# Cultivar-specific metabolomic and morpho-physiological responses reveal distinct salt tolerance mechanisms in rice (Oryza sativa L.)

## TL;DR

This study identifies how different rice cultivars respond to salt stress through morphological and metabolic changes, with Sakha 108 showing the highest tolerance.

## Contribution

The study reveals cultivar-specific metabolic strategies for salt tolerance in rice, including conserved and unique metabolite responses.

## Key findings

- Salt stress reduced fresh weight and RWC across all cultivars, with Sakha 108 showing the highest tolerance.
- Metabolomic analysis identified 114 leaf and 97 root metabolites, with 40 having VIP scores greater than 1.
- Cultivar-specific responses included enhanced amino acid metabolism in Giza 177 and lipid metabolism in Sakha 108.

## Abstract

Salt stress significantly limits rice productivity worldwide, highlighting the need for a thorough understanding of cultivar-specific tolerance mechanisms. This study explored the morpho-physiological and metabolomicresponses of four rice cultivars to salinity stress, aiming to identify potential adaptation strategies and candidate tolerance markers. The four rice cultivars (Giza 177, Giza 178, Sakha 104, and Sakha 108) were subjected to 200 mM NaCl treatment for 14 days under controlled conditions. Morpho-physiological parameters measured included fresh weight, relative water content (RWC), proline content, and plant height. Comprehensive metabolomic profiling was performed using GC-MS analysis of leaf and root tissues, followed by multivariate statistical analyses, including principal component analysis (PCA) and variable importance in projection (VIP) scores. Salt stress significantly decreased fresh weight and RWC across all cultivars (p < 0.001) and led to substantial proline accumulation. Sakha 108 showed superior salt tolerance (78.6% tolerance index), maintaining higher biomass and water content under stress conditions. PCA distinguished control from salt-treated samples (PC1: 75.2% variance). Metabolomic analysis identified 114 metabolites in leaf tissues and 97 in roots, with 40 metabolites exhibiting VIP scores greater than 1. Cultivar-specific responses included enhanced amino acid metabolism in Giza 177 and activated lipid metabolism pathways in Sakha 108. Hierarchical clustering highlighted tissue-specific metabolic reprogramming, with only six metabolites displaying conserved expression patterns across all cultivars in leaves. The rice cultivars employed different metabolic strategies for salt tolerance, with Sakha 108 demonstrating integrated mechanisms that combine osmotic adjustment, metabolic flexibility, and water retention. These findings offer initial insights for breeding salt-tolerant rice varieties and understanding plant stress adaptation at the metabolomic level within this experimental system.

The online version contains supplementary material available at 10.1186/s12870-025-08086-1.