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7 results for “Ascochyta”
Raw data for "The role of conidia in the dispersal of *Ascochyta rabiei*"
<p>Raw data associated with the pre-print, “<em>The role of conidia in the dispersal of </em>Ascochyta rabiei”, <a href="https://doi.org/10.1101/2020.05.12.091827">https://doi.org/10.1101/2020.05.12.091827</a></p> <p>There are six data files associated with this manuscript. Five are raw data, one was generated as a course of the analysis, “weather_summary.csv”. All files are in .csv format. Details for each including the number of columns and column contents and units follow.</p> <p><strong>Files and Content Descriptions</strong></p> <ul> <li><strong>BCG_weather_data.csv</strong> – 15-minute interval weather data from the Birchip Ag Group automated weather station near Curyo, Victoria, Australia for the time period of 01/10/2019 to 31/10/2019</li> <li><strong>Curyo_SPA_2019_weather.csv </strong>– 10-minute interval weather data from AgVictoria’s automated weather station at Curyo, Victoria, Australia from 22/01/2019 to 06/12/2019 recorded with Measurement Engineering Australia, Adelaide, Australia equipment</li> <li><strong>Dispersal_experiment_dates.csv</strong> – Data detailing each spread event at each location including the time trap plants were put out and brought in and date assessed</li> <li><strong>Horsham_SPA_2019_weather.csv</strong> – 10-minute interval weather data from AgVictoria’s automated weather station at Horsham, Victoria, Australia from 01/01/2019 to 06/12/2019 recorded with Measurement Engineering Australia, Adelaide, Australia equipment</li> <li><strong>lesion_counts.csv </strong>– Data detailing lesion counts on trap plants for each location and spread event</li> <li><strong>weather_summary.csv</strong>– Summary weather data detailing for each location and spread event</li> </ul> <p><em><strong>BCG_weather_data.csv </strong></em>The file “BCG_weather_data.csv” contains six columns:</p> <ul> <li><strong>Reading Time </strong>– the time at which the data was recorded</li> <li><strong>Rainfall</strong> – the amount of rainfall (mm)</li> <li><strong>Humidity</strong> – relative humidity (%)</li> <li><strong>Temperature</strong> – air temperature (˚C)</li> <li><strong>Wind Speed</strong> – wind speed (km/p)</li> <li><strong>Wind Direction</strong> – direction in which the wind was blowing from (cardinal directions)</li> </ul> <p><em><strong>Curyo_SPA_2019_weather.csv</strong></em> and H<em><strong>orsham_SPA_2019_weather.csv </strong></em>The files “Curyo_SPA_2019_weather.csv” and “Horsham_SPA_2019_weather.csv” both contain 22 columns:</p> <ul> <li><strong>Time</strong></li> <li><strong>Air Temperature - average (ºC)</strong></li> <li><strong>Soil Temperature - average (ºC)</strong></li> <li><strong>Relative Humidity - average (%)</strong></li> <li><strong>Wind Speed - minimum (km/h)</strong></li> <li><strong>Wind Speed - average (km/h)</strong></li> <li><strong>Wind Speed - maximum (km/h)</strong></li> <li><strong>Wind Direction - average (º)</strong></li> <li><strong>Solar Radiation - average (W/m^2)</strong></li> <li><strong>Sigma - average (deg)</strong></li> <li><strong>Rainfall - (mm)</strong></li> <li><strong>Voltage - minimum (V)</strong></li> <li><strong>Voltage - average (V)</strong></li> <li><strong>Voltage - maximum (V)</strong></li> <li><strong>Apparent Temperature - average (ºC)</strong></li> <li><strong>Dew Point - average (ºC)</strong></li> <li><strong>Delta T - average (ºC)</strong></li> </ul> <p><em><strong>Dispersal_experiment_dates.csv </strong></em>The file “Dispersal_experiment_dates.csv” contains five columns:</p> <ul> <li><strong>site </strong>– The experiment location</li> <li><strong>rep </strong>– Spread event number for each location</li> <li><strong>time out </strong>– date and time on which the trap plants were deployed in the paddock for the spread event (rainfall)</li> <li><strong>time removed </strong>– date and time on which the trap plants were retrieved from the paddock after the spread event (rainfall)</li> <li><strong>assessment date</strong>– date on which trap plants were assessed for number of lesions</li> </ul> <p><em><strong>lesion_counts.csv </strong></em>The file "lesion_counts.csv” contains thirteen columns:</p> <ul> <li><strong>site </strong>– The experiment location</li> <li><strong>rep </strong>– Spread event number for each location</li> <li><strong>distance </strong>– Distance from infection source (m)</li> <li><strong>station – </strong>Trap plant units (number of trap plants at each point along transect)</li> <li><strong>transect – </strong>One of ten repeating lines along which the trap plant stations were deployed in a 90˚ arc downwind of the infection source</li> <li><strong>dist_stat – </strong>A concatenation of the ‘dist’ and ‘station’ columns</li> <li><strong>plant_no – </strong>Total number of plants at a given station</li> <li><strong>pot_no </strong>– Individually assigned pot number for each individual transect (1 – 56)</li> <li><strong>counts_p1 – </strong>Lesion counts for Pot 1</li> <li><strong>counts_p2 – </strong>Lesion counts for Pot 2</li> <li><strong>counts_p3 – </strong>Lesion counts for Pot 3</li> <li><strong>counts_p4 – </strong>Lesion counts for Pot 4</li> <li><strong>counts_p5 – </strong>Lesion counts for Pot 5</li> </ul> <p><em><strong>weather_summary.csv </strong></em>The file “weather_summary.csv” contains six columns that summarise the weather conditions during each of the six spread events at three experiment plot locations.</p> <ul> <li><strong>site </strong>– The experiment location</li> <li><strong>rep</strong> – Spread event number for each location</li> <li><strong>mws</strong> – Mean wind speed for the spread event (m/s)</li> <li><strong>ws_sd </strong>– Wind speed standard deviation for the spread event</li> <li><strong>mwd </strong>– Mean wind direction for the spread event (˚)</li> <li><strong>sum_</strong>rain – Total precipitation during spread event including both natural rainfall and overhead sprinkler irrigation (mm)</li> </ul>
Variant dataset and code for "Population-level whole genome sequencing of Ascochyta rabiei identifies genomic loci associated with isolate aggressiveness"
<p>This dataset contains genetic variants (SNPs) of <em>Ascochyta rabiei</em> isolates and the R code used in their analysis to generate the results and figures described in the manuscript "<strong>Population-level whole genome sequencing of <em>Ascochyta rabiei</em> identifies genomic loci associated with isolate aggressiveness</strong>".</p> <div> <div> </div> </div>
Novel Genomic Regions linked to Ascochyta blight Resistance in two differentially resistant cultivars of chickpea
<p><em>Ascochyta</em> blight (AB) caused by the fungal pathogen <em>Ascochyta rabiei</em> is a devastating foliar disease of chickpea (<em>Cicer arietinum</em> L.). Genotyping-by-sequencing (GBS) has been used in the current study for the identification of AB associated quantitative trait loci (QTLs) and their gene(s). We evaluated genotyping-by-sequencing (GBS)-based approach for mapping QTLs associated with AB resistance in chickpea using two recombinant inbred lines populations (AB<sub>3279</sub> and AB<sub>482</sub>) derived from two crosses ILC 1929 X ILC 3279 and ILC 1929 X ILC 482, under six different environments. In total, twenty-one different genomic regions were identified on linkage groups CalG02 and CalG04 pertaining to AB resistance in both populations AB<sub>3279</sub> and AB<sub>482</sub>. Four genomic regions were detected on CalG02 in the population AB<sub>3279</sub> and nine major genomic regions were associated with AB resistance on CaLG04, five out of them were common to both resistant parents ‘ILC3279’ and ‘ILC482’, and eight minor genomic regions with two out of them common between both populations. These regions contain 1,118 SNPs significantly associated (p ≤ 0.001) with AB resistance. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, with most important genes belonging to resistance gene families including Leucine-Rich Repeat (LRR), and transcription factors families. Our results may refer to the flowering-associated gene GIGANTEA as a possible key factor in AB resistance in chickpea. The results have narrowed the AB resistance associated regions on the chickpea physical map and the associated markers will help in breeding programs for chickpea improvement.</p>
Dataset and code release for "Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia"
<p>This upload contains the raw DArTseq data and code for reproducible analysis and production of output tables and plots to accompany the publication "Current population structure and pathogenicity patterns of <em>Ascochyta rabiei</em> in Australia".<br> The analysis is performed primarily in R and is run using the `A_rabiei_DArT.R` file.</p> <p>A version-controlled repository of this upload is maintained at GitHub at the following link: <a href="https://github.com/IdoBar/A_rabiei_DArT">https://github.com/IdoBar/A_rabiei_DArT</a></p> <p>The archived file is structured as follows:</p> <ul> <li>Main analysis code is in <strong>A_rabiei_DArT.R</strong></li> <li>Raw DArTseq data and <em>A. rabiei</em> isolate metadata can be found in in the <strong><em>data </em></strong>folder</li> <li>Output tables and plots in <em><strong>output</strong></em> folder</li> <li>General information (partial and slightly outdated) in the markdown <strong>A_rabiei_DArT.Rmd </strong>and knitted <strong>A_rabiei_DArT.html </strong>files</li> <li>Australian chickpea production stats and figures in <strong>Chickpea_production.R</strong></li> </ul>
Lens orientalis contributes quantitative trait loci and candidate genes associated with Ascochyta blight resistance in lentil
GEO Series GSE176412. Lens culinaris; Lens orientalis; Lens culinaris x Lens orientalis. 142 samples. Type: Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Other.
Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei
GEO Series GSE4660. Lathyrus sativus; Cicer arietinum; Lens culinaris. 20 samples. Type: Expression profiling by array.
Transcriptional profiling of Ascochyta blight resistance in Lentil
GEO Series GSE11374. Lathyrus sativus; Cicer arietinum; Lens culinaris; Lens culinaris subsp. culinaris. 10 samples. Type: Expression profiling by array.
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