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Study of gene expression in Chromolaena odorata cuttings using a combination of RNA-seq and digital gene expression analysis

ABSTRACT: 4,392 differentially expressed genes were generated by DGE analysis, and 3,074 had good comparability with known gene sequences in existing species. 1,152 differentially expressed sequences were mapped to the reference canonical pathways in the KEGG database, and were assigned to 110 KEGG pathways, 11 pathways less then with the transcriptome database. Differentially expressed genes were classed according to their function, which includes phytohormones, growth and developmental processes, defense, peroxidase and P450-related genes. Pathway analysis also revealed that the principal secondary metabolites in the C. odorata cuttings were phytohormones and flavonoids.

ORGANISM(S): Chromolaena odorata

PROVIDER: GSE42283 | GEO | 2012/11/16

SECONDARY ACCESSION(S): PRJNA181144

REPOSITORIES: GEO

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Project description:The loss of rooting capability following the transition from the juvenile to the mature phase is a known phenomenon in woody plant development. Eucalyptus grandis was used here as a model system to study the differences in gene expression between juvenile and mature cuttings. RNA was prepared from the base of the two types of cuttings before root induction and hybridized to a DNA microarray of E. grandis. In juvenile cuttings, 363 transcripts were specifically upregulated, enriched in enzymes of oxidation/reduction processes. In contrast, in mature cuttings, 245 transcripts were specifically upregulated, enriched in transcription factors involved in the regulation of secondary metabolites. A gene encoding for nitrate reductase (NIA), an enzyme that is known to be involved in nitric oxide (NO) production, was among the genes that were upregulated in juvenile cuttings. Concomitantly, a transient burst of NO upon excision was higher in juvenile cuttings than in mature ones. Treatment with a NO donor improved rooting of both juvenile and mature cuttings. A single NIA gene was found in the newly released E. grandis genome sequence, the cDNA of which was isolated, overexpressed in Arabidopsis plants and shown to increase NO production. Therefore, higher levels of NIA in E. grandis juvenile cuttings might lead to their better ability to produce NO and form adventitious roots. The Arabidopsis transgenic plants did not exhibit significantly increased lateral or adventitious roots, suggesting that spatial and temporal rather than a constitutive increase in NO is favorable for root formation. E. grandis seedlings were grown from seeds to the age of 6-7 months. The seedlings were pruned either at 10-15 cm or at 150-200 cm above the ground. The newly developed shoots were used as cuttings. To induce rooting, auxin (6000 ppm of K-IBA), was applied by quick dipping (20 sec). Stem cuttings taken from low-pruned seedlings were found to be easy-to root, exhibiting 45% rooting after 14 days and 60% after 35 days. These cuttings were defined as juvenile (RNA from two biological replicates was extracted). In contrast, stem cuttings taken from high pruned seedlings, barely rooted (5%) after 35 days, and were defined as mature (RNA from two biological replicates was extracted). The two biological replicates was used to dye swap experimental design.

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Study of gene expression in Chromolaena odorata cuttings using a combination of RNA-seq and digital gene expression analysis

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