Whole-Transcriptome Profiling in Developing Tubers of the Jerusalem Artichoke
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PROVIDER: PRJNA549527 | ENA |
REPOSITORIES: ENA
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Project description:Helianthus tuberosus L., known as the Jerusalem Artichoke, is a hexaploid plant species, adapted to low nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 ESTs from a H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3) and at tuber physiological maturity (Tm), in “VR” and “K8-HS142”clones. The former was selected as an early tuberizing, the latter as a late-tuberizing clone. We quantified inulin and starch levels, and q-RT PCR confirmed the expression of key genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.
2020-01-13 | GSE132955 | GEO
Project description:Jerusalem artichoke (JA) tubers are an important bio-economy developing crop because of its invaluable bioproducts in both food and biofuel aspects. However, the molecular mechanism of its tuberization, and the differences among different cultivars have been little studied to date. Here, we conducted a comparative proteome profiling of the JA tubers of three different cultivars including PJA, DJA, and HJA, showing phenotypic characteristics. Tuber epidermal pigmentation and underground tuberization habit were different phenological characters in the three cultivars and inulin content was also a physiological character exceptionally DJA regardless of the similar level of total carbohydrate amount. We identified a total of 420 proteins in the tubers and out of 114 showed significantly modulated among the cultivars. GO classification of the DEPs revealed biosynthesis amino acid and carbohydrate metabolic enzymes were differentially expressed in the three cultivar tubers. Integrated physiological inulin content and the biosynthetic protein expression levels among the cultivars suggest that Sucrose:sucrose 1-fructosyltransferase (1-SST) prioritizes inulin biosynthesis rather than rate-limiting enzyme fructan:fructan 1-fructosyltransferases (1-FFT). Furthermore, we confirmed the relationship between transcript-protein expression levels was in discord within inulin biosynthesis enzymes 1-SST and 1-FFT with the terms in previous RT-qPCR results using the same tubers. Our data represent the first report that comparative proteome profiling in JA tubers among the different cultivars and provides the metabolic and molecular basis for understanding carbohydrate metabolism in storage tuber tissue.
2019-05-29 | PXD010835 | Pride
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:<p><strong>INTRODUCTION: </strong>Earliness of tuberisation and the quality of potato tubers are important traits in potato breeding. The qualitative traits rely on the metabolite profile of tubers, which are storage organs and net importers of assimilates. Thus, the quality of tubers largely depends on the metabolites transported from leaves to developing tubers.</p><p><strong>OBJECTIVES: </strong>To test the influence of canopy on the quality of tubers by metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts.</p><p><strong>METHODS:</strong> Potatoes were grown under greenhouse conditions, grafted and the tubers harvested at the end of the scions' vegetation period. Metabolite profiling of freshly harvested tubers was performed using gas chromatography coupled with mass spectrometry. Statistical analyses were applied to determine the significant differences between the different tubers.</p><p><strong>RESULTS:</strong> 99 metabolites were identified and an additional 181 peaks detected in chromatograms, out of which 186 were polar and 94 non-polar compounds. The concentrations of 113 metabolites were significantly different in the tubers from the early-maturing CE3130 and the late-maturing CE3027 line. Hetero-grafting resulted in considerable changes in the metabolite content of tubers. Especially, the effect of CE3027 on the metabolite composition of tubers formed on CE3130 rootstocks was readily apparent. Nevertheless, many compounds were present at similar levels in the tubers of hetero-grafted plants as was found in the tubers of their scion counterparts.</p><p><strong>CONCLUSION:</strong> Hetero-grafting resulted in many compounds at similar concentrations in rootstock tubers as in scion tubers suggesting that these are transported from the source leaves to tubers.</p>
2023-09-12 | MTBLS4445 | MetaboLights
Project description:X-ray CT was used to determine the growth velocity of individual tubers. RNA was extracted from tubers growing at different velocities and used for microarray hybridisation.
2010-02-08 | E-MEXP-2484 | biostudies-arrayexpress
Project description:Transcriptome sequencing was performed to reveal the physiological changes of potato tubers after injury at the transcriptome level
2021-06-22 | GSE178602 | GEO
Project description:Helianthus tuberosus L., known as the Jerusalem artichoke, is a hexaploid plant species, adapted to low-nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 expressed sequence tags (ESTs) from an H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3), and at tuber physiological maturity (Tm), in "VR" and "K8-HS142"clones. The former was selected as an early tuberizing and the latter as a late-tuberizing clone. We quantified inulin and starch levels, and qRT-PCR confirmed the expression of critical genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady-state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.
| S-EPMC7046554 | biostudies-literature