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Background <p>Pepper(<i>Capsicum annuum</i> L.) faces multiple biotic and abiotic stresses throughout the phases of peppers’ growth and development, with salinity being a major constraint. Recent research shows that cation proton antiporters (CPAs) are vital for ion balance and enhancing plant resilience during abiotic stress. Although the <i>CPA</i> gene family plays important roles in pepper, its characteristics and biological significance have not been systematically characterized. Analyzing the functions of pepper <i>CPA</i> family genes is of great significance for revealing the molecular mechanism of improving adaptability to adversity.</p> Methods and results <p>Our investigation revealed 33 distinct <i>CaCPA</i> genes within the pepper genome. Phylogenetic analysis coupled with whole genome duplication studies demonstrated that these <i>CaCPA</i> genes can be classified into three distinct subfamilies (<i>CaCHXs</i>,<i> CaNHXs</i> and <i>CaKEAs</i>). Analysis of the cis-acting elements showed that the highest enrichment was for the adversity stress response element. Available transcriptome expression data showed <i>CaCHXs</i> highly expressed in floral tissues, while <i>CaNHXs</i> and <i>CaKEAs</i> displayed varied expression patterns. RNA-seq and RT-qPCR analyses revealed that <i>CaNHX2</i> exhibited the most pronounced upregulation under 200 mM NaCl, with expression levels increasing 7-fold after 3&#xa0;h of treatment compared to the 0&#xa0;h control. This suggests its potential importance in salt tolerance. The functional role of <i>CaCHX2</i> requires further experimental validation.</p> Conclusions <p>Collectively, these findings shed new light on the CPA gene family, yielding important clues about its evolutionary patterns and functional roles in pepper. This study provides fundamental insights for future efforts aimed at breeding salt-resistant pepper varieties.</p>

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Genome-wide analysis of cation-proton antiporter (CPA) family involved in salt stress tolerance in pepper (Capsicum annuum L.)

  • 期刊论文

  • 发表日期：

    2025年10月28日

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  • Yitong Cheng,
  • Yuanyuan Ding,
  • Jiaxue Guo,
  • Yuyang Li,
  • Shengbao Yang,
  • Lijun Ou

摘要

Background

Pepper(Capsicum annuum L.) faces multiple biotic and abiotic stresses throughout the phases of peppers’ growth and development, with salinity being a major constraint. Recent research shows that cation proton antiporters (CPAs) are vital for ion balance and enhancing plant resilience during abiotic stress. Although the CPA gene family plays important roles in pepper, its characteristics and biological significance have not been systematically characterized. Analyzing the functions of pepper CPA family genes is of great significance for revealing the molecular mechanism of improving adaptability to adversity.

Methods and results

Our investigation revealed 33 distinct CaCPA genes within the pepper genome. Phylogenetic analysis coupled with whole genome duplication studies demonstrated that these CaCPA genes can be classified into three distinct subfamilies (CaCHXs, CaNHXs and CaKEAs). Analysis of the cis-acting elements showed that the highest enrichment was for the adversity stress response element. Available transcriptome expression data showed CaCHXs highly expressed in floral tissues, while CaNHXs and CaKEAs displayed varied expression patterns. RNA-seq and RT-qPCR analyses revealed that CaNHX2 exhibited the most pronounced upregulation under 200 mM NaCl, with expression levels increasing 7-fold after 3 h of treatment compared to the 0 h control. This suggests its potential importance in salt tolerance. The functional role of CaCHX2 requires further experimental validation.

Conclusions

Collectively, these findings shed new light on the CPA gene family, yielding important clues about its evolutionary patterns and functional roles in pepper. This study provides fundamental insights for future efforts aimed at breeding salt-resistant pepper varieties.