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Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10900 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1019270_1.fastq.gz | Fastqsanger.gz | |||
| ERR1019270_2.fastq.gz | Fastqsanger.gz | |||
| ERR1019280_1.fastq.gz | Fastqsanger.gz | |||
| ERR1019280_2.fastq.gz | Fastqsanger.gz | |||
| ERR1019290_1.fastq.gz | Fastqsanger.gz |
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Project description:We prepared QTL map of tuber starch content in potato diploid population. Then, we examined expression level of enzyme ADP-glucose pyrophosphorylase (AGPase) taking part in starch biosynthesis (marker AGPaseS-a). Based on starch content and AGPaseS-a expression, we constructed four bulks prepared from RNA isolated from tubers of F1 individuals H1 and H2 consisted of high TSC genotypes, bulks L1 and L2 were made of low TSC genotypes. Plants in bulks H1 and L1 strongly expressed AGPaseS-a, whereas those in bulks H2 and L2 exhibited low levels. Then we used RNA-seq technology for selection of genes displaying differential expression between RNA pools. For selected candidate genes we mapped expression QTL (e-QTL) and found eQTL of eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5). We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers and suggests that cruciferin may be a novel PTST protein in potato tubers.
2020-06-24 | GSE153031 | GEO
Project description:Sweet potato (Ipomoea batatas), a starchy root and tuber crop, is an important source of carbohydrates for the human diet and a valuable resource in many industrial applications. Here, we performed a spatiotemporally distributed proteome analysis using leaves and storage roots of two F1 individuals, H283 (high starch) and L423 (low starch), of similar high yield to underly regulatory networks governing starch accumulation.
2024-07-30 | PXD048050 | Pride
Project description:Although significant work has been undertaken regarding the response of model and crop plants to heat shock during the acclimatory phase, few studies have examined the steady state response to the mild heat stress encountered in temperate agriculture. In the present work we therefore exposed tuberising potato plants to mildly elevated temperatures (30/20C), day/night) for up to five weeks and compared tuber yield, physiological and biochemical responses, and leaf and tuber metabolomes and transcriptomes with plants grown under optimal conditions (22/16C). Growth at elevated temperature reduced tuber yield despite an increase in net foliar photosynthesis. This was associated with major shifts in leaf and tuber metabolite profiles, a significant decrease in leaf glutathione redox state and decreased starch synthesis in tubers. Furthermore, growth at elevated temperature had a profound impact on leaf and tuber transcript expression with large numbers of transcripts displaying a rhythmic oscillation at the higher growth temperature. RT-PCR revealed perturbation in the expression of circadian clock transcripts including StSP6A, previously identified as a tuberisation signal. Our data indicate that potato plants grown at moderately elevated temperatures do not exhibit classic symptoms of abiotic stress but that tuber development responds via a diversity of biochemical and molecular signals. In this submission we are looking at gene expression changes with respect to both temperature and time, every 4h over a 24h period whereby diurnal changes may be apparent.
2013-08-01 | E-MTAB-1655 | biostudies-arrayexpress
Project description:For many potato cultivars, tuber yield is optimal at average day time temperatures in the range of 14-22 ⁰C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. In our previous work we observed that the steady-state expression level of the core circadian clock gene, TIMING OF CAB EXPRESSION 1 (TOC1), in potato tubers increased at moderately elevated temperature, whereas expression of the tuberisation signal gene StSP6A decreased along with tuber yield. In this study we investigated the potential roles of StTOC1 in linking environmental signalling and potato tuberisation. We show that transgenic lines with decreased expression of StTOC1 exhibit enhanced StSP6A transcript levels in tuberising stolons, and show changes in gene expression consistent with elevated tuber sink strength.
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Project description:Cycling Dof Factor (CDF) transcription factors have been implicated in different aspects of plant growth and development. In Arabidopsis and tomato, two members of this family CDF1 and CDF3 have recently been associated with the regulation of primary metabolism and abiotic stress responses, but their roles in crop production under open field conditions remain unknown. In this study, we compared growth and tuber yield and composition of wild-type (WT) potato plants and plants ectopically expressing the CDF1/3 genes from Arabidopsis under the control of the 35S promoter cultured under growth chamber and open field conditions. In growth chambers, the 35S::AtCDF1 and 35S::AtCDF3 potato plants showed higher than WT biomass production and tuber yield. Under field conditions, 35S::AtCDF1 plants showed significant increases in tuber yield with a significant increase in tuber weight, whereas 35S::AtCDF3 plants showed no significant changes in yield, but produced more than WT number of tubers. Metabolomic analysis revealed that tubers of 35S::AtCDF1 plants cultured under open field conditions accumulated higher levels of glucose, starch and amino acids than WT tubers. Comparative proteomic analysis of tubers of 35S::AtCDF1 and control plants cultured under open field revealed that these changes can be accounted for by changes in the expression of proteins involved in energy production and different aspects of C and N metabolism. Results from this study advance our collective understanding of the role of CDFs and are of interest to improve yield and breeding of crop plants
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Project description:Transcript profiling of tuber samples of 94 genotypes deriving from a segregating diploid potato population
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Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates. Keywords: direct comparison
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Project description:We identified germline single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL) and its subtypes. Using the Affymetrix 500K Mapping array and publicly available genotypes, we identified 18 SNPs whose allele frequency differed (P<1x10-5) between a pediatric ALL population (n=317) and non-ALL controls (n=17,958). Six of these SNPs differed (P≤0.05) in allele frequency among four ALL subtypes. Two SNPs in ARID5B not only differed between ALL and non-ALL groups (rs10821936, P=1.4x10-15, odds ratio[OR]=1.91; rs10994982, P=5.7x10-9, OR=1.62) but also distinguished B-hyperdiploid ALL from other subtypes (rs10821936, P=1.62 x10-5, OR=2.17; rs10994982, P=0.003, OR 1.72). These ARID5B SNPs also distinguished B-hyperdiploid ALL from other subtypes in an independent validation cohort (n=124 children with ALL) (P=0.003 and P=0.0008, OR 2.45 and 2.86, respectively) and were associated with methotrexate accumulation and gene expression pattern in leukemic lymphoblasts. We conclude that germline genomic variations affect susceptibility to and characteristics of specific ALL subtypes.
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Project description:We identified germline single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL) and its subtypes. Using the Affymetrix 500K Mapping array and publicly available genotypes, we identified 18 SNPs whose allele frequency differed (P<1x10-5) between a pediatric ALL population (n=317) and non-ALL controls (n=17,958). Six of these SNPs differed (P≤0.05) in allele frequency among four ALL subtypes. Two SNPs in ARID5B not only differed between ALL and non-ALL groups (rs10821936, P=1.4x10-15, odds ratio[OR]=1.91; rs10994982, P=5.7x10-9, OR=1.62) but also distinguished B-hyperdiploid ALL from other subtypes (rs10821936, P=1.62 x10-5, OR=2.17; rs10994982, P=0.003, OR 1.72). These ARID5B SNPs also distinguished B-hyperdiploid ALL from other subtypes in an independent validation cohort (n=124 children with ALL) (P=0.003 and P=0.0008, OR 2.45 and 2.86, respectively) and were associated with methotrexate accumulation and gene expression pattern in leukemic lymphoblasts. We conclude that germline genomic variations affect susceptibility to and characteristics of specific ALL subtypes. We used microarrays to detail the global program of gene expression in primary leukemic blasts cells from children diagnosed with acute lymphoblastic leukemia.
2009-08-16 | E-GEOD-17195 | biostudies-arrayexpress
Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. While cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers, cv. Sante is resistant and thus not affected by the virus. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Moreover, the differences in the response of the sensitive and resistant cultivar can pinpoint the genes involved in differential sensitivity of the cultivars. Differential gene expression in the early response of potato cvs. Igor and Sante to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 0.5 and 12 hours after inoculation.
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