Isolation of genes differentially expressed during development and ripening of Fragaria chiloensis fruit by suppression subtractive hybridization

Pimentel, Paula; Salvatierra, Ariel; Moya-León, Marı́a Alejandra; Herrera, Raúl

doi:10.1016/j.jplph.2010.03.006

Cited by 24 publications

(25 citation statements)

References 62 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These results further confirmed the hypothesis that ASR acts as a component of the transduction pathway for ABA signaling and is involved in non-climacteric fruit ripening, as reported in grape berry [34], and also in climacteric fruit such as tomato [44], [60]. Our data represent the response of whole strawberry fruit (receptacle plus achenes) [18], [46], [73], which differs from numerous other studies whereby the fleshy receptacle and achenes have been evaluated separately [12], [49], [74], [75]. It has been shown that free auxin levels peak in the receptacle and achenes prior to the white stage and subsequently decline as the fruit matures.…”

Section: Discussionsupporting

confidence: 90%

Molecular Characterization of a Strawberry FaASR Gene in Relation to Fruit Ripening

et al. 2011

View full text Add to dashboard Cite

BackgroundABA-, stress- and ripening-induced (ASR) proteins have been reported to act as a downstream component involved in ABA signal transduction. Although much attention has been paid to the roles of ASR in plant development and stress responses, the mechanisms by which ABA regulate fruit ripening at the molecular level are not fully understood. In the present work, a strawberry ASR gene was isolated and characterized (FaASR), and a polyclonal antibody against FaASR protein was prepared. Furthermore, the effects of ABA, applied to two different developmental stages of strawberry, on fruit ripening and the expression of FaASR at transcriptional and translational levels were investigated.Methodology/Principal Findings FaASR, localized in the cytoplasm and nucleus, contained 193 amino acids and shared common features with other plant ASRs. It also functioned as a transcriptional activator in yeast with trans-activation activity in the N-terminus. During strawberry fruit development, endogenous ABA content, levels of FaASR mRNA and protein increased significantly at the initiation of ripening at a white (W) fruit developmental stage. More importantly, application of exogenous ABA to large green (LG) fruit and W fruit markedly increased endogenous ABA content, accelerated fruit ripening, and greatly enhanced the expression of FaASR transcripts and the accumulation of FaASR protein simultaneously.ConclusionsThese results indicate that FaASR may be involved in strawberry fruit ripening. The observed increase in endogenous ABA content, and enhanced FaASR expression at transcriptional and translational levels in response to ABA treatment might partially contribute to the acceleration of strawberry fruit ripening.

show abstract

Section: Discussionsupporting

confidence: 90%

Molecular Characterization of a Strawberry FaASR Gene in Relation to Fruit Ripening

et al. 2011

View full text Add to dashboard Cite

show abstract

“…The SSH method has been used to identify genes differentially expressed at the mRNA level from different plant species under a wide range of biotic and abiotic stresses. Applications of SSH range from biological characteristics, such as the development and ripening of fruit [99], flowering [100], morphological differences with different physical function [12], the molecular processes underlying salt and water stress tolerance development [101][102][103], the molecular mechanism of plant defense against different pathogens [104][105][106][107][108], the identification of mineral upregulated responsive genes as food bio-fortification [109], and in improving the tolerance of plants under different chemical component stresses [110][111][112][113][114]. The results of a study considering the micropylar endosperm of germinated cress seeds using a tissue-specific subtracted cDNA library revealed the role of three peroxidase SALK activities in the germination phenotype.…”

Section: Application Of Different Techniques Involved In Gene Expressmentioning

confidence: 99%

“…(1) Differentiate homologous gene copies which is an advantage over microarray (2) The specificity and sensitivity of this technique detects poorly expressed genes as well as distinguishes between homologous sequences Amaranthus caudatus SSH Calcium stress-induced genes [111] Camellia sinensis cDNA microarray Analysis of albescent stages from 'Anji Baicha [253] Camellia sinensis Microarray Large-scale gene expression [174] Camellia sinensis SSH Formation of adventitious root induced by indole-3-butyric acid [254] Carthamus tinctorius cDNA-AFLP Effect of CT-wpr expression on hydroxysafflor yellow A [255] Carthamus tinctorius cDNA-AFLP Transcripts related to biosynthetic of hydroxysafflor yellow A [256] Carthamus tinctorius cDNA-AFLP Expression of CTL-hsyapr in associate with hydroxysafflor yellow A [257] Catharanthus roseus cDNA-AFLP Responsive genes against wheat blue dwarf phytoplasma [258] Chrysanthemum lavandulifolium cDNA-AFLP salt-inducible genes [259] Citrus aurantifolia SSH Resistance responsive genes against citrus tristeza virus [104] Citrus reticulata Blanco Microarray Transcriptome analysis of a citrus late-ripening [260] Cucumis sativus SSH Powdery mildew-resistant genes [105] Disambiguation SSH Ethylene climacteric-induced genes [112] Eustoma grandiflorum Microarray Floral transcriptome [261] Festuca arundinacea Microarray Responsive genes involved in endophyte infection [262] Fragaria chiloensis SSH Responsive genes in development and ripening of fruit [99] Glycine max SSH Salt stress-induced genes [101] Gossypium arboreum SSH Resistance responsive genes against Apolygus lucorum [106] Gossypium hirsutum cDNA-AFLP Responsive genes against infection of Verticillium dahliae [263] Gossypium hirsutum Microarray Salt-responsive genes [264] Helianthus annuus SSH Phosphorus stress-induced genes [113,115] Lepidium sativum SSH Peroxidases [115] Melon Fruit SSH Expressed genes during ethylene climacteric [112] Musa acuminate SSH Tolerance to Fusarium oxysporum [107] Nicotiana tabacum cDNA-AFLP Responsive genes against tobacco mosaic virus …”

Section: Sshmentioning

confidence: 99%

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

et al. 2015

View full text Add to dashboard Cite

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

show abstract

“…Suppression subtractive hybridization (SSH) is helpful in identifying differentially expressed genes. Extensive studies showed that SSH is a powerful tool in the analysis of stress resistance [13], pathological mechanism [14] and developmental physiology [15]. Moreover, Wang et al found that light could be effective for activation of the biosynthesis of phenylpropanoids by establishing SSH cDNA libraries of tea calli [16].…”

Section: Introductionmentioning

confidence: 99%

Isolation of biosynthesis related transcripts of 2,3,5,4'-tetrahydroxy stilbene-2-O-β-D-glucoside from Fallopia multiflora by suppression subtractive hybridization

et al. 2014

View full text Add to dashboard Cite

2,3,5,4'-tetrahydroxy stilbene-2-O-ß-D-glucoside (THSG) exerts multiple pharmacodynamic actions, found in Fallopia multiflora, but the biosynthesis pathway of THSG is still unclear. To clear this ambiguity, we constructed suppression subtractive hybridization (SSH) libraries to screen the genes involved in THSG biosynthesis from two F. multiflora varieties, which vary significantly in THSG content. Twelve non-redundant differentially expressed sequence tags were obtained and the full lengths of 4 unreported fragments were amplified by rapid amplification of cDNA ends. We totally got 7 fulllength transcripts, and all of them were aligned to the transcriptome and digital gene expression tag profiling database of four F. multiflora tissues (root, stem and leaf from Deqing F. multiflora and another root from Chongqing F. multiflora; data unpublished) using local BLAST. The results showed that there was a significant, organ specific difference in the expression of fragments and full-length sequences. All the sequences were annotated by aligning to nucleotide and protein databases. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that THSG biosynthesis was correlated with multiple life activities.

show abstract

Isolation of genes differentially expressed during development and ripening of Fragaria chiloensis fruit by suppression subtractive hybridization

Cited by 24 publications

References 62 publications

Molecular Characterization of a Strawberry FaASR Gene in Relation to Fruit Ripening

Molecular Characterization of a Strawberry FaASR Gene in Relation to Fruit Ripening

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Isolation of biosynthesis related transcripts of 2,3,5,4'-tetrahydroxy stilbene-2-O-β-D-glucoside from Fallopia multiflora by suppression subtractive hybridization

Contact Info

Product

Resources

About