Exploring large-scale gene coexpression networks in peach (Prunus persica L.): a new tool for predicting gene function
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Author
García-Gómez, Beatriz E.
Orduña-Rubio, Luis
Tomás Matus, José
Publication date
2024-01-02ISSN
2052-7276
Abstract
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a
complex task. A gene coexpression network (GCN) capable of capturing stable gene–gene relationships would help researchers overcome
the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created
four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations
using an algorithm based on the ‘guilty-by-association’ principle. The GCN with the best performance was COO300, encompassing
21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes
involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted
and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results
with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion
and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate.
In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression
network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful
tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction
analysis are available at https://github.com/felipecobos/PeachGCN.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
13
Publisher
Oxford University Press
Is part of
Horticulture Research
Citation
De Los Cobos, Felipe Pérez, Beatriz Ester García-Gómez, Luis Orduña-Rubio, I. Batlle, Pere Arús, José Tomás Matus, and Iban Eduardo. 2024. “Exploring Large-scale Gene Coexpression Networks in Peach (Prunus Persica L.): A New Tool for Predicting Gene Function.” Horticulture Research, 11 (2): uhad294. doi:10.1093/hr/uhad294.
Grant agreement number
FEDER/ / /EU/ /
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I y Programa Estatal de I+D+I orientada a los retos de la sociedad/PID2020-118612RR-I00/ES/Mejora genética de variedades de almendro/
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I y Programa Estatal de I+D+I orientada a los retos de la sociedad/PID2019-110599RR-I00/ES/Aplication of Marker Assisted Introgression and Resynthesis in peach/MAIRES
MICINN/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2021-128865NB-I00/ES/Validación y visualización de redes reguladoras del metabolismo especializado de plantas integrando métodos ómicos/
MINECO/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/RYC-2017-23645/ES/ /
Program
Fructicultura
Genòmica i Biotecnologia
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- ARTICLES CIENTÍFICS [2555]
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