Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor
Ontology highlight
ABSTRACT:
ORGANISM(S): Manihot esculenta Manihot esculenta subsp. flabellifolia
PROVIDER: GSE60743 | GEO | 2014/12/31
SECONDARY ACCESSION(S): PRJNA259412
REPOSITORIES: GEO
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Project description:In this study, β-carotene concentrations in cassava storage roots were enhanced by co-expression of transgenes for deoxyxylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin type-1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 μg/g DW, a 15- to 20-fold increase relative to roots from non-transgenic plants. Approximately 85-90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. β-carotene-accumulating storage roots displayed delayed onset of post-harvest physiological deterioration, a major constraint limiting utilization of cassava products. Significant metabolite changes were detected in β-carotene enhanced storage roots. Most significantly, an inverse correlation was observed between β-carotene and dry matter contents, with reductions of 50% to 60% of dry matter content in the highest carotenoid accumulating storage roots of different cultivars. Further analysis confirmed concomitant reduction in starch content, and increased levels of total fatty acids, triacylglycerols, soluble sugars, and abscisic acid. Irish potato engineered to co-express DXS and crtB displayed a similar correlation between β-carotene accumulation, reduced dry matter and starch content, and elevated oil and soluble sugars in tubers. Transcriptome analyses revealed reduced expression of starch biosynthetic genes, ADP-glucose pyrophosphorylase genes, in transgenic, carotene-accumulating cassava roots relative to non-transgenic roots. These findings highlight unintended metabolic consequences of provitamin A biofortification of starch-rich organs and point to strategies for redirecting metabolic flux to restore starch production.
2017-06-22 | GSE100319 | GEO
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:Purpose: The goals of this study are to compare differentially expressed transcripts in roots and leaves of spinach cultivars with distinct oxalate contents using transcriptome profiling (RNA-seq)
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Project description:In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. Our analyses showed that conserved miRNAs have higher expression levels and more family members as well as more targets than other miRNAs. Meanwhile, these conserved miRNAs were found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes in plants, which will help further understanding regulatory mechanisms of C. gigantea miRNAs. The samples were collected from the young roots, tender shoots, young leaves and flower buds of wild C. gigantea growing in Jiangsu Province. TRIzol reagent (Invitrogen, USA) was used to extract the total RNAs [20]. An Illumina next-generation sequencing system, i.e. the 1 G Genome Analyzer sequencing platform, was utilized for sRNA sequencing. An Illumina HiSeq 2000 (LC Sciences, USA) was used for degradome sequencing.
2016-03-10 | E-GEOD-66754 | biostudies-arrayexpress
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.
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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
Project description:In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress. Screenning of sRNA transcriptome of sugarcane plants under drougth stress
2012-11-24 | E-GEOD-42483 | 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:Root development of fibrous and storage roots of cassava (Manihot esculenta Crantz, TMEB419) were monitored over time by destructive sampling. Tissues of fibrous roots, storage roots, sink and source leaves were taken 30, 34, 38, 42, 52, 60 and 68 days after planting (dap). Samples of 30, 38 and 60 dap were sequenced in biological triplicates for total RNA.
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Project description:In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. Our analyses showed that conserved miRNAs have higher expression levels and more family members as well as more targets than other miRNAs. Meanwhile, these conserved miRNAs were found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes in plants, which will help further understanding regulatory mechanisms of C. gigantea miRNAs.
2016-03-10 | GSE66754 | GEO