Selection of candidate housekeeping controls in tomato plants using EST data

Coker, Jeffrey Scott; Davies, Eric

doi:10.2144/03354st04

Cited by 83 publications

(68 citation statements)

References 21 publications

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“…The cDNA abundance of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a cytosol and plastid glycolytic enzyme, was similarly high in both libraries, four ESTs in each ( Table 3), suggesting that it is perhaps one of the housekeeping genes, a view also supported by a recent analysis of tomato ESTs (Coker and Davies 2003). However, since several nuclear-encoded isoforms of GAPDH exist in plant cells, we conducted a close bioinformatic analysis of GAPDH ESTs via manual BLAST search against the Arabidopsis protein database.…”

Section: Clustering Analysis To Generate Unique Transcriptsmentioning

confidence: 69%

Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx

Hui

Dhanaraj

Rowland³

et al. 2005

Planta

109

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An expressed sequence tag (EST) analysis approach was undertaken to identify major genes involved in cold acclimation of Rhododendron, a broad-leaf, woody evergreen species. Two cDNA libraries were constructed, one from winter-collected (cold-acclimated, CA; leaf freezing tolerance -53 degrees C) leaves, and the other from summer-collected (non-acclimated, NA; leaf freezing tolerance -7 degrees C) leaves of field-grown Rhododendron catawbiense plants. A total of 862 5'-end high-quality ESTs were generated by sequencing cDNA clones from the two libraries (423 from CA and 439 from NA library). Only about 6.3% of assembled unique transcripts were shared between the libraries, suggesting remarkable differences in gene expression between CA and NA leaves. Analysis of the relative frequency at which specific cDNAs were picked from each library indicated that four genes or gene families were highly abundant in the CA library including early light-induced proteins (ELIP), dehydrins/late embryogenesis abundant proteins (LEA), cytochrome P450, and beta-amylase. Similarly, seven genes or gene families were highly abundant in the NA library and included chlorophyll a/b-binding protein, NADH dehydrogenase subunit I, plastidic aldolase, and serine:glyoxylate aminotransferase, among others. Northern blot analyses for seven selected abundant genes confirmed their preferential expression in either CA or NA leaf tissues. Our results suggest that osmotic regulation, desiccation tolerance, photoinhibition tolerance, and photosynthesis adjustment are some of the key components of cold adaptation in Rhododendron.

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Section: Clustering Analysis To Generate Unique Transcriptsmentioning

confidence: 69%

Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx

Hui

Dhanaraj

Rowland³

et al. 2005

Planta

109

View full text Add to dashboard Cite

show abstract

“…Sequence-based approaches such as EST, SAGE were also used in housekeeping gene studies (Velculescu et al 1999;Coker and Davies 2003;Zhu et al 2008), however most of them are relatively low throughput ). Until recently high-throughput next-generation sequencing based RNA-seq provided an appealing alternative to mining housekeeping genes in a high-throughput and relatively unbiased fashion.…”

Section: Discussionmentioning

confidence: 99%

“…For example, Zhu et al (2008) analyzed human EST libraries and found 3,140 to 6,909 annotated genes were universally expressed. Coker and Davies (2003) used EST data to select candidate housekeeping controls in tomato. However, EST based method is relatively low throughput, expensive and generally not quantitative ).…”

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confidence: 99%

Genome-wide identification of housekeeping genes in maize

et al. 2014

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In the wake of recent progress of high throughput transcriptome profiling technologies, extensive housekeeping gene mining has been conducted in humans. However, very few studies have been reported in maize (Zea mays L.), an important crop plant, and none were conducted on a genome -wide level. In this study, we surveyed housekeeping genes throughout the maize transcriptome using RNA-seq and microarray techniques, and validated the housekeeping profile with quantitative polymerase chain reaction (qPCR) under a series of conditions including different genotypes and nitrogen supplies. Seven microarray datasets and two RNA-seq libraries representing 40 genotypes at more than 20 developmental stages were selected to screen for commonly expressed genes. A total of 1,661 genes showed constitutive expression in both microarray and RNA-seq datasets, serving as our starting housekeeping gene candidates. To determine for stably expressed housekeeping genes, NormFinder was used to select the top 20 % invariable genes to be the more likely candidates, which resulted in 48 and 489 entries from microarray and RNA-seq data, respectively. Among them, nine genes (2OG-Fe, CDK, DPP9, DUF, NAC, RPN, SGT1, UPF1 and a hypothetical protein coding gene) were expressed in all 40 maize diverse genotypes tested covering 16 tissues at more than 20 developmental stages under normal and stress conditions, implying these as being the most reliable reference genes. qPCR analysis confirmed the stable expression of selected reference gene candidates compared to two widely used housekeeping genes. All the reference gene candidates showed higher invariability than ACT and GAPDH. The hypothetical protein coding gene exhibited the most stable expression across 26 maize lines with different nitrogen treatments with qPCR, followed by CDK encoding the cyclin-dependent kinase. As the first study to systematically screen for housekeeping genes in maize, we identified candidates by examining the transcriptome atlas generated from RNA-seq and microarray technologies. The nine top-ranked qPCR-validated novel housekeeping genes provide a valuable resource of reference genes for maize gene expression analysis.

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“…The tubulin cDNA was used as reference. Tubulin has been accepted widely as housekeeping gene in growing plants (Coker and Davies 2003). PCR was carried out in a 0.02 cm 3 reaction containing a 1 × SYBR Green PCR master mix (Tiangen, Beijing, China), 500 nM forward and reverse primers, and 0.002 cm 3 of cDNA template.…”

Section: Methodsmentioning

confidence: 99%

Antioxidative defence under drought stress in a wheat stay-green mutant

Tian¹,

Zhang²,

Wang³

et al. 2015

Biol. plant.

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A wheat stay-green mutant, named tasg1, was generated using the mutagen ethyl methane sulphonate applied to wheat (Triticum aestivum L.) cv. HS2. A drought stress was imposed by controlling irrigation and sheltering plants from rain. The antioxidant defence was characterized in the flag leaves of the tasg1 and wild-type (WT). Compared with WT, tasg1 had higher reduced ascorbate/oxidized ascorbate ratio, reduced glutathione/oxidized glutathione ratio, and antioxidant enzyme activities during senescence under both normal and drought stress conditions. The DHAR gene expression remained higher in tasg1 than in WT during the drought stress and tasg1 had a higher antioxidant defence competence which may contribute towards the delayed leaf senescence. The different transcriptional responses of some wheat senescence-associated genes to the drought stress between tasg1 and WT were observed. These results suggest that the competent antioxidative capacity might play an important role in the enhanced drought tolerance in tasg1.

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Selection of candidate housekeeping controls in tomato plants using EST data

Cited by 83 publications

References 21 publications

Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx

Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx

Genome-wide identification of housekeeping genes in maize

Antioxidative defence under drought stress in a wheat stay-green mutant

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