Unravelling MADS-box gene family in Eucalyptus spp.: a starting point to an understanding of their developmental role in trees

Dias, Beatriz Fonseca de Oliveira; Simões‐Araújo, Jean Luiz; Russo, Carlo; Margis, Rogério; Alves‐Ferreira, Márcio

doi:10.1590/s1415-47572005000400004

Cited by 10 publications

(3 citation statements)

References 52 publications

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“…In order to search for MADS-box sequences, a MADS-box consensus sequence was used. This consensus was generated by the COBBLER program (COnsensus Biasing By Locally Embedding Residues, http://blocks.fhcrc.org/blocks/cobbler.html ) from all identified MADS-box amino acid sequences "MGRKKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEV ALIVFSPSGrlyeyannni" [ 30 ]. Searches were conducted using the tBLASTN algorithm with the BLOSUM62 scoring matrix [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data

et al. 2010

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BackgroundNormalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.ResultsBy the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development.ConclusionWe have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; GhACT4 and GhUBQ14 for flower development, GhACT4 and GhFBX6 for the floral organs and GhMZA and GhPTB for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.

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Section: Methodsmentioning

confidence: 99%

Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data

et al. 2010

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“…Even if most reports have related their role in flowering, several authors have shown that MADS-box genes are expressed in differentiating primary/secondary xylem and phloem during wood formation in poplar 44 . In eucalyptus, MADS-box TFs have been detected in vegetative tissues 45 , and xylem tissue of white spruce 6 . Nine MADS-box genes have been identified in P. radiata (PrMADS 1 to 9), which have been detected in vegetative outbreak, floral organs and roots, all of them orthologues of TOMATO MADS3 (TM3).…”

Section: Introductionmentioning

confidence: 99%

Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy

Cruz

Méndez

Ramos

et al. 2019

Sci Rep

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The molecular mechanisms underlying inclination responses in trees are unclear. In this study, we identified a MADS-box transcription factor differentially expressed early after inclination in the stems of Pinus radiata D. Don. PrMADS10 has a CDS of 582 bp and encodes a group II MADS-box transcription factor. We measured highest accumulation of this transcript on the lower side of inclined pine stems. In an effort to identify putative targets, we stably transformed Arabidopsis thaliana with a 35S::PrMADS10 construct. Transcriptome analysis revealed 1,219 genes differentially-expressed, with 690 and 529 genes up- and down-regulated respectively, when comparing the transgenic and wild-type. Differentially-expressed genes belong to different biological processes, but were enriched in cell wall remodeling and phenylpropanoid metabolic functions. Interestingly, lignin content was 30% higher in transgenic as compared to wild-type plants consistent with observed changes in gene expression. Differentially expressed transcription factors and phenylpropanoid genes were analyzed using STRING. Several MYB and NAC transcription factors showed interactions with genes of the phenylpropanoid pathway. Together, these results implicate PrMADS10 as a regulatory factor, triggering the expression of other transcription factors and genes involved in the synthesis of lignin.

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“…The fact that transcript of MADS type I proteins were not found can be explained by the hypothesis of low expression level or because they were expressed under conditions not monitored in transcriptome projects (Dias et al 2005). Parenicová et al (2003) reported that it would be possible that members of MIKC group controlled many phenotypic effects obvious and redundant in different studied mutants (Férrandiz et al 2000;Pelaz et al 2000;Liljegren et al 2000), but the Mα, Mβ, Mγ, and Mδ groups would control much more subtle functions, probably not always related to development.…”

Section: Resultsmentioning

confidence: 99%

In Silico and Quantitative Analyses of MADS-Box Genes in Coffea arabica

et al. 2010

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MADS-box genes comprise a family of transcription factors that act as key regulators in many cellular development processes of several organisms. Members of this family have highly conserved regions and play important roles as transcription factors, activating target genes. The present work aimed at analyzing the MADS-box gene family present in a database generated by the Brazilian Coffee Genome Project (CAFEST) as well as of observing their respective sites of expression within these data. Through the use of bioinformatics tools, it was possible to identify and classify 26 expressed sequence tag contigs, 13 of them were expressed exclusively in vegetative tissues, 11 in reproductive tissues, and two in both. Later, quantitative analysis by quantitative reverse transcriptase PCR was carried out for three of them belonging to the groups of genes APETALA3 (B genes), AGAMOUS (C genes), and SEPALLATAS (E genes), which could be compared with the expression profile of in silico analysis and of its putative orthologous genes. Therefore, this study aims at a better understanding of the development processes performed by this family of genes in Coffea arabica, mainly in reproductive organs, as well as to compare functions of MADS-box orthologous studied in other species.

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Unravelling MADS-box gene family in Eucalyptus spp.: a starting point to an understanding of their developmental role in trees

Cited by 10 publications

References 52 publications

Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data

Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data

Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy

In Silico and Quantitative Analyses of MADS-Box Genes in Coffea arabica

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