# Physiological and biochemical variations in different pepper (Capsicum annuum var. conoides) varieties under salt stress

## TL;DR

This study explores how different pepper varieties respond to salt stress, identifying physiological and molecular mechanisms that help some peppers tolerate salt better than others.

## Contribution

The study is the first to systematically reveal the role of the alkaloid pathway in pepper salt stress response using multi-omics approaches.

## Key findings

- Salt-tolerant pepper variety P47 showed better maintenance of chlorophyll and antioxidant enzyme activities under stress.
- Transcriptomic and metabolomic analyses identified key genes and pathways involved in salt tolerance, including alkaloid biosynthesis.
- Salt-sensitive variety P18 exhibited severe cellular damage and disrupted ion homeostasis under salt stress.

## Abstract

Pepper (Capsicum annuum L.), an annual herbaceous plant of the Solanaceae family, is extensively cultivated as both a fresh vegetable and a condiment, ranking among the most widely grown vegetable crops globally. Pod pepper (Capsicum annuum var. conoides), major variety of pepper, often suffers from salt stress during growth, leading to reduced yield and quality. However, systematic multi-omics studies on the salt stress response in pod pepper remain limited.

To elucidate physiological responses and salt tolerance mechanisms in pepper plants, this study screened 63 pod pepper accessions and selected salt-tolerant (P47) and salt-sensitive (P18) varieties for comparative analysis. Integrated physiological, transcriptomic and metabolomic analyses revealed that P47 exhibited lower leaf relative electrical conductivity, malondialdehyde content, and Na⁺/K⁺ ratio, along with better maintenance of chlorophyll a content and antioxidant enzyme activities. Transmission electron microscopy showed that P47 maintained intact mesophyll cell ultrastructure under stress, while P18 exhibited severe damage, including chloroplast membrane disintegration and starch grain degradation. Integrated transcriptomic and metabolomic analysis further revealed significant enrichment of differential metabolites in pathways such as phenylpropanoid biosynthesis, tyrosine metabolism, alkaloid biosynthesis, and glycerophospholipid metabolism. Key salt-responsive genes, including SAUR, ARF7, and TAT, involved in plant hormone signal transduction, tyrosine metabolism, and alkaloid biosynthesis, were identified.

This study, for the first time, systematically reveals the involvement of the alkaloid pathway in the salt stress response of pod pepper through integrated multi-omics approaches. It elucidates the physiological and molecular mechanisms by which the salt-tolerant variety enhances antioxidant capacity, regulates ion homeostasis, and maintains cellular structural integrity under salt stress. These findings provide a theoretical basis and genetic resources for targeted breeding of salt-tolerant pepper cultivars.

The online version contains supplementary material available at 10.1186/s12870-025-07873-0.