QTL analysis using SNP allele frequencies calculated from genome sequences of individual segregants.

(A) Cross 1 (Pp2_BGL5 × CBS_BGL9). Left axis: Black dots show the frequency of the Pp2 allele among the 30 superior segregants, and orange dots show its frequency among the 30 inferior segregants, at each of the 42,262 polymorphic sites segregating on the 4 K. phaffii chromosomes in this cross. The gray horizontal lines at allele frequency 0.5 represent unbiased segregation. Right axis: Blue bars show the statistical significance of bias in allele frequency (log10 scale; Fisher’s exact test with Bonferroni correction for multiple testing over all SNPs on a chromosome). (B) Cross 2 (Pp4_BGL3 × CBS_BGL9). Black dots show the frequency of the Pp4 allele among the 30 superior segregants, and orange dots show its frequency among the 30 inferior segregants, at each of the 41,552 polymorphic sites segregating in this cross. Other details are as in (A). Numerical data are listed in S2 Data.