Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes
Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF)...
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PeerJ Inc.
2019-10-01
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| author | Ana O. Quintana-Escobar Geovanny I. Nic-Can Rosa María Galaz Avalos Víctor M. Loyola-Vargas Elsa Gongora-Castillo |
| author_facet | Ana O. Quintana-Escobar Geovanny I. Nic-Can Rosa María Galaz Avalos Víctor M. Loyola-Vargas Elsa Gongora-Castillo |
| author_sort | Ana O. Quintana-Escobar |
| collection | DOAJ |
| description | Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process. |
| first_indexed | 2024-03-09T06:35:39Z |
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| language | English |
| last_indexed | 2024-03-09T06:35:39Z |
| publishDate | 2019-10-01 |
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| spelling | doaj.art-dc409c8e88aa4f00984156e02282ad6d2023-12-03T10:58:50ZengPeerJ Inc.PeerJ2167-83592019-10-017e775210.7717/peerj.7752Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genesAna O. Quintana-Escobar0Geovanny I. Nic-Can1Rosa María Galaz Avalos2Víctor M. Loyola-Vargas3Elsa Gongora-Castillo4Unidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, MéxicoCONACYT Research Fellow-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, MexicoUnidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, MéxicoUnidad de Bioquímica y Biologia Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, MéxicoCONACYT Research Fellow-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, MéxicoBackground Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.https://peerj.com/articles/7752.pdfAuxin responseCellular differentiationGrowth regulatorsSomatic embryogenesisSignalingCellular totipotency |
| spellingShingle | Ana O. Quintana-Escobar Geovanny I. Nic-Can Rosa María Galaz Avalos Víctor M. Loyola-Vargas Elsa Gongora-Castillo Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes PeerJ Auxin response Cellular differentiation Growth regulators Somatic embryogenesis Signaling Cellular totipotency |
| title | Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes |
| title_full | Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes |
| title_fullStr | Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes |
| title_full_unstemmed | Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes |
| title_short | Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes |
| title_sort | transcriptome analysis of the induction of somatic embryogenesis in coffea canephora and the participation of arf and aux iaa genes |
| topic | Auxin response Cellular differentiation Growth regulators Somatic embryogenesis Signaling Cellular totipotency |
| url | https://peerj.com/articles/7752.pdf |
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