Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments

Li, Yunhe; Zhang, Hongna; Wu, Qingsong; Muday, Gloria K.

doi:10.1007/s00425-017-2677-9

Cited by 17 publications

(9 citation statements)

References 67 publications

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“…Therefore, in the present study, treatment with IBA was chosen to override the effects from endogenous auxin. Similar results and methods were previously reported in mango [33] and petunia [34]: Indicating that endogenous and exogenous auxin play key roles in regulating AR formation via similar signalling pathways to some extent.…”

Section: Discussionsupporting

confidence: 88%

Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock

Liang

Xing

et al. 2018

IJMS

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Adventitious roots (AR) play an important role in the vegetative propagation of apple rootstocks. The potential role of hormone, wounding, and sugar signalling pathways in mediating AR formation has not been adequately explored and the whole co-expression network in AR formation has not been well established in apple. In order to identify the molecular mechanisms underlying AR formation in ‘T337’ apple rootstocks, transcriptomic changes that occur during four stages of AR formation (0, 3, 9 and 16 days) were analyzed using high-throughput sequencing. A total of 4294 differentially expressed genes were identified. Approximately 446 genes related to hormones, wounding, sugar signaling, root development, and cell cycle induction pathways were subsequently selected based on their potential to be involved in AR formation. RT-qPCR validation of 47 genes with known functions exhibited a strong positive correlation with the RNA-seq data. Interestingly, most of the candidate genes involved in AR formation that were identified by transcriptomic sequencing showed auxin-responsive expression patterns in an exogenous Indole-3-butyric acid (IBA)-treatment assay: Indicating that endogenous and exogenous auxin plays key roles in regulating AR formation via similar signalling pathways to some extent. In general, AR formation in apple rootstocks is a complex biological process which is mainly influenced by the auxin signaling pathway. In addition, multiple hormones-, wounding- and sugar-signaling pathways interact with the auxin signaling pathway and mediate AR formation in apple rootstocks.

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Section: Discussionsupporting

confidence: 88%

Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock

Liang

Xing

et al. 2018

IJMS

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“…MmiR51876 was a miRNA that targeted to auxin responsive protein. The pentose and glucoronate interconversions pathway, phenlypropanoid biosynthesis pathway and alpha-linolenic acid metabolism pathway were KEGG pathway involved in the adventitious root formation of mango cotyledon segments [44]. In this study, 9 miRNAs bound to 8 target genes involved in these three pathways for mango root formation.…”

Section: Discussionmentioning

confidence: 63%

Computational Identification of miRNAs and Temperature Responsive lncRNAs from Mango (Mangifera indica, L.)

Moh¹,

Zhang

Chen

et al. 2020

Preprint

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Background Mango is a major tropical fruit in the world and is known as the king of fruits because of its flavour, aroma, taste, and nutritional values. Moreover, various parts of mango trees have been used for medical purposes. Although various regulatory roles of miRNAs and lncRNAs have been investigated in many plants, there is yet an absence of study in mango. This is the first study to provide information on ncRNAs of mango with the aim of identifying miRNAs and lncRNAs of mango and discovering of their potential functions by the interaction prediction of the miRNAs, lncRNAs and their target genes. Results In this analysis, 104 miRNAs and 7,610 temperature responsive lncRNAs were identified and the target genes of these ncRNAs were characterized. By analysing the interaction of miRNAs and their target genes, it was observed that miRNAs are mainly involved in growth, development, and stress responses of mango. For the lncRNAs, cold responsive lncRNAs bound to low temperature responsive proteins expressed at low temperature stress. GO enrichment analysis of heat and cold responsive lncRNAs revealed that they involved in all three basic processes; biological process, cellular component, and molecular function. Moreover, mango lncRNAs can target miRNAs to reduce the stability of lncRNAs and can function as molecular decoys or sponges of miRNAs. Conclusion This paper would provide the new information about miRNAs and lncRNAs of mango and would help for the further investigation of mango ncRNAs.

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“…This is mainly because the development of adventitious roots is quite different from other biological processes, which include root primordium initiation, callus differentiation, adventitious root emergence and elongation process [46, 47]. During this process, tissue morphology and structure have undergone dramatic changes, and gene expression patterns varied tremendously [48–50]. Therefore, the genes expressed stably in other tissues or developmental stages may not have stable expression values during AR developmental stages.…”

Section: Discussionmentioning

confidence: 99%

Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar

et al. 2019

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Background: Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a rapid and sensitive approach to identify miRNA and protein-coding gene expression in plants. However, because of the specially designated reverse transcription and shorter PCR products, very few reference genes have been identified for the quantitative analysis of miRNA expression in plants, and different internal reference genes are needed to normalize the expression of miRNAs and mRNA genes respectively. Therefore, it is particularly important to select the suitable common reference genes for normalization of quantitative PCR of miRNA and mRNA. Results: In this study, a modified reverse transcription PCR protocol was adopted for selecting and validating universal internal reference genes of mRNAs and miRNAs. Eight commonly used reference genes, four stably expressed novel genes in Populus tremula, three small noncoding RNAs and three conserved miRNAs were selected as candidate genes, and the stability of their expression was examined across a set of 38 tissue samples from four developmental stages of poplar clone 84K (Populus alba × Populus glandulosa). The expression stability of these candidate genes was evaluated systematically by four algorithms: geNorm, NormFinder, Bestkeeper and DeltaCt. The results showed that Eukaryotic initiation factor 4A III (EIF4A) and U6-2 were suitable for samples of the callus stage; U6-1 and U6-2 were best for the seedling stage; Protein phosphatase 2A-2 (PP2A-2) and U6-1 were best for the plant stage; and Protein phosphatase 2A-2 (PP2A-2) and Oligouridylate binding protein 1B (UBP) were the best reference genes in the adventitious root (AR) regeneration stage. Conclusions: The purpose of this study was to identify the most appropriate reference genes for qRT-PCR of miRNAs and mRNAs in different tissues at several developmental stages in poplar. U6-1, EIF4A and PP2A-2 were the three most appropriate reference genes for qRT-PCR normalization of miRNAs and mRNAs during the plant regeneration process, and PP2A-2 and UBP represent the best reference genes in the AR regeneration stage of poplar. This work will benefit future studies of expression and function analysis of miRNAs and their target genes in poplar.

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Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments

Cited by 17 publications

References 67 publications

Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock

Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock

Computational Identification of miRNAs and Temperature Responsive lncRNAs from Mango (Mangifera indica, L.)

Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar

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