Transcriptomics

Dataset Information

18

Gene expression profiling of developing cassava storage roots


ABSTRACT: Mechanisms related to the development of cassava storage roots and starch accumulation remain largely unknown. To evaluate genome-wide expression patterns during cassava tuberization, a 60-mer oligonucleotide microarray representing 20,840 cassava genes was designed to identify differentially expressed transcripts in fibrous root, developing storage root and mature storage root. Using a random variance model and the traditional two-fold change method for statistical analysis, 912 and 3386 differentially expressed genes were identified related to the three different phases. Among 25 significant pathways identified, glycolysis/gluconeogenesis was the most important pathway signature due to its effects on other pathways. Rate-limiting enzymes were identified from each individual pathway, such as pectinesterase, enolase, L-lactate dehydrogenase and aldehyde dehydrogenase in glycolysis/gluconeogenesis, and ADP-glucose pyrophosphorylase, starch branching enzyme and glucan phosphorylase in sucrose and starch metabolism. This study revealed that dynamic changes in at least 16% of the transcriptome, including hundreds of transcription factors, oxidoreductases/transferases/hydrolases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this biological process. The reliability of differentially expressed genes in microarray analysis was further verified by quantitative real-time RT-PCR. The genome-wide transcription analysis facilitates our understanding of the formation of the storage root and deciphers key genes for further cassava improvement. Overall design: Fibrous roots (FR), developing storage roots (DR) and mature storage roots (MR) were collected for RNA extractions from three independent healthy 4 month-old cassava (cultivar TMS60444) plants in the field .Two RNA samples extracted from stored storage root slices were used as technical repeats (TR) for quality control.

INSTRUMENT(S): SIPPE Cassava 44k v1.0

ORGANISM(S): Manihot esculenta  

SUBMITTER: Jun Yang   

PROVIDER: GSE25813 | GEO | 2011-05-13

SECONDARY ACCESSION(S): PRJNA135617

REPOSITORIES: GEO

altmetric image

Publications

Sorry, this publication's infomation has not been loaded in the Indexer, please go directly to PUBMED or Altmetric.

Similar Datasets

2012-03-27 | E-GEOD-25813 | ArrayExpress
| GSE100319 | GEO
| GSE31073 | GEO
| GSE82279 | GEO
2014-06-02 | E-GEOD-31073 | ArrayExpress
| GSE80675 | GEO
| GSE51862 | GEO
| PRJNA135617 | ENA
2008-12-23 | GSE13809 | GEO
2014-06-02 | E-GEOD-13809 | ArrayExpress