Cassava Peel Heap samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA488516 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. It has been reported that landraces lose CMD resistance after regeneration through de novo morphogenesis. We sequenced WGBS data of 14 samples.
2022-05-27 | GSE192748 | GEO
Project description:The quality of the pepper fruit is significantly influenced by the properties of its surface such as color, glossiness and texture. The fruit surface is composed of a peel containing several layers including the cuticle, epidermis and the hypodermis. The peel acts as a protective barrier against biotic and abiotic stresses and is the most critical tissue affecting water loss during post harvest storage. The peel is composed of an outer epidermis with thick waxy (lipid) cuticle and few cell layers of thick-walled hypodermal cells. Despite its agronomic importance and due to the fact that the majority of studies in fruits have been conducted using flesh and peel tissues as a whole, the biochemical and genetic bases of variation in peel properties are largely unknown. In this proposal we aim to determine peel-specific gene expression in pepper by micro array hybridizations of peel and flesh RNA extracted at different developmental stages of the fruit. The cultivar Celica (Capsicum annuum) that has a large blocky fruit will be used for studying gene expression in the peel and flesh. Plants were grown in the greenhouse during the spring of 2006. Fruits were harvested at three developmental stages: young- 10 days after anthesis, mature green- 30 days after anthesis and ripe red- 45 days after anthesis. These stages were chosen because each represents a distinct phase in fruit development. At each stage, a biological replicate consists of bulked tissue from 3 fruits from each of 3 plants (a total of 9 fruits). We have a total of 4 biological replicates. For each fruit, the peel was separated from the flesh by manual dissection using thin forceps and scalpel blade. Peel and flesh samples were immediately frozen in liquid nitrogen and stored at -800C until RNA extraction. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep kit (Sigma). Keywords: Reference design
2007-09-01 | GSE8282 | 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: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:Analysis of transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease transcriptome analysis of two varieties of cassava that differ in their level of resistance to cassava brown streak virus.
2014-04-03 | E-GEOD-56467 | biostudies-arrayexpress
Project description:Analysis of transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease
2014-04-03 | GSE56467 | GEO
Project description:The quality of the pepper fruit is significantly influenced by the properties of its surface such as color, glossiness and texture. The fruit surface is composed of a peel containing several layers including the cuticle, epidermis and the hypodermis. The peel acts as a protective barrier against biotic and abiotic stresses and is the most critical tissue affecting water loss during post harvest storage. The peel is composed of an outer epidermis with thick waxy (lipid) cuticle and few cell layers of thick-walled hypodermal cells. Despite its agronomic importance and due to the fact that the majority of studies in fruits have been conducted using flesh and peel tissues as a whole, the biochemical and genetic bases of variation in peel properties are largely unknown. In this proposal we aim to determine peel-specific gene expression in pepper by micro array hybridizations of peel and flesh RNA extracted at different developmental stages of the fruit. The cultivar Celica (Capsicum annuum) that has a large blocky fruit will be used for studying gene expression in the peel and flesh. Plants were grown in the greenhouse during the spring of 2006. Fruits were harvested at three developmental stages: young- 10 days after anthesis, mature green- 30 days after anthesis and ripe red- 45 days after anthesis. These stages were chosen because each represents a distinct phase in fruit development. At each stage, a biological replicate consists of bulked tissue from 3 fruits from each of 3 plants (a total of 9 fruits). We have a total of 4 biological replicates. For each fruit, the peel was separated from the flesh by manual dissection using thin forceps and scalpel blade. Peel and flesh samples were immediately frozen in liquid nitrogen and stored at -800C until RNA extraction. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep kit (Sigma). Keywords: Reference design 12 hybs total
2007-08-31 | E-GEOD-8282 | biostudies-arrayexpress
Project description:Cassava mosaic disease caused by cassava begomoviruses is the most serious disease of cassava in Africa. However, the molecular mechanisms leading to symptom development of infected cassava plants are poorly understood. Here a high throughput digital gene expression profiling (DGE) based on Illumina Solexa sequencing technology was used to investigate the global transcriptional response of cassava to the African cassava mosaic virus infection. Results showed that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis related genes were most affected, which was consistent with the chlorotic symptom on the infected leaves. The upregulation of chlorophyll degradation genes, e.g. the genes encoding chlorophyllase and pheophorbide a oxygenase, as well as the downregulation of the major apoproteins genes in light harvesting complex II (LHCII) identified by the DGE analysis were confirmed by qRT-PCR. Together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, this study reveals that the degradation of chlorophyll plays an important role during ACMV symptom development for the first time. Meanwhile, we believe that the non-lethal effect on photosystem is a trick for virus to avoid fierce host immune response and a result of the long-term co-evolution. This study will provide a road map for future investigations into virus symptom development. ACMV-infected cassava leaves mixture from three independent replicates were collected for RNA extractions at 20 dpi. Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.
2014-04-01 | E-GEOD-47224 | biostudies-arrayexpress
Project description:Purpose:The red coloration of apple (Malus × domestica Borkh.) is due to the accumulation of anthocyanins in the fruit peel. Light is essential for anthocyanin biosynthesis in apple.Apple peel can quickly turn red under light conditions after unbagging. Therefore, the implementation of transcriptome sequencing to find genes that promote anthocyanin accumulation in response to light signals is necessary to clarify the mechanism of light-induced anthocyanin accumulation in apple peel.
2021-10-02 | GSE185089 | GEO