Figure 1.
Histograms of sporulation efficiencies for progeny.
In each graph, the offspring are shown in blue, with 24 replicates each of the oak parent in green, the vineyard parent in purple, and the hybrid in yellow for comparison. Number of isolates is on the y-axis, while sporulation efficiency is along the x-axis in bins of 5 percent, where 5 indicates the bin containing all isolates with sporulation efficiencies from 0%–5%, 10 contains 5%–10%, etc. A) Offspring from cross 1. Average sporulation efficiency for UCD51 is 25.8%, for YPS606 it is 98.1% and for the hybrid it is 90.6%. B) Offspring from cross 2. Average sporulation efficiency for M5 is 35.2%, for YPS606 it is 99.3% and for the hybrid it is 82.6%.
Figure 2.
LOD traces from cross 1 (YPS606×UCD51) are shown in blue; cross 2 (YPS606×M5) is overlaid in red. The thresholds for significance were set using 1000 permutations of each dataset; the threshold for cross 1 was 3.2 LOD while cross 2 was 3.3 LOD.
Table 1.
Markers nearest QTL peak apex.
Table 2.
Cross 1 linear model coefficients using nearest marker to QTL apex.
Table 3.
Cross 2 linear model coefficients using nearest marker to QTL apex.
Figure 3.
Reciprocal hemizygosity analysis.
Bar color and allele label correspond to the allele present in the hemizygous strain; green – vineyard allele knockout, oak allele remaining, purple – oak allele knockout, vineyard allele remaining. Error bars show standard deviation among at least 4 independent knockouts (t-test, *** indicates P<0.001, * indicates P<0.01).
Figure 4.
Single allele replacement analysis.
All replacements were performed in the BC248 oak background. WT indicates unaltered oak strain. Error bars indicate standard deviation among at least 4 replicates (t-test, *** indicates P<0.001). A) RIM101 replacements. V RIM101 indicates the full (coding and noncoding) RIM101 gene was replaced with the M5 vineyard version; all other bars are single allele replacements as indicated. B) RIM15 single allele replacement.
Table 4.
Causal SNP frequency in oak and vineyard isolates.
Table 5.
RIM101 allele replacement panel linear model.
Table 6.
RIM15 allele replacement panel linear model.
Figure 5.
Schematic of sporulation pathway.
The regulation of IME1 involves inputs such as ploidy (blue), pH (orange), and nutrient availability (green). The induction of IME1 modifies the activity of many genes, including those involved in meiosis (brown) and spore formation (purple). Genes identified as QTL are highlighted with red text. Only a subset of sporulation-involved genes are shown. For more detail, please see [14], [15], [17], [38]–[40].