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20 results for “pimpinellifolium”
EMMA-X GWAS results on S. pimpinellifolium RSA traits - part 2
<p>The results of GWAS run through EMMA-X pipeline, on root system architecture traits of S. pimpinellifolim (wild tomato) exposed to control and salt stress conditions on agar plates. Traits are abbreviated as: aLRG for average lateral root growth rate, aLRL for average lateral root length, aLRLpTRS for the ratio between average lateral root length and total root size. The treatments are abbreviated with C or S for control or 100 mM NaCl treatments. The numbers in file name (0-4) indicate the days post transfer to agar plates containing treatment. </p>
EMMA-X GWAS results on S. pimpinellifolium RSA traits - part 1
<p>The results of GWAS run through EMMA-X pipeline, on root system architecture traits of S. pimpinellifolim (wild tomato) exposed to control and salt stress conditions on agar plates. Traits are abbreviated as: aLRG for average lateral root growth rate, aLRL for average lateral root length, aLRLpTRS for the ratio between average lateral root length and total root size. The treatments are abbreviated with C or S for control or 100 mM NaCl treatments. The numbers in file name (0-4) indicate the days post transfer to agar plates containing treatment. </p>
Manhattan and QQ plots of GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)
<p>The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>. The raw GWAS outputs can be found <a href="https://zenodo.org/badge/DOI/10.5281/zenodo.5856310.svg">here</a>. This dataset represents Manhattan plots and QQ plots made out of the data. </p>
Lycopersicon pimpinellifolium (L.) Mill. (BR0000010151600)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Lycopersicon pimpinellifolium (L.) Mill. (BR0000024927833)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Solanum pimpinellifolium input data collected from the TPA - used for GWAS
<p>The GWAS input data used for mapping the candidate genes in S. pimpinellifolium collection, exposed to salt stress in The Plant Accelerator experiment (TPA). The phenotypic data was collected in an experiment was performed by Mitchell Morton while being a PhD student in the group of Prof. Mark Tester at KAUST. The genotypic data was collected by Magdalena Julkowska, and used for sequencing. The SNPs were called by Elodie Ray, and subsequently curated by Magdalena Julkowska for GWAS analysis. The GWAS was conducted by Magdalena Julkowska. </p>
Solanum pimpinellifolium L. (BR0000012564415)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
EMMA-X GWAS results on S. pimpinellifolium RSA traits - part 3
<p>The results of GWAS run through EMMA-X pipeline, on root system architecture traits of S. pimpinellifolim (wild tomato) exposed to control and salt stress conditions on agar plates. Traits are abbreviated as: LRnG for increase in lateral root number, LRno for lateral root number, MR.GR for main root growth rate, MRL for main root length. The treatments are abbreviated with C or S for control or 100 mM NaCl treatments. The numbers in file name (0-4) indicate the days post transfer to agar plates containing treatment. </p>
GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)
<p>The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>. </p>
Deciphering salt stress responses in Solanum pimpinellifolium through high-throughput phenotyping
Open the record for dataset details and reuse information.
Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions
<p>Marker genotypes, linkage map and phenotypic data used for QTL analysis included in the manuscript by Gonzalo et al. <em>in press "</em>Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between <em>S. pimpinellifolium</em> and <em>S. lycopersicum</em> Accessions".</p>
Transcriptome sequencing of 7 tissues of S. lycopersicum and 2 of its closely related wild ancestor S. pimpinellifolium
GEO Series GSE33507. Solanum lycopersicum; Solanum pimpinellifolium. 9 samples. Type: Expression profiling by high throughput sequencing.
Expression analysis of S. pimpinellifolium accession LA1589 wild type, lc, fas and lc/fas NILs, SlCLV3 RNAi and SlCLV3-complementation lines during tomato floral development.
GEO Series GSE129901. Solanum pimpinellifolium. 72 samples. Type: Expression profiling by high throughput sequencing.
Expression analysis of tomato S. pimpinellifolium accession LA1589 wild type and the Nearly Isogenic Lines lc, fas and lc/fas NILs during floral development.
GEO Series GSE129809. Solanum pimpinellifolium. 60 samples. Type: Expression profiling by high throughput sequencing.
Dissection of the style’s response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species
GEO Series GSE67654. Solanum pimpinellifolium; Solanum chilense. 12 samples. Type: Expression profiling by high throughput sequencing.
Expression of genes in red fruit of Andean tomato (Solanum lycopersicum) and Solanum pimpinellifolium
GEO Series GSE125476. Solanum lycopersicum; Solanum pimpinellifolium. 30 samples. Type: Expression profiling by array.
Transcriptome analyses of a pair of near-isogenic lines (NILs) from the cross Solanum lycopersicum var. cerasiforme (E9) x S. pimpinellifolium line (L5) under multistress conditions
GEO Series GSE79307. Solanum lycopersicum x Solanum pimpinellifolium; Solanum lycopersicum. 16 samples. Type: Expression profiling by array.
3' Tag RNA-seq analysis of wild type (S. pimpinellifolium accession LA1589) and SUN NIL during tomato fruit development.
GEO Series GSE135764. Solanum pimpinellifolium. 56 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptome analysis of responses to water deficit in Solanum lycopersicum and S. pimpinellifolium roots
GEO Series GSE39894. Solanum lycopersicum; Solanum pimpinellifolium. 46 samples. Type: Expression profiling by array.
The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium
GEO Series GSE62196. Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pimpinellifolium. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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OpenNeuro
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