DOI: 10.6084/m9.figshare.29820191
title: Continuous phenotyping files

description: The folder contains .ods files of continuous phenotyping data. The data were acquired by the Pyphe hard- and software. Yeast colonies were grown on solid media plates and continuously scanned. Their growth was monitored by continuous image acquisition, coordinated by the Pyphe toolbox. Growth values, i.e. colony sizes, were extracted from a series of images.Biologically, the testing strains were generated by BY × CEN.PK biparental (back)crossing of two <i>Saccharomyces cerevisiae</i> yeast strains. The most salt tolerant haploid segregant of each generation was selected based on its tolerance against NaCl. The strain panel included parental strains BY, Y7092 and CEN.PK from a yeast collection, as well as 13 segregants from the BY × CEN.PK crosses, 7 of which represented individuals with the most extreme trait values from each generation of crossing.Candidate quantitative trait genes (QTGs) for salt tolerance were selected by QTL mapping method based on variant effect criteria. The candidate genes were: <i>ENA</i> locus, <i>ASG1</i>, <i>AYR1</i>, <i>KGD1</i>, <i>MET18</i>, <i>QDR2</i>, <i>RRT14</i>. Within each of 16 strains from the panel, each of the 7 candidate genes was firstly deleted. In the second step, the allele variant from the opposite parental strain was introduced by the CRISPR-Cas9 procedure. With this approach, we generated 3 isogenic variants of each strain from the panel for each candidate QTG: source wild-type variant, deletion variant, and allele-swapped variant.The growth of each variant was continuously monitored for five consecutive days on solid YPD agar plates, supplemented with NaCl in concentrations from 0.25 M to 2.25 M in increment of 0.25 M.The files contain spreadsheets regarding the analysed gene. In each experiment, 4 solid agar plates were placed within the scanner (plate1-4), of which the first plate was a control without supplemented NaCl (plate1_ctrl) for to the normalization purposes during the analysis. In the first round (1), plate2, plate3, and plate4 correspond to 0.25 M, 0.75 M, and 1.00 M of supplemented NaCl, in the second round (2), plate2, plate3, and plate4 correspond to 1.00 M, 1.25 M, and 1.50 M supplemented NaCl, and in the third round (3), plate2, plate3, and plate4 correspond to 1.75 M, 2.00, and 2.25 M of supplemented NaCl, respectively. Colony positions (16 rows and 24 columns) are indicated in the first row of each spreadsheet, with the corresponding layout plan with strain names in the layout_wide_chrIV/chrIX.csv files. The corresponding strain genotypes regarding loci on chrIV and chrIX are indicated in the allele.txt file. The growthcurves.ods files contain quantitative growth parameter values: i) initial biomass, ii) lag phase duration, iii) t_max, iv) max_slope, v) r2 of for the fitting, vi) y-intercept of the growth curve, vii) x-intercept of the growth curve, viii) sum_fo_values_(AUC), ix) maximum of the growth curve. Growth values (i.e. colony sizes) were first extracted from the acquired scan images and then fitted to the growth curve model. Quantitative parameters describing the growth curve were extracted by the Pyphe software.<br>