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Transcriptomic analysis of bell pepper (Capsicum annuum L.) revealing key mechanisms in response to low temperature stress

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Abstract

Background

Bell pepper (Capsicum annuum L.) is one of the most economically and nutritionally important vegetables worldwide. However, its production can be affected by various abiotic stresses, such as low temperature. This causes various biochemical, morphological and molecular changes affecting membrane lipid composition, photosynthetic pigments, accumulation of free sugars and proline, secondary metabolism, as well as a change in gene expression. However, the mechanism of molecular response to this type of stress has not yet been elucidated.

Methods and results

To further investigate the response mechanism to this abiotic stress, we performed an RNA-Seq transcriptomic analysis to obtain the transcriptomic profile of Capsicum annuum exposed to low temperature stress, where libraries were constructed from reads of control and low temperature stress samples, varying on average per treatment from 22,952,190.5–27,305,327 paired reads ranging in size from 30 to 150 bp. The number of differentially expressed genes (DEGs) for each treatment was 388, 417 and 664 at T-17 h, T-22 h and T-41 h, respectively, identifying 58 up-regulated genes and 169 down-regulated genes shared among the three exposure times. Likewise, 23 DEGs encoding TFs were identified at T-17 h, 30 DEGs at T-22 h and 47 DEGs at T-42 h, respectively. GO analysis revealed that DEGs were involved in catalytic activity, response to temperature stimulus, oxidoreductase activity, stress response, phosphate ion transport and response to abscisic acid. KEGG pathway analysis identified that DEGs were related to flavonoid biosynthesis, alkaloid biosynthesis and plant circadian rhythm pathways in the case of up-regulated genes, while in the case of down-regulated genes, they pertained to MAPK signaling and plant hormone signal transduction pathways, present at all the three time points of low temperature exposure. Validation of the transcriptomic method was performed by evaluation of five DEGs by quantitative polymerase chain reaction (q-PCR).

Conclusions

The data obtained in the present study provide new insights into the transcriptome profiles of Capsicum annuum stem in response to low temperature stress. The data generated may be useful for the identification of key candidate genes and molecular mechanisms involved in response to this type of stress.

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Data availability

Data presented in this study are available on fair request to the corresponding author.

Abbreviations

DEGs:

Differential expression genes

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

LT:

Low temperature

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Acknowledgements

The authors would like to thank Q.F.B. Jesús Héctor Carrillo Yáñez for his technical assistance.

Funding

This work was supported by FOSEC SEPINVESTIGACIÓN BÁSICA, Proyecto No. A1-S-8466. Cátedras CONACYT: Proyecto No. 784. Lightbourn Research. Convenio: 589683, Proyecto: Análisis Transcripcional de Pimiento Morrón (Capsicum annuum L.) bajo estrés abiótico.

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Authors and Affiliations

  1. Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo (CIAD) A.C., Carretera Culiacán-Eldorado Km 5.5 Col. Campo el Diez, C.P. 80110, Culiacán, Sinaloa, Mexico

    Jesús Christian Grimaldi-Olivas, Brandon Estefano Morales-Merida, J. Basilio Heredia & Josefina León-Félix

  2. Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), CONAHCYT-Instituto Politécnico Nacional (IPN), Unidad Sinaloa. Blvd. Juan de Dios Bátiz Paredes #250 Col. San Joachin, C.P. 81049, Guasave, Sinaloa, Mexico

    Abraham Cruz-Mendívil

  3. Laboratorio de Biología Molecular y Genómica Funcional, CONAHCYT-Centro de Investigación en Alimentación y Desarrollo (CIAD) A.C., Carretera Culiacán-Eldorado Km 5.5, Campo el Diez, C.P. 80110, Culiacán, Sinaloa, Mexico

    Claudia Villicaña

  4. Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional (IPN), Unidad Sinaloa. Blvd. Juan de Dios Bátiz Paredes #250 Col. San Joachin, C.P. 81049, Guasave, Sinaloa, Mexico

    Melina López-Meyer

  5. Laboratorio de Genética, Instituto de Investigación Lightbourn, A. C., C.P. 33981, Ciudad Jiménez, Chihuahua, Mexico

    Rubén León-Chan & Luis Alberto Lightbourn-Rojas

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Contributions

JLF, BH and LLR, who designed and coordinated the study. JCGO performed the experimental analysis. BEMM, ACM, JLF, MLM, CV and JCGO analyzed the results. Contribution of reagents/materials/analytical tools: RLC, JLF, LLR and BH. CV, MLM and ACM edited the English grammar of the manuscript. All authors drafted, read and approved the manuscript.

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Correspondence to Josefina León-Félix.

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Grimaldi-Olivas, J.C., Morales-Merida, B.E., Cruz-Mendívil, A. et al. Transcriptomic analysis of bell pepper (Capsicum annuum L.) revealing key mechanisms in response to low temperature stress. Mol Biol Rep 50, 8431–8444 (2023). https://doi.org/10.1007/s11033-023-08744-3

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