Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava.
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ABSTRACT:
SUBMITTER: Kamsen R
PROVIDER: S-EPMC8062692 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon - the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.
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Project description:Cassava roots are complex structures comprising several distinct types of root. The number and size of the storage roots are two potential phenotypic traits reflecting crop yield and quality. Counting and measuring the size of cassava storage roots are usually done manually, or semi-automatically by first segmenting cassava root images. However, occlusion of both storage and fibrous roots makes the process both time-consuming and error-prone. While Convolutional Neural Nets have shown performance above the state-of-the-art in many image processing and analysis tasks, there are currently a limited number of Convolutional Neural Net-based methods for counting plant features. This is due to the limited availability of data, annotated by expert plant biologists, which represents all possible measurement outcomes. Existing works in this area either learn a direct image-to-count regressor model by regressing to a count value, or perform a count after segmenting the image. We, however, address the problem using a direct image-to-count prediction model. This is made possible by generating synthetic images, using a conditional Generative Adversarial Network (GAN), to provide training data for missing classes. We automatically form cassava storage root masks for any missing classes using existing ground-truth masks, and input them as a condition to our GAN model to generate synthetic root images. We combine the resulting synthetic images with real images to learn a direct image-to-count prediction model capable of counting the number of storage roots in real cassava images taken from a low cost aeroponic growth system. These models are used to develop a system that counts cassava storage roots in real images. Our system first predicts age group ('young' and 'old' roots; pertinent to our image capture regime) in a given image, and then, based on this prediction, selects an appropriate model to predict the number of storage roots. We achieve 91% accuracy on predicting ages of storage roots, and 86% and 71% overall percentage agreement on counting 'old' and 'young' storage roots respectively. Thus we are able to demonstrate that synthetically generated cassava root images can be used to supplement missing root classes, turning the counting problem into a direct image-to-count prediction task.
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Project description:ABSTARCT:Regulation of storage root development by source strength remains largely unknown. The cassava storage root delay (srd) T-DNA mutant postpones storage root development but manifests normal foliage growth as wild-type plants. The SRD gene was identified as an orthologue of ?-glucan, water dikinase 1 (GWD1), whose expression is regulated under conditions of light/dark cycles in leaves and is associated with storage root development. The GWD1-RNAi cassava plants showed both retarded plant and storage root growth, as a result of starch excess phenotypes with reduced photosynthetic capacity and decreased levels of soluble saccharides in their leaves. These leaves contained starch granules having greatly increased amylose content and type C semi-crystalline structures with increased short chains that suggested storage starch. In storage roots of GWD1-RNAi lines, maltose content was dramatically decreased and starches with much lower phosphorylation levels showed a drastically reduced ?-amylolytic rate. These results suggested that GWD1 regulates transient starch morphogenesis and storage root growth by decreasing photo-assimilation partitioning from the source to the sink and by starch mobilization in root crops.
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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:Pseudomonas protegens shows a high degree of lifestyle plasticity since it can establish both plant-beneficial and insect-pathogenic interactions. While P. protegens protects plants against soilborne pathogens, it can also invade insects when orally ingested leading to the death of susceptible pest insects. The mechanism whereby pseudomonads effectively switch between lifestyles, plant-beneficial or insecticidal, and the specific factors enabling plant or insect colonization are poorly understood. We generated a large-scale transcriptomics dataset of the model P. protegens strain CHA0 which includes data from the colonization of wheat roots, the gut of Plutella xylostella after oral uptake and the Galleria mellonella hemolymph after injection. We identified extensive plasticity in transcriptomic profiles depending on the environment and specific factors associated to different hosts or different stages of insect infection. Specifically, motor-activity and Reb toxin-related genes were highly expressed on wheat roots but showed low expression within insects, while certain antimicrobial compounds (pyoluteorin), exoenzymes (a chitinase and a polyphosphate kinase), and a transposase exhibited insect-specific expression. We further identified two-partner secretion systems as novel factors contributing to pest insect invasion. Finally, we use genus-wide comparative genomics to retrace the evolutionary origins of cross-kingdom colonization.
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Project description:Background:Root and tuber crops are becoming more important for their high source of carbohydrates, next to cereals. Despite their commercial impact, there are significant knowledge gaps about the environmental and inherent regulation of storage root (SR) differentiation, due in part to the innate problems of studying storage roots and the lack of a suitable model system for monitoring storage root growth. The research presented here aimed to develop a reliable, low-cost effective system that enables the study of the factors influencing cassava storage root initiation and development. Results:We explored simple, low-cost systems for the study of storage root biology. An aeroponics system described here is ideal for real-time monitoring of storage root development (SRD), and this was further validated using hormone studies. Our aeroponics-based auxin studies revealed that storage root initiation and development are adaptive responses, which are significantly enhanced by the exogenous auxin supply. Field and histological experiments were also conducted to confirm the auxin effect found in the aeroponics system. We also developed a simple digital imaging platform to quantify storage root growth and development traits. Correlation analysis confirmed that image-based estimation can be a surrogate for manual root phenotyping for several key traits. Conclusions:The aeroponic system developed from this study is an effective tool for examining the root architecture of cassava during early SRD. The aeroponic system also provided novel insights into storage root formation by activating the auxin-dependent proliferation of secondary xylem parenchyma cells to induce the initial root thickening and bulking. The developed system can be of direct benefit to molecular biologists, breeders, and physiologists, allowing them to screen germplasm for root traits that correlate with improved economic traits.
| S-EPMC6842211 | biostudies-literature
Project description:BackgroundCassava (Manihot esculenta Crantz) storage root provides a staple food source for millions of people worldwide. Increasing the carotenoid content in storage root of cassava could provide improved nutritional and health benefits. Because carotenoid accumulation has been associated with storage root color, this study characterized carotenoid profiles, and abundance of key transcripts associated with carotenoid biosynthesis, from 23 landraces of cassava storage root ranging in color from white-to-yellow-to-pink. This study provides important information to plant breeding programs aimed at improving cassava storage root nutritional quality.ResultsAmong the 23 landraces, five carotenoid types were detected in storage root with white color, while carotenoid types ranged from 1 to 21 in storage root with pink and yellow color. The majority of storage root in these landraces ranged in color from pale-to-intense yellow. In this color group, total β-carotene, containing all-E-, 9-Z-, and 13-Z-β-carotene isomers, was the major carotenoid type detected, varying from 26.13 to 76.72 %. Although no α-carotene was observed, variable amounts of a α-ring derived xanthophyll, lutein, was detected; with greater accumulation of α-ring xanthophylls than of β-ring xanthophyll. Lycopene was detected in a landrace (Cas51) with pink color storage root, but it was not detected in storage root with yellow color. Based on microarray and qRT-PCR analyses, abundance of transcripts coding for enzymes involved in carotenoid biosynthesis were consistent with carotenoid composition determined by contrasting HPLC-Diode Array profiles from storage root of landraces IAC12, Cas64, and Cas51. Abundance of transcripts encoding for proteins regulating plastid division were also consistent with the observed differences in total β-carotene accumulation.ConclusionsAmong the 23 cassava landraces with varying storage root color and diverse carotenoid types and profiles, landrace Cas51 (pink color storage root) had low LYCb transcript abundance, whereas landrace Cas64 (intense yellow storage root) had decreased HYb transcript abundance. These results may explain the increased amounts of lycopene and total β-carotene observed in landraces Cas51 and Cas64, respectively. Overall, total carotenoid content in cassava storage root of color class representatives were associated with spatial patterns of secondary growth, color, and abundance of transcripts linked to plastid division. Finally, a partial carotenoid biosynthesis pathway is proposed.
| S-EPMC4902922 | biostudies-literature
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