ZmVQ56) exhibited opposite results. These findings provide insights into the genetic basis of water‑nitrogen interactions and suggest a role for ZmVQ56 in regulating low nitrogen and drought tolerance, offering potential for molecular breeding in maize.