Generation and analysis of an Eucalyptus globulus cDNA library constructed from seedlings subjected to low temperature conditions

Rasmussen-Poblete, Susana; Valdés, Jorge Hernández; Gamboa, María Cecilia; Valenzuela, Pablo; Krauskopf, Erwin

doi:10.2225/vol11-issue2-fulltext-14

Cited by 19 publications

(13 citation statements)

References 39 publications

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“…The analysis of a cDNA library (available at NCBI) constructed from E. globulus seedlings subjected to low temperature conditions (Rasmussen-Poblete et al 2008) and a 454 cDNA library constructed from two genotypes of E. globulus subjected to low temperature conditions (data not published) allowed the identification of three putative dehydrins. Three E. globulus ESTs sequences were found in the NCBI database (supplementary Table S1), two of which were named EuglDHN1 and EuglDHN10.…”

Section: Screening Of Cdna Library and Dna Sequence Analysismentioning

confidence: 99%

“…Considerable effort has been directed towards understanding how E. globulus responds and adapts to low temperature due to its low freezing resistance (Travert et al 1997;Moraga et al 2006;Costa e Silva et al 2008;Fernández et al 2006;Rasmussen-Poblete et al 2008). The majority of plants in temperate climates are capable of developing a certain degree of frost resistance when exposed for some days to low but nonfreezing temperatures (Chinusamy et al 2007).…”

Section: Introductionmentioning

confidence: 99%

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Isolation and characterization of three cold acclimation-responsive dehydrin genes from Eucalyptus globulus

Fernández

Águila

Arora

et al. 2011

Tree Genetics & Genomes

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The molecular and physiological work related to cold hardiness in Eucalyptus globulus and the coldresponsive dehydrins is reported. The identification and full-length gene sequence of three dehydrins of 10, 20, and 30 kDa and the comparison of their promoters regarding to potential stress and hormone response elements in E. globulus are shown. The categorization of cold-responsive proteins as dehydrin was based on the similarity in amino acid composition with selected sequenced peptides from chilling-responsive dehydrin reported for other woody plants and the increasing of gene expression level during cold acclimation. The transcript accumulation for these three dehydrin genes increased with cold acclimation and decreased with deacclimation in leaf and stem tissues, being higher in a freezing-resistant genotype of E. globulus compared to a sensitive genotype. By western blot, five dehydrin peptides were identified which increased their expression, under cold stress in leaf and stem tissues. These results provide valuable information about cold acclimation and gene regulation in eucalypt genotypes that differ in their ability to tolerate frost temperature.

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Section: Screening Of Cdna Library and Dna Sequence Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of three cold acclimation-responsive dehydrin genes from Eucalyptus globulus

Fernández

Águila

Arora

et al. 2011

Tree Genetics & Genomes

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“…The ELIP gene was chosen as the gene of interest, and two additional genes, NCED and GS, were analyzed with the most stable internal control genes. The sequences for the genes (Table 1) were retrieved from Arabidopsis thaliana and BLAST via two E. globulus cDNA libraries available in the National Center for Biotechnology Information (NCBI) (Rasmussen-Poblete et al 2008). Primers were designed for each individual gene using the Primer Express 2.0 software (PE, Applied Biosystems, Foster City, CA, USA) using the default parameters for a real-time assay.…”

Section: Primer Designmentioning

confidence: 99%

“…Considerable effort has thus been directed towards understanding how E. globulus responds and adapts to low temperature. Most of these studies have been based on the quantification of compatible solutes (Travert et al 1997;Moraga et al 2006;Costa e Silva et al 2008), the detection of molecular markers associated with freezing resistance (Fernández et al 2006), and expressed sequence tags (Rasmussen-Poblete et al 2008). A large amount of EST sequencing data is available for cold stress studies (Dhanaraj et al 2004;Joosen et al 2006;Keller et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Validation of reference genes for real-time qRT-PCR normalization during cold acclimation in Eucalyptus globulus

Fernández

Villarroel

Balbontín

et al. 2010

Trees

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During the last few years, many studies have directed their efforts at elucidating the molecular mechanisms that regulate plant response to cold stress using gene expression analysis. Quantitative real-time qRT-PCR has great advantages compared to traditional transcriptional detection methods due to its high sensibility, reproducibility, and specificity for the detection of low quantities of RNA. However, this technique requires the use of one or several housekeeping genes. In this work, the expression stabilities of six housekeeping genes (EF1a, ACT, a-TUB, PDF, SAND, and UBC) during the cold acclimation of E. globulus plants was analyzed. An ELIP gene that responds to photooxidative stress caused by light and cold stress was used as the target gene to identify the most suitable internal control for normalizing real-time qRT-PCR. Two additional genes involved in the ABA biosynthesis pathway (NCED) and sugar metabolism (GS) were analyzed with the most stable internal control genes in order to check the results found with the ELIP gene. The expressions of UBC, a-TUB and EF1a were the most stable across acclimation and de-acclimation treatments. The expressions of the other housekeeping genes tested varied depending upon the conditions. The relative quantification of ELIP changed according to identities and the number of reference genes used, thus demonstrating the importance of selecting an appropriate number of reference genes in order to achieve an accurate and reliable normalization of gene expression during cold acclimation in E. globulus.

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“…The availability at the NCBI database of 8737 ESTs from E. globulus submitted to low temperature (Rasmussen-Poblete et al 2008) prompted us to find cold-regulated genes, but the identification of genes being expressed during CA offers a wider spectrum of data that will allow to better understand the mechanisms underlying this process in this species. RNA-Seq is a cost-effective approach offering a sequencing strategy to generate transcriptome profiles with high efficiency and speed for gene discovery and for in silico gene expression analysis, where differentially expressed genes can be identified by measuring the reads mapped for each transcript.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profile in Response to Frost Tolerance in Eucalyptus globulus

2015

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The genetic improvement of trees for freezing tolerance is one of the most important goals to extend the plantations to colder areas. RNA-Seq technology has become a key tool in transcriptome studies. It can quantify overall expression levels for each gene simultaneously with high efficiency and speed through in silico gene expression, where differentially expressed genes can be identified by measuring the reads mapped for each transcript. In this study, the results of ESTs libraries from two Eucalyptus globulus genotypes showing contrasting differences in frost tolerance after cold acclimation using mRNA-Seq and in silico gene expression are discussed. A total of 14,265 non-redundant transcripts were predicted, where 163 corresponded to upregulated and 537 to downregulated genes. Pathway analyses of upregulated transcripts indicated that differences in frost tolerance might be regulated by the tree response to chemical and osmotic stimulus and organic substances, principally by overexpressing proteins that respond to hormone stress. These results suggest that genes coding for dehydrins, outer envelope, and voltage-dependent anion channel proteins are likely to participate in the regulation of the cold acclimation process and may have an important role in frost tolerance. The transcription factor analysis allowed identifying that those most differentially expressed in a resistant genotype were participating in the regulation of transcription, hormone regulation, photosynthesis, and response to stress. Additionally, the screening of polymorphic EST-SSR in silico and the validation of these markers in a reference population lead to identify a polymorphic EST-SSR with potential use for plant breeding and genotype discrimination.

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Generation and analysis of an Eucalyptus globulus cDNA library constructed from seedlings subjected to low temperature conditions

Cited by 19 publications

References 39 publications

Isolation and characterization of three cold acclimation-responsive dehydrin genes from Eucalyptus globulus

Isolation and characterization of three cold acclimation-responsive dehydrin genes from Eucalyptus globulus

Validation of reference genes for real-time qRT-PCR normalization during cold acclimation in Eucalyptus globulus

Transcriptome Profile in Response to Frost Tolerance in Eucalyptus globulus

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