Carrot root transcriptome
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REPOSITORIES: ENA
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Project description:Cultivated carrot (Daucus carota L. ssp. sativus) was domesticated from wild carrot (Daucus carota L. ssp. carota) with radical different traits. The aim of this study was to compare the root transcriptomes between cultivated and wild carrots for SNP discovery, inferring domestication process, and identifying domestication genes. Six cultivated carrots representing main European carrot root types and five wild carrot populations from widely dispersed sites were used. The root transcriptomes were sequenced with multiplexing paried-end sequencing in Illumina Genome Analyzer IIx.
2013-10-24 | E-MTAB-1340 | biostudies-arrayexpress
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray. Near isogenic recombinant inbred lines B8788 and B8750, derived from a cross between white rooted wild carrot (QAL) and orange-rooted B493 were used for comparative analyzes to minimize background genetic differences. B8788 is true breeding for orange color whereas B8750 is true breeding for white storage root color. Carrots were grown in three pots for each genotype under greenhouse conditions and carrots were selected arbitrarily from these pots for harvest. Roots were harvested at approximately 11 weeks post planting when carotenoid accumulation becomes apparent in the storage root. Storage root tissue from sixteen individual carrot roots was pooled into three one-gram tissue pools of four carrots for each genotype.
2014-08-13 | E-GEOD-49873 | biostudies-arrayexpress
Project description:Comparing root transcriptomes of cultivated and wild carrots
| PRJEB3356 | ENA
Project description:Purple carrots can accumulate large quantities of anthocyanins in their roots. Depending on the genetic background, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns, confined to the root phloem or xylem tissues. Within the phloem, the tissue usually contributing most of the overall anthocyanin concentration in the carrot root, purple pigmentation can be found in the outer phloem (OP) (also called cortex) and inner phloem (IP) tissues, or it can be confined exclusively to the OP. The latter is a fairly-common phenotype in many purple carrot cultivars. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping, transcriptome (RNA-seq), phylogenetic, and gene expression (RT-qPCR) analyses in two genetic backgrounds; an F2 mapping population (3242) and the inbred line B7262. Genetic mapping of the ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed co-localization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors (4 MYBs, 1 bHLH, 1 MADS-box, 1 ERF), seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, which roots present purple pigmentation only in the outer phloem, DcMYB113 conditions ROPAP
2021-10-27 | GSE181611 | GEO
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray.
2014-08-13 | GSE49873 | GEO
Project description:To test the impacts of drought on the host and fungus, we inoculated carrots (Daucus carota cv. ‘Napoli’) with spores of Rhizophagus irregularis DAOM 197198. Carrots grew in a greenhouse, and at the beginning of taproot development, were exposed to a 10-day water restriction. We evaluated plant growth and physiological responses, colonization level, and plant and fungal gene expression.
2023-06-30 | GSE189806 | GEO
Project description:ra04-07_pgpr - profiling of the root architecture response to phyllobacterium - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. - Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sawn on agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on a fresh agar mineral medium inoculated or not with Phyllobacterium STM196 (2.108 cfu/ml). 6 days later, root and leaves were collected, froze on liquid nitrogen and stored at -80degreeC. Keywords: treated vs untreated comparison
2007-06-20 | GSE7991 | GEO
Project description:BackgroundUnderstanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses.ResultsThe root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication.ConclusionsWestern carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
| S-EPMC4213543 | biostudies-literature
Project description:The impact of nitrate on the proteome of the primary root tip of Medicago truncatula were compared in R108, a wild and sensitive genotype, and npf6.8, a mutant and insensitive line by shotgun analysis. Each genotype were cultivated in N-free condition or with 5mM of nitrate in three independent biological replicate. Sample collection was performed of 10 days old seedlings
2022-05-20 | PXD030547 | Pride
Project description:Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.
2022-05-02 | GSE180100 | GEO