ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
This article is part of the Research TopicGenomics-Driven Advances in Crop Productivity and Stress Resilience, Volume IIView all articles
Transcriptome profiling reveals tissue-wide gene expression in chile pepper (Capsicum annuum L.) under infection by Phytophthora capsici
Provisionally accepted
Dennis Nicuh Lozada1*
Cristian Cabrales-Arellano2
Jerlie Mhay Matres1
Jorge Gil C Angeles3
Victor Velazquez-Martinez4
Navdeep Kaur5Efren Delgado1
Soum Sanogo1- 1New Mexico State University, Las Cruces, United States
- 2Eastern New Mexico University, Portales, United States
- 3University of the Philippines Los Banos, Laguna, Philippines
- 4Universidad Veracruzana, Veracruz, Mexico
- 5Texas A&M University, College Station, United States
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Phytophthora blight, manifested by root, stem, and fruit rot, caused by the oomycete Phytophthora capsici, is an important disease affecting chile pepper production globally. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) and shared genetic resistance mechanisms across different tissues upon infection by the pathogen. RNA-seq revealed the dynamic transcriptome of leaf, stem, and root tissues from resistant (R; CM-334) and susceptible (S; Early Jalapeno) varieties under different times of infection by P. capsici. There were 149,531 differentially expressed genes (DEGs) from 39 different R vs. S, time vs. time, and tissue vs. tissue comparisons. A total of 75,520 DEGs (51%) showed higher expression, whereas 74,011 (49%) demonstrated lower expression across all tissues and times of post-inoculation. The total number of DEGs with higher expression for the different tissue samples decreased across times of post-inoculation, where the 72h post-inoculation showed the least number of genes. The roots generally showed a higher number of DEGs compared to the stems and the leaves. Network analyses of DEGs demonstrated that genes with functions related to defense response to fungal infection were also involved with carbohydrate metabolism and ADP binding. Genes related to immune response to fungal infection and amino acid metabolism (e.g., homoserine kinase activity) showed higher gene expression across all times of infection and tissue samples. Chile pepper transcriptome under P. capsici infection provides evidence of shared gene expression across multiple tissues which can be leveraged for breeding and selection for broad-spectrum resistance in current Capsicum germplasm.
Keywords: candidate genes, Disease Resistance, Functional Genomics, Gene Expression, Phytophthora root rot, RNA-sequencing
Received: 13 Nov 2025; Accepted: 22 Jan 2026.
Copyright: © 2026 Lozada, Cabrales-Arellano, Matres, Angeles, Velazquez-Martinez, Kaur, Delgado and Sanogo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dennis Nicuh Lozada
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