scholarly journals Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jens Theine ◽  
Daniela Holtgräwe ◽  
Katja Herzog ◽  
Florian Schwander ◽  
Anna Kicherer ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Expression Profiles ◽  
Climatic Conditions ◽  
Pinot Noir ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Potential Candidate ◽  
Berry Development ◽  
Ripening Time ◽  
Berry Ripening

Abstract Background Grapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars ‘Pinot Noir’ (PN) and ‘Pinot Noir Precoce’ (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years. Results The difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP. Conclusions Many of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.

scholarly journals Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential ripening-regulative genes

2021 ◽  
Author(s):  
Jens Theine ◽  
Daniela Holtgräwe ◽  
Katja Herzog ◽  
Florian Schwander ◽  
Anna Kicherer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory Genes ◽  
Pinot Noir ◽  
Differentially Expressed ◽  
Berry Development ◽  
Ripening Time ◽  
Berry Ripening

Background Grapevine cultivars of the Pinot family represent in the broader sense clonally propagated mutants with clear-cut phenotypes, such as different color or shifted ripening time, that result in major phenotypic and physiological differences as well as changes in important viticultural traits. Specifically, the cultivars 'Pinot Noir' (PN) and 'Pinot Noir Precoce' (PNP, early ripening) flower at the same time, but vary for the beginning of berry ripening (véraison) and consequently for the harvest time. Apart from the genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible ripening-regulatory genes affecting the timing of the start of ripening, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and in two years. Results The difference in the duration of berry formation between PN and PNP was quantified to be about two weeks under the growth conditions applied, using plant material with a proven clonal relationship of PN and PNP. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the beginning of ripening at the level of gene expression profiles. Functional annotation of these DEGs fits to phenotypic and physiological changes during berry development. In total, we observed between PN and PNP 3,342 DEGs in 2014 and 2,745 DEGs in 2017. The intersection of both years comprises 1,923 DEGs. Among these, 388 DEGs were identified as véraison-specific and 12 were considered as candidates for a regulatory effect on berry ripening time. The expression profiles revealed two candidate genes for Ripening Time Control, designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively) that may contribute to controlling the phenotypic difference between PN and PNP. Conclusions Many of the 1,923 DEGs identified show highly similar expression profiles in both cultivars as far as accelerated berry formation of PNP is concerned. Putative ripening-regulatory genes differentially expressed between PNP and PN as well as véraison-specific genes were identified. We point out potential connections of these genes to molecular events during berry development and discuss potential ripening time controlling candidate genes, two of which are already differentially expressed in the early berry development phase. Several down-regulated genes are annotated to encode auxin response factors / ARFs. Conceivably, changes in auxin signaling may realize the earlier ripening phenotype of PNP.

scholarly journals Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2775 ◽  
Author(s):  
Nahid Safari-Alighiarloo ◽  
Mostafa Rezaei-Tavirani ◽  
Mohammad Taghizadeh ◽  
Seyyed Mohammad Tabatabaei ◽  
Saeed Namaki
Keyword(s):  
Multiple Sclerosis ◽  
Cerebrospinal Fluid ◽  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Biological Pathways ◽  
Differentially Expressed ◽  
Potential Candidate ◽  
Functional Modules ◽  
Ppi Networks

BackgroundThe involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate interactome (protein–protein interaction (PPI)) and transcriptomes data to construct and analyze PPI networks for MS disease.MethodsGene expression profiles in paired cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) samples from MS patients, sampled in relapse or remission and controls, were analyzed. Differentially expressed genes which determined only in CSF (MSvs.control) and PBMCs (relapsevs.remission) separately integrated with PPI data to construct the Query-Query PPI (QQPPI) networks. The networks were further analyzed to investigate more central genes, functional modules and complexes involved in MS progression.ResultsThe networks were analyzed and high centrality genes were identified. Exploration of functional modules and complexes showed that the majority of high centrality genes incorporated in biological pathways driving MS pathogenesis. Proteasome and spliceosome were also noticeable in enriched pathways in PBMCs (relapsevs.remission) which were identified by both modularity and clique analyses. Finally, STK4, RB1, CDKN1A, CDK1, RAC1, EZH2, SDCBP genes in CSF (MSvs.control) and CDC37, MAP3K3, MYC genes in PBMCs (relapsevs.remission) were identified as potential candidate genes for MS, which were the more central genes involved in biological pathways.DiscussionThis study showed that network-based analysis could explicate the complex interplay between biological processes underlying MS. Furthermore, an experimental validation of candidate genes can lead to identification of potential therapeutic targets.

scholarly journals Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Pietro Delfino ◽  
Sara Zenoni ◽  
Zahra Imanifard ◽  
Giovanni Battista Tornielli ◽  
Diana Bellin
Keyword(s):  
Candidate Genes ◽  
Genetic Control ◽  
Developmental Stages ◽  
Regulation Of Gene Expression ◽  
Climatic Conditions ◽  
Grape Berry ◽  
Genetic Maps ◽  
Berry Development ◽  
Comprehensive Overview ◽  
Berry Ripening

Abstract Background High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates. Results With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition. Conclusion Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.

scholarly journals Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation

2016 ◽  
Vol 33 (8) ◽  
pp. 1017-1025 ◽  
Author(s):  
Erika M. Munch ◽  
Amy E. Sparks ◽  
Jesus Gonzalez Bosquet ◽  
Lane K. Christenson ◽  
Eric J. Devor ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Human Embryos ◽  
Potential Candidate ◽  
Blastocyst Formation

Trascriptome Analysis of Bone Marrow CD14+ Monocytes Revealed Differential Expression Profiles in Symptomatic Multiple Myeloma (MM) Compared to Smoldering MM and Monoclonal Gammopathy of Undetermined Significance

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1811-1811
Author(s):  
Marco Peronaci ◽  
Paola Storti ◽  
Domenica Ronchetti ◽  
Luca Agnelli ◽  
Marina Bolzoni ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Differentially Expressed Genes ◽  
Monoclonal Gammopathy ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Potential Candidate ◽  
Molecular Alterations ◽  
Potential Candidate Gene

Abstract Abstract 1811 Symptomatic multiple myeloma (MM), smoldering MM (SMM) and monoclonal gammopathy of uncertain significance (MGUS) are well known different pathological and clinical entities of plasma cell (PC) disorders. Nevertheless molecular studies performed on clonal CD138+ PC do not clear distinguished these disorders that share common alterations. Studies focusing on the presence of potential molecular alterations in the microenvironment cells are ongoing. Because monocytes are the cells primarily involved in osteoclastogenesis, angiogenesis and immune system disfuction, that are the hallmark of symptomatic MM compared to SMM and MGUS, in this study we have analyzed the transcriptional profile of the bone marrow (BM) CD14+ cells in these settings of patients. BM CD14+ monocytes were purified from a total cohort of 36 patients with PC disorders including 21 patients with symptomatic MM, 8 patients with SMM and 7 patients with MGUS. CD14+ cells were isolated from the CD138 negative fraction of BM samples of patients by immunomagnetic method with anti-CD14 monoclonal antibody conjugated with microbeads. The presence of potential haemopoietic and CD138+ contaminating cells was excluded by FACS analysis. Only samples with CD14 purity greater than 95% were analyzed by microarrays by GeneChip® HG-U133Plus 2.0 arrays (Affymetrix®) (13 MM, 8 SMM and 7 MGUS). Data obtained were then validated on selected genes by Real-Time quantitative PCR. A multiclass analysis identified 14 differentially expressed genes, which characterized MGUS vs SMM vs symptomatic MM. A supervised analysis between symptomatic MM vs. SMM and MGUS samples identified 101 genes differentially expressed in CD14+ (58 genes up-regulated in MM vs SMM and MGUS and 43 genes donwregulated). Interestingly, among the differentially expressed genes we found that cytokines and cytokine receptors (IL21, IL21R, IL15, IL15R), chemokines (CXCL10, CXCL11) and interferon-inducible proteins (IFI27, IFI44) were up-regulated in CD14+ of MM patients as compared to SMM and MGUS. A supervised analysis between MM and MGUS identified 6 differentially expressed genes in CD14+ whereas 37 genes distinguished MM and SMM patients. Notably the SLAMF7 (CS1) gene recently indentified as a therapeutic target in CD138+ MM cells was up-regulated in CD14+ monocytes of MM patients as compared either to MGUS alone or to MGUS plus SMM could be a potential candidate gene. Overall our preliminary results indicate that a different transcriptional fingerprint may be identified in BM CD14+ cells of patients with symptomatic MM as compared to those with indolent PC disorders such as SMM and MGUS with a greater number of differentially expressed genes between symptomatic MM and SMM patient rather than between MM and MGUS. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5975
Author(s):  
Suthasinee Somyong ◽  
Kitti Walayaporn ◽  
Nukoon Jomchai ◽  
Chaiwat Naktang ◽  
Tanapong Yodyingyong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Palm ◽  
Fruit Development ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Parthenocarpic Fruit ◽  
Rna Seq ◽  
Auxin Treatment ◽  
Auxin Signaling Pathway ◽  
Average Size

Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy.

scholarly journals Construction of potential periodontitis-related miRNA-mRNA regulatory network

2020 ◽  
Author(s):  
Zheng Zhang ◽  
Youli Zheng ◽  
Xiaowei Bian ◽  
Mingguang Jin
Keyword(s):  
Candidate Genes ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Multivariate Logistic Regression Analysis ◽  
Gene Expression Profiles ◽  
Mirna Expression Profile ◽  
Differentially Expressed ◽  
B Cell Differentiation

Abstract Background MicroRNAs (miRNAs) are found to be involved in the pathogenesis of periodontitis, a major cause of tooth loss in adults. However, a comprehensive miRNA-mRNA regulatory network has still not been established. Methods One miRNA expression profile and 2 gene expression profiles were downloaded from the GEO database and analyzed using GEO2R. Candidate genes commonly appeared in differentially expressed mRNAs (DE-mRNAs) and target genes of differentially expressed miRNAs (DE-miRNAs) were selected for functional and pathway enrichment analyses using Enrichr database. Multivariate Logistic regression analysis was used to screen independent variables among candidate genes. The diagnostic values of screened genes were determined by the area under the receiver operating characteristic (ROC) curve (AUC). Results A total of 5 DE-miRNAs (4 upregulated and 1 downregulated) and 11 candidate genes (3 upregulated and 8 downregulated) were screened. After the construction of miRNA-mRNA regulatory network, 12 miRNA-mRNA pairs were identified. In the network, the upregulated genes were significantly enriched in cellular triglyceride homeostasis and positive regulation of B cell differentiation, whereas the downregulated genes were enriched in vesicle organization, negative regulation of lymphocyte and leukocyte migration. EPCAM and RAB30 were screened as risk factors of periodontitis. The combined AUC of these 2 genes was 0.896 (GSE10334) and 0.916 (GSE16134). Conclusion In this study, we established a potential periodontitis-related miRNA-mRNA regulatory network, which brings new insights into the molecular mechanisms and provides key clues in seeking novel therapeutic targets for periodontitis. In the future, more experiments need to be carried out to validate our current findings.

scholarly journals Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Sayed Haidar Abbas Raza ◽  
Chengcheng Liang ◽  
Wang Guohua ◽  
Sameer D. Pant ◽  
Zuhair M. Mohammedsaleh ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Muscle Tissue ◽  
Microarray Data ◽  
Muscle Development ◽  
The Other ◽  
Differentially Expressed ◽  
Regulatory Mechanisms ◽  
Potential Candidate ◽  
Differential Genes

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

scholarly journals Apomixis-related genes identified from a coexpression network inPaspalum notatum, a Neotropical grass

2018 ◽  
Author(s):  
Fernanda A. de Oliveira ◽  
Bianca B. Z. Vigna ◽  
Carla C. da Silva ◽  
Alessandra P. Fávero ◽  
Frederico de P. Matta ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Expression Profiles ◽  
Mother Plant ◽  
Differentially Expressed ◽  
Coexpression Network ◽  
Paspalum Notatum ◽  
Great Promise ◽  
Expression Data ◽  
Breeding Programs ◽  
Reproductive Process

AbstractApomixis is a highly desirable trait in modern agriculture, due to the maintenance of characteristics of the mother plant in the progeny. However, incorporating it into breeding programs requires a deeper knowledge of its regulatory mechanisms.Paspalum notatumis considered a good model for such studies because it exhibits both sexual and apomictic cytotypes, facilitating the performance of comparative approaches. Therefore, we used comparative transcriptomics between contrastingP. notatumcytotypes to identify novel candidate genes involved in the regulation of the expression of this phenotype. We assembled and characterized a transcriptome from leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids ofP. notatumaccessions, and then assembled a coexpression network based on pairwise correlation between transcripts expression profiles. We identified genes exclusively expressed in each cytotype and differentially expressed genes between pairs of cytotypes. Gene ontology enrichment analyses were performed for the interpretation of data. Wede novoassembled 114,306 of reference transcripts. 536 novel candidate genes for the control of apomixis were detected through statistical analyses of expression data, contains in this set, the interactions among genes potentially linked to the apomixis-controlling region, differentially expressed, several genes also already reported in the literature and their neighbors transcriptionally related in the coexpression network. The reference transcriptome obtained in this study represents a robust set of expression data forP. notatum. Additionally, novel candidate genes identified in this work represent a valuable resource for future grass breeding programs.Author SummaryClonal mode of reproduction by seeds is termed apomixis, which results from the failure of gamete formation (meiosis) and fertilization in the sexual female reproductive pathway. The manipulation of seeds production genetically identical to the mother plant bears great promise for agricultural applications, however clarification regarding gene interactions involved in reproductive process is needed.Paspalumis considered a model genus for the analysis of apomixis mechanisms. Here, we describe an overall analysis of the expression profiles ofPaspalum notatumtranscripts in response to changes in reproductive mode (sexual to apomictic), which allowed us to identify several candidate apomixis genes. Among these, we found genes potentially associated with the apomixis control region, in addition to genes already described in the literature forPaspalum, which highlights the representativeness of assembled transcriptome. For the first time in the literature, we explored the main biological processes involved in controlling the expression of apomictic reproduction based on co-regulatory networks of candidate apomixis genes.

scholarly journals Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7752 ◽  
Author(s):  
Ana O. Quintana-Escobar ◽  
Geovanny I. Nic-Can ◽  
Rosa María Galaz Avalos ◽  
Víctor M. Loyola-Vargas ◽  
Elsa Gongora-Castillo
Keyword(s):  
Somatic Embryogenesis ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Coffea Canephora ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Quantitative Expression ◽  
Sequencing Technologies ◽  
Auxin Signaling Pathway

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.

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