Leveraging the Round Robin design to identify causative variants.
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(A) A QTL on chromsome 15 affects salt and caffeine resistance in crosses 7 and 8 (with smaller effects in other crosses). The CLIB219 is shared between the two crosses and in both cases it contributes the allele is selected against, suggesting that the causative variant is private to CLIB219. (B) We determined the association of coding variants within this QTL interval with the observed pattern of LOD scores. The highest association scores were exhibited by four variants private to CLIB219; one a frame-shift mutation in WHI2. (C) Allele replacements of WHI2 in the CLIB219 strain background. The CLIB219-specific frame shift mutation resulted in decreased growth in the presence of both high salt and caffeine. (D) Identification of a quantitative trait nucleotide (QTN) within the caffeine resistance QTL on chromosome 10. The QTL was identified in eight crosses and is multi-allelic as specific alleles were beneficial or deleterious depending on a particular cross. (E) Measuring the association of variants and LOD scores confirmed that no single variant could explain the observed pattern of QTL and indicated a TOR1 SNP (3875 G -> A) as a QTN (red circle). (F) Introduction of the TOR13875A variant into two strain backgrounds, YJM269 and 273614x, reduced resistance to caffeine. For each allele replacements two independent transformants are shown.