Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1083414 | ENA |
REPOSITORIES: ENA
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Project description:Cassava (Manihot esculenta) is one of the most important staple food crops worldwide. Its starchy tuberous roots supply over 800 million people with carbohydrates. Yet, surprisingly little is known about the processes involved in filling of those vital storage organs. A better understanding of cassava carbohydrate allocation and starch storage is key to improve storage root yield. In this work, we studied cassava morphology and phloem sap flow from source to sink using transgenic pAtSUC2::GFP plants, the phloem tracers esculin and 5(6)-carboxyfluorescein diacetate (CFDA), as well as several staining techniques. We show that cassava performs apoplasmic phloem loading in source leaves and symplasmic unloading into phloem parenchyma cells of tuberous roots. We demonstrate that vascular rays play an important role in radial transport from the phloem to xylem parenchyma cells in tuberous roots. Furthermore, enzymatic and proteomic measurements of storage root tissues confirmed high abundance and activity of enzymes involved in the sucrose synthase-mediated pathway and indicated that starch is stored most efficiently in the outer xylem layers of tuberous roots. Our findings represent a first basis for biotechnological approaches aimed at improved phloem loading and enhanced carbohydrate allocation and storage in order to increase tuberous root yield of cassava.
2019-07-08 | PXD014001 | Pride
Project description:Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid (SA), and indole-3-acetic acid conjugated with aspartic acid (IAAsp) on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.
2021-12-29 | GSE143278 | GEO
Project description:To screen genes related to the development of sweet potato tuberous roots, the high throughput sequencing of different stages of sweet potato tuberous roots was performed. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed lines were used for transcriptome analysis. Totally, we identified 5488 differentially expressed genes between different stage tuberous roots of Taizhong6 and 14312 differentially expressed genes between the tuberous roots of Taizhong6 and MBP3 overexpressed lines, by calculating the gene FPKM in each sample and conducting differential gene analysis. This study provides a foundation for the mechanism analysis of sweet potato tuberous root development.
2023-10-12 | GSE245185 | GEO
Project description:Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava
| PRJNA599583 | 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:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized. 7 samples are examined: young leaves, mature leaves, stems, fibrous roots, initial tuberous roots, expanding tuberous roots and harvest tuberous roots.
2012-02-18 | E-GEOD-35929 | biostudies-arrayexpress
Project description:Investigation of whole transcriptome gene expression level during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87 Identification of transcription factors (TFs) during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87 A total of 7 samples were analyzed using RNA isolated from sweetpotato roots at 10, 15, 20, 30, 60, 90, 120days after transplanting. Each sample had two biological replicates.
2015-07-12 | E-GEOD-48834 | 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. 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
Project description:Cassava’s storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in Sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant’s metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes towards carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understandings of cassava’s metabolism as well as a data resource for targeted genetic improvement.
2023-06-21 | PXD038813 | Pride