# Multiomics Profiling Unveils Key Genes and Metabolites Involved in the Salt Tolerance of Gossypium hirsutum

## TL;DR

This study uses multiomics to identify genes and metabolites in cotton that help it tolerate salt stress, offering insights into improving crop resilience.

## Contribution

The study provides a novel multiomics analysis of salt tolerance in Gossypium hirsutum, identifying key genes and metabolic pathways.

## Key findings

- 33,975 differentially expressed genes were identified, enriched in hormone signaling and metabolism pathways.
- 6292 metabolites were detected, showing metabolic reprogramming under salt stress.
- ABC transporters and starch metabolism pathways were highlighted as key for salt tolerance.

## Abstract

Background: Salt stress is a primary abiotic constraint on cotton growth, significantly impairing yield and fiber quality. Methods: To elucidate the regulatory mechanisms underlying salt stress responses in Gossypium hirsutum, we performed transcriptomic and metabolomic profiling at multiple time points following salt treatment. Results: We identified 33,975 differentially expressed genes (DEGs), with significant enrichment in pathways related to plant hormone signal transduction, amino acid metabolism, and starch and sucrose metabolism. K-means clustering grouped the DEGs into six expression modules corresponding to distinct response stages. Additionally, UPLC–MS analysis identified 6292 metabolites—spanning lipids, carbohydrates, and amino acids—and revealed substantial metabolic reprogramming with increasing stress duration. An integrated multiomics analysis highlighted the ABC transporter and starch and sucrose metabolism pathways as key regulatory modules for salt tolerance and identified critical genes within them. Conclusions: Collectively, these findings provide a comprehensive view of the transcriptional and metabolic dynamics of G. hirsutum under salt stress, offering valuable insights for understanding the molecular mechanisms of salt tolerance.