Role of TAO3 in sporulation efficiency. (A) Comparison of genomic sequences of TAO3 (4441–4500) across the SGRP collection (). The 4477th position of TAO3 consists of the sporulation causative variant where identical nucleotides are indicated by the same color. Identity indicates the percentage match between the nucleotides in the shown region of the gene. The strains are ordered according to their mean sporulation efficiency (): high (60–100%), intermediate (10–60%), low (0–10%) and ND (not determined). (B) Bar plots represents the mean sporulation efficiency after 48 hr of the SK1, T and S strains. The sporulation efficiency data are indicated as circles. (C) Line graphs represent the mean sporulation efficiency of the S, T, and SK1 strains measured until saturation, i.e., until sporulation efficiency did not vary for three consecutive days. (D) Percentage of one-, two- and four-nuclei states of the T strain (y-axis) vs. time in sporulation medium (x-axis). One-nucleus stage is indicated as red circles (G₀/G₁ phase), two-nuclei state as yellow circles (completion of Meiosis I, MI phase), and blue circles is four-nuclei stage (completion of Meiosis II, MII phase). (E) Bootstrap distribution of the time to initiate meiosis and the rate of transition from G₁/G₀ into MI, estimated from time courses in (D). See Materials and Methods for details. (F) Conditional expression of TAO3(4477C) during sporulation in P_Tet-TAO3(4477C) strain. The y-axis is the mean sporulation efficiency in 48 hr. No doxycycline in growth (YPD) or spo (YPA + sporulation) medium is depicted as “–” condition on the x-axis, and addition of doxycycline is depicted as “+” under those conditions. The “+3h” condition in Spo indicates that doxycycline was present throughout in the growth medium, and in the sporulation medium until 3 hr, after which cells were sporulated in the absence of doxycycline. The “+6h” condition indicates that doxycycline was present throughout in both the growth and sporulation medium until 6 hr, after which cells were sporulated in the absence of doxycycline. P values were calculated by an unpaired t-test. Error bars are SEM.

The role of TAO3 in meiosis is distinct from its role during mitosis. (A) Expression profile (log₂ fold change t₀) of TAO3 is given in the y-axis for the T (purple) and S strains (red), and the x-axis denotes the time in sporulation medium (data in Table S1 and Table S11). (B) Heatmap showing gene expression of RAM network genes and Ace2-regulated genes in the T and S strains. Gene names in green show differential expression (data in Table S1 and Table S11). (C) Bar plots represent the mean sporulation efficiency after 48 hr of the SK1 and T wild type (wt) and ace2∆ deletion strains. Pair and interaction tests (Materials and Methods) were performed to test significance.

Global gene expression variation in presence of causative TAO3 allele. (A) Temporal heatmap of meiotic genes in the T and S strains. The gene names shown in green are differentially expressed in the presence of TAO3(4477C). (B) The expression profile (log₂ fold change t₀) for the meiotic landmark genes is given in the y-axis, and the x-axis denotes the time in sporulation medium. The red line represents the expression profile of the respective gene in the S strain, and the blue line is the same in the T strain. (C) Heatmap of the T and S strains showing differentially expressed genes across time, clustered according to expression profiles in T strain. Each row represents a single gene, and columns are time points of each strain (for gene list in each cluster, see Table S2). The order of genes is based on clustering of the T strain. Both the heatmap and boxplot consists of genes in each cluster of the T strain, and represent their expression profiles in both T and S strains. Functional GO categories of genes in each cluster of T strain are shown on left. The boxplots on the right represent the average expression profile of each cluster in the T, and the same genes in S strains. The number of genes in each cluster in a strain is indicated in brackets.

Identifying candidate genes mediating the allele-specific effects of TAO3 during sporulation using the temporal gene expression data. (A) Regulatory network of candidate genes predicted to mediate the effects of TAO3(4477C) in sporulation. The candidate mediating genes are shown as bigger nodes (large circles), with their target genes (small circles) connected to them as straight lines. The box contains the protein network interactions of the candidate genes with the core sporulation gene UME6, obtained from YEASTRACT (Materials and Methods). Colors inside the nodes were calculated as an average of the first six time points in sporulation (early phase). For a complete list of interacting genes and their expression values, see Table S5 and Table S11, respectively. (B) Genetic model for functional validation of allele-specific interactors mediating sporulation efficiency variation. The wild type effect comparison of the two alleles A1 and A2 of the YFG1 gene is shown inside the box. A1 is associated with high sporulation efficiency (wild type genotype and phenotype shown), and A2 is associated with low sporulation efficiency (wild type genotype and phenotype shown). Genetic interaction of these YFG1 alleles with candidate mediating genes (YFG2) is represented: (i) representation of nonmediating gene associated with genotype only, or is a consequence of the phenotype, since yfg2∆ in the presence of A1 does not affect the wild type phenotype of A1; (ii) representation of nonmediating gene associated with the phenotype independent of the allele, since yfg2∆ in the presence of both A1 and A2 lowers (low) the phenotype; (iii) representation of causal mediating gene since yfg2∆ only in presence of allele A1 lowers the phenotype, and in the presence of allele A2 does not change the wild type phenotype of A2. (C) Bar plots represent the mean sporulation efficiency after 48 hr of the T and S wild type (wt), and the ert1∆, pip2∆, and gat3∆ strains. Pair and interaction tests (Materials and Methods) were performed to test significance. For the T strain, gat1∆ was nonsignificant, but ert1∆ (P = 2.1 × 10⁻¹²), pip2∆ (P = 6.1 × 10⁻¹³), and gat3∆ (P = 9.6 × 10⁻¹⁰) significantly reduced the mean sporulation efficiency. Significant interaction terms were obtained between the genetic backgrounds (S and T) and ert1∆ (P = 2.3 × 10⁻⁴) and pip2∆ (P = 0.04).