Fig 4. The HS and MS classes are each specified by two predominant multi-locus genotypes.

(A) We previously showed that two distinct multi-locus genotypes underlie trait expression at 30°C [10,11], and in this paper we determined that these same genotypes underlie the MS class. In addition to ira2Δ2933, these genotypes both involve FLO8^3S and MSS11^BY. However, individuals carrying END3^BY also require TRR1^3S (‘END3^BY-dependent genotype’), while individuals carrying END3^3S instead require MGA1^BY and SFL1^BY (‘END3^3S-dependent genotype’). We refer to the fact that both of these multi-locus genotypes specify the same trait as ‘genotypic heterogeneity’. When such genotypic heterogeneity is present, alleles involved in only one of the multi-locus genotypes can be masked. For example, in the bulk segregant mapping data for the MS class, only the alleles involved in the genotype that involves END3^BY were detected. (B) In the current data, we found evidence for genotypic heterogeneity in the HS class. By partitioning individuals in the HS class from the 3S backcross population and calculating their allele frequencies across the genome, we determined that two predominant multi-locus genotypes underlie this temperature sensitivity class. These genotypes are FLO8^3S ira2Δ2933 MSS11^BY (‘MSS11^BY-dependent genotype’) and XII^3S END3^BY FLO8^3S ira2Δ2933 MGA1^BY MSS11^3S SFL1^BY (‘MSS11^3S-dependent genotype’). As described in the main text, XII^3S refers to a locus that was detected specifically among HS individuals carrying MSS11^3S. The same coloring scheme is used in this figure as in Fig 2.