# Identification and Expression Analysis of the CHX Gene Family in Capsicum annuum L

## TL;DR

This study identifies and analyzes the CHX gene family in pepper, revealing their roles in flower development and stress responses, which could help breed more resilient pepper varieties.

## Contribution

The first comprehensive genomic and transcriptomic analysis of the CHX gene family in pepper.

## Key findings

- Twenty-three CHX genes were identified and classified into six groups across ten pepper chromosomes.
- Most CaCHX genes are highly expressed in flowers, suggesting a role in reproductive development.
- CaCHX1, CaCHX20, and CaCHX23 show distinct expression patterns under salt and hormone treatments, indicating involvement in stress responses.

## Abstract

Pepper is an important vegetable crop, but its growth is often threatened by environmental stresses such as high soil salinity, which affects yield and quality. This study comprehensively identifies and analyzes the cation/H+ exchanger (CHX) gene family in pepper, which helps plants to maintain internal chemical balance under stress. Twenty-three CHX genes, which were unevenly distributed across ten chromosomes, were identified and classified into six groups. Expression analysis revealed that most of these genes are highly active in flowers, suggesting a role in flower development. Under salt and hormone treatments, genes such as CaCHX1, CaCHX20, and CaCHX23 showed distinct expression patterns: CaCHX1 was rapidly induced, CaCHX20 was suppressed, and CaCHX23 decreased initially but later increased. These findings suggest that CHX genes may help pepper to cope with stress and regulate reproductive growth. This study provides valuable gene resources for the future breeding of stress-resistant pepper varieties.

The cation/H+ exchanger (CHX) gene family plays a vital role in maintaining K+/Na+ homeostasis in plants, yet its functional characterization in pepper (Capsicum annuum L.) remains largely unexplored. To elucidate the potential roles of CHX genes in stress adaptation and development in pepper, a genome-wide identification and systematic analysis of this gene family was performed. Using a combination of Hidden Markov Model (HMM) searches, phylogenetic reconstruction, conserved motif and promoter analysis, and expression profiling across tissues and under multiple stress conditions, a total of 23 CaCHX genes were identified, which are unevenly distributed across 10 chromosomes and classified into 6 phylogenetic subfamilies. Expression profiling revealed that most CaCHX genes were highly expressed in flowers, suggesting their potential involvement in reproductive development, while only CaCHX12 and CaCHX17 were detected in leaves. Under treatments such as abscisic acid (ABA), gibberellic acid (GA), NaCl, and jasmonic acid (JA), CaCHX1, CaCHX20, and CaCHX23 exhibited distinct temporal expression patterns, suggesting their involvement in hormone-mediated stress responses. This study provides the first comprehensive genomic and transcriptomic overview of the CHX family in pepper, offering novel insights into its regulatory roles in flower development and stress tolerance and, thus supplying valuable genetic resources for molecular breeding aimed at enhancing pepper resilience.