Fei Zhang#, Boming Ji#, Si Wu#, Jie Zhang, Hui Zhang, Fei Wang, Baoxing Song, Qing Sang, Wenjie Huang, Shijuan Yan, Mustafa Bulut, Yariv Brotman*, Mingqiu Dai*

Genome Biology, volume 26, Article number: 275 (2025) ,Published: 10 September 2025

Abstract

Background

Soil salinization represents a critical global challenge to agricultural productivity, profoundly impacting crop yields and threatening food security. Plant salt-responsive is complex and dynamic, making it challenging to fully elucidate salt tolerance mechanism and leading to gaps in our understanding of how plants adapt to and mitigate salt stress.

Results

Here, we conduct high-resolution time-series transcriptomic and metabolomic profiling of the extremely salt-tolerant maize inbred line, HLZY, and the salt-sensitive elite line, JI853. Utilizing advanced data mining techniques, we identify key factors underlying the divergence in salt tolerance between these two lines and discover a series of novel genes and metabolites essential for maize salt tolerance. Additionally, we develop an innovative decision algorithm that enabled the construction of a high-confidence gene regulatory network for important salt-responsive metabolites. Comprehensive genetic and molecular studies further reveal the pivotal role of a hub gene, ZmGLN2, in regulating metabolite biosynthesis and salt tolerance in maize.

Conclusions

Our study provides the first high-resolution transcriptomic and metabolomic dataset for crop salt response, uncovering novel maize salt-responsive genes and metabolites. These findings demonstrate the effectiveness of high-resolution multi-omics in deciphering the mechanisms underlying complex crop traits. Furthermore, we develop a systematic analytical framework for mining time-series multi-omics data, which can be broadly applied to other species or traits.

论文链接：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03766-5