Development of a high-density oligo microarray of cassava, an important tropical crop
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ABSTRACT:
ORGANISM(S): Manihot esculenta subsp. peruviana Manihot esculenta
PROVIDER: GSE31749 | GEO | 2012/06/15
SECONDARY ACCESSION(S): PRJNA145325
REPOSITORIES: GEO
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Project description:We developed a 60-mer oligonucleotide Agilent microarray representing about 20,000 cassava genes and applied it to expression profiling under drought stress. We demonstrated that our microarray is an useful tool for analyzing the cassava transcriptome and that it can be applied to various cassava species. After cutting of shoots from the cassava plants, the shoots were grown in a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark). The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for 1 hour under 40-80 M-NM-<mol photons m-2 sec-1 at 30M-BM-:C in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.
2012-06-14 | E-GEOD-31749 | biostudies-arrayexpress
Project description:Development of a high-density oligo microarray of cassava, an important tropical crop
| PRJNA145325 | ENA
Project description:Cassava (Manihot esculenta) is the food security crop that feeds approximately 800 million people worldwide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content. Cassava improvement programs are focused on addressing these constraints but are hindered by the crop’s high heterozygosity, difficulty in synchronizing flowering, low seed production and a poor understanding of the physiology of this plant. Among the major food crops, cassava is unique in its ability to develop massive, underground storage roots. Despite the importance of these structures, their basic physiology remains largely unknown, especially the molecular genetic basis of storage root development. Similarly, in cassava, the favored target tissue for transgene integration and genome editing is a friable embryogenic callus (FEC). Little is known concerning gene expression in this tissue, or its relatedness to the somatic organized embryogenic structures (OES) from which it originates. Here, we provide molecular identities for eleven cassava tissue types through RNA sequencing and develop an open access, web-based interface for further interrogation of the data. Through this dataset, we report novel insight into the physiology of cassava and identify promoters able to drive specified tissue expression profiles. The information gained from this study is of value for both conventional and biotechnological improvement programs.
2016-06-07 | GSE82279 | GEO
Project description:Cassava Anthracnose Disease (CAD) that caused by the fungus Colletotorichum anthracnose is a serious disease of cassava in worldwide. In this study, we aim to establish the cassava oligo-DNA microarray representing approximately 30,000 cassava genes and apply it to investigate the molecular mechanisms against fungal infection using two cassava cultivars; Huay Bong 60 (HB60, resistant line for CAD) and Hanatee (HN, sensitive line for CAD). Based on expression profiling, we showed that the expression of various biotic stress-inducible genes, such as detoxification enzyme related genes is higher in HB60 under the treated conditions and non-treated condition, compared with HN. These results show that stress-inducible signaling pathways including ROS detoxification are constitutively activated in HB60 even under normal growth conditions without stress. These results suggest that our microarray is a useful tool for analyzing the cassava transcriptome and add new insight into the host responses of cassava against fungal infection.
2016-12-31 | GSE63223 | GEO
Project description:Cassava is an important crop that provides food security and income generation in many tropical countries and is known for its adaptability to various environmental conditions. Despite its global importance, the development of cassava microarray tools has not been well established. Here, we describe the development of a 60-mer oligonucleotide Agilent microarray representing ?20,000 cassava genes and how it can be applied to expression profiling under drought stress using three cassava genotypes (MTAI16, MECU72 and MPER417-003). Our results identified about 1300 drought stress up-regulated genes in cassava and indicated that cassava has similar mechanisms for drought stress response and tolerance as other plant species. These results demonstrate that our microarray is a useful tool for analysing the cassava transcriptome and that it is applicable for various cassava genotypes.
| S-EPMC3415295 | biostudies-literature
Project description:Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7°C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including ‘Response to abiotic and biotic stimulus’, ‘Response to stress’, ‘Transcription factor activity’, and ‘Chloroplast’. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including ‘Plant hormone signal transduction’, ‘Starch and sucrose metabolism’, and ‘Plant-pathogen interaction’. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement.
2013-01-17 | GSE31073 | GEO
Project description:Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including M-bM-^@M-^XResponse to abiotic and biotic stimulusM-bM-^@M-^Y, M-bM-^@M-^XResponse to stressM-bM-^@M-^Y, M-bM-^@M-^XTranscription factor activityM-bM-^@M-^Y, and M-bM-^@M-^XChloroplastM-bM-^@M-^Y. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including M-bM-^@M-^XPlant hormone signal transductionM-bM-^@M-^Y, M-bM-^@M-^XStarch and sucrose metabolismM-bM-^@M-^Y, and M-bM-^@M-^XPlant-pathogen interactionM-bM-^@M-^Y. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement. Apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h were collected for RNA extractions from three independent healthy 3-month-old cassava (cultivar TMS60444) plants in the greenhouse.
2013-01-17 | E-GEOD-31073 | biostudies-arrayexpress
Project description: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.
2011-05-13 | GSE25813 | GEO
Project description:Cassava is the most important root crop in the tropics but rapid post-harvest physiological root deterioration (PPD) is a major constraint to commercial cassava production. We used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2400 unique proteins were identified in the cassava root and nearly 300 proteins showed significant abundance regulation during PPD. A candidate gene for reducing PPD was identified from the regulated proteins with enzymatic assays and afterwards verified with a transgene approach. This demonstrates the relevance of proteomics approach for crop improvements.
2014-06-03 | PXD000587 | Pride
Project description: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. 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.
2011-05-13 | E-GEOD-25813 | biostudies-arrayexpress