Mapping QTLs and modifiers.

<p>(A) QTL mapping has evolved from the classical approach of individual segregant analysis to the X-QTLs and iQTLs approaches with higher mapping sensitivity and resolution. Analysis of time series data in iQTLs allows dynamic monitoring of allele frequency values <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002912#pgen.1002912-Illingworth1" target="_blank">[56]</a>. (B) A possible approach to map genetic modifiers using iQTLs. A conditional essential gene, <i>y</i>, is deleted from its original chromosomal location and maintained on a plasmid. This hybrid is intercrossed multiple times to allow reshuffling of parental genomes. Upon loss of gene <i>y</i>, viability relies on the presence of genetic modifier/s, and allelic combinations that result in lethality (dashed cells) will decrease in allele frequency. These modifiers can be detected by comparing allele frequencies of the pool before and after the plasmid loss. When many modifiers are involved, the lethal combinations will be present in low frequency, making them difficult to detect. Further rounds of intercrosses, after loss of gene <i>y</i>, will allow reshuffling of alleles and the generation of more cells with unviable combinations.</p

Experimental measures of natural variation.

<p>Yeasts offer a unique opportunity to engineer changes to measure the impact of phenotypic variants on traits. (A) Reciprocal hemizygosity has high throughput and can be used to test a large number of candidates. Hybrids that differ only in which of two alleles is present/deleted are compared. Deletion collections of multiple strains will soon be available allowing genome-wide systematic studies using hybrids to test all candidates easily or even for discovery of phenotypic effects directly. (B) Allele swapping is less high throughput but allows testing phenotypic effects of specific alleles in different genetic backgrounds. This is more precise than reciprocal hemizygosity. (C) Site-directed mutagenesis is a rapid and precise way of testing known and novel base changes for phenotypic effects. (D) Synthetic biology has the potential of simultaneously testing multiple variants, both natural or artificial, in a single gene <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002912#pgen.1002912-Hietpas1" target="_blank">[55]</a> or scattered through the genome <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002912#pgen.1002912-Dymond1" target="_blank">[47]</a>.</p

Additional file 6: Table S2. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

List of genes used in the RH analysis with the BY4741 strain that are present in the subtelomeric regions and are not essential. (XLSX 13 kb

Inference of recombination from simulated data.

<p>a) A histogram of estimated recombination rates from simulated data under uniform recombination using our likelihood calculation together with the <i>interval</i> tool from <i>LDhat </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062266#pone.0062266-McVean1" target="_blank">[9]</a>. Input recombination rates were chosen to cover a biologically realistic range and were well recovered by the inference. Each of the 100 simulations has 100 segregating sites at 1 kb intervals (other parameters ). b) Inference of recombination rate for a simulation with varying rate. The simulated recombination profile (blue) had three recombination hotspots, with (50,25,50)-fold higher rate than the background; other parameters as before. The inferred profile is in good agreement with the input (red band: 95% confidence interval from 300 bootstrap samples of the single realisation of the crossing simulation).</p

Additional file 3: Figure S2. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

Workflow of populations’ selection and sequencing. Cells were grown in complete media (YPD) and synthetic must (SM), and were incubated at either optimum temperature (28 °C) or low temperature (15 °C) until the stationary phase was reached. At this time, the volume required to inoculate at an OD of 0.2 was re-inoculated into 60 mL of fresh medium. The experiment was carried out 8 times after which the selected populations were analyzed and sequenced. (PDF 43 kb

Additional file 2: Figure S1. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

Distribution of private nonsynonymous SNPs in P5 and P24 compared to S288c. An external circle indicates P24 and an internal circle indicates P5. Homozygous changes are colored in green, while heterozygous changes are marked in red. (PDF 243 kb

Measurement of promoter band intensities on chromatin blot confirmed mating-type dependent changes.

<p>Measurements were made on the autoradiograph of the chromatin blot of strains with a telomeric reporter at XI-L. Intensities were measured along a vertical line drawn through the three promoter bands produced by digestion with the highest concentration of MNase I. The graphs show intensity versus distance in inches along the line. Arrows indicate the band positions. The left hand peak corresponds to the top promoter band on the auroradiograph. Strains on graphs: haploid (blue), dipoid (red), diploid <i>mata-</i>delta (green).</p

Power to discover recombination hot and cold regions under different crossing designs.

<p>Red (blue) curves show the ability to correctly recover the hottest (coldest) recombining kb at resolution and number of crossing rounds . <b>a, b</b>) Results for an advanced intercross design, comprising 12 generations of crossing. Curves are calculated by comparing the locations of the hottest and coldest regions from the landscapes inferred for each of the ten simulated crossing experiments to the corresponding locations in the true input landscape (that inferred for the two-way cross), taking the mean value of the size of the overlap. <b>c, d</b>) Results for a single generation cross. The advanced intercross design has a clear advantage over single generation experiment.</p

Neither Sir3 nor Sir4 are limiting at <i>HML</i> in diploid cells.

<p>A single copy of <i>SIR3</i> or <i>SIR4</i> was deleted from diploid cells and fluorescence levels were measured by flow cytometry. Strains on histogram plot: haploid (n, red), diploid (2n, blue), <i>SIR3</i>/<i>sir3-</i>Δ (pink), <i>SIR4</i>/<i>sir4-</i>Δ (turquoise).</p

Additional file 7: Figure S5. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

Outline of the construction of advanced intercross lines. We carried out a strategy that forces yeast cells through multiple rounds of random mating and sporulation to create advanced intercross lines (AILs). This step can improve genetic mapping in two ways: increasing resolution by reducing linkage and unlinking nearby QTLs. (PDF 168 kb