Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process

Octavio Martínez; Magda L. Arce-Rodríguez; Fernando Hernández-Godínez; Christian Escoto-Sandoval; Felipe Cervantes-Hernández; Corina Hayano-Kanashiro; José J. Ordaz-Ortiz; M. Humberto Reyes-Valdés; Fernando G. Razo-Mendivil; Ana Garcés-Claver; Neftalí Ochoa-Alejo

doi:10.3390/plants10030585

Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process

Octavio Martínez^*, Magda L. Arce-Rodríguez, Fernando Hernández-Godínez, Christian Escoto-Sandoval, Felipe Cervantes-Hernández, Corina Hayano-Kanashiro, José J. Ordaz-Ortiz, M. Humberto Reyes-Valdés, Fernando G. Razo-Mendivil, Ana Garcés-Claver, Neftalí Ochoa-Alejo^*

^*Corresponding author for this work

Departamento de Investigaciones Científicas y Tecnológicas

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

Original language	English
Article number	585
Pages (from-to)	1-20
Number of pages	20
Journal	Plants
Volume	10
Issue number	3
DOIs	https://doi.org/10.3390/plants10030585
State	Published - Mar 2021

Bibliographical note

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Capsicum
Domestication
Fruit
Gene expression
RNA-Seq
Transcriptome

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10.3390/plants10030585

Cite this

Martínez, O., Arce-Rodríguez, M. L., Hernández-Godínez, F., Escoto-Sandoval, C., Cervantes-Hernández, F., Hayano-Kanashiro, C., Ordaz-Ortiz, J. J., Humberto Reyes-Valdés, M., Razo-Mendivil, F. G., Garcés-Claver, A., & Ochoa-Alejo, N. (2021). Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process. Plants, 10(3), 1-20. Article 585. https://doi.org/10.3390/plants10030585

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title = "Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process",

abstract = "Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.",

keywords = "Capsicum, Domestication, Fruit, Gene expression, RNA-Seq, Transcriptome",

author = "Octavio Mart{\'i}nez and Arce-Rodr{\'i}guez, {Magda L.} and Fernando Hern{\'a}ndez-God{\'i}nez and Christian Escoto-Sandoval and Felipe Cervantes-Hern{\'a}ndez and Corina Hayano-Kanashiro and Ordaz-Ortiz, {Jos{\'e} J.} and {Humberto Reyes-Vald{\'e}s}, M. and Razo-Mendivil, {Fernando G.} and Ana Garc{\'e}s-Claver and Neftal{\'i} Ochoa-Alejo",

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year = "2021",

month = mar,

doi = "10.3390/plants10030585",

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Martínez, O, Arce-Rodríguez, ML, Hernández-Godínez, F, Escoto-Sandoval, C, Cervantes-Hernández, F, Hayano-Kanashiro, C, Ordaz-Ortiz, JJ, Humberto Reyes-Valdés, M, Razo-Mendivil, FG, Garcés-Claver, A & Ochoa-Alejo, N 2021, 'Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process', Plants, vol. 10, no. 3, 585, pp. 1-20. https://doi.org/10.3390/plants10030585

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AU - Martínez, Octavio

AU - Arce-Rodríguez, Magda L.

AU - Hernández-Godínez, Fernando

AU - Escoto-Sandoval, Christian

AU - Cervantes-Hernández, Felipe

AU - Hayano-Kanashiro, Corina

AU - Ordaz-Ortiz, José J.

AU - Humberto Reyes-Valdés, M.

AU - Razo-Mendivil, Fernando G.

AU - Garcés-Claver, Ana

AU - Ochoa-Alejo, Neftalí

PY - 2021/3

Y1 - 2021/3

N2 - Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

AB - Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

KW - Capsicum

KW - Domestication

KW - Fruit

KW - Gene expression

KW - RNA-Seq

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ER -

Transcriptome analyses throughout chili pepper fruit development reveal novel insights into the domestication process

Abstract

Bibliographical note

Keywords

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