Table 2.

Hotspot description

Hotspot	Localization a	Number of eQTL b	Functional enrichment	Phenotypic QTL	Knowon or candidate gene regulator	Functional validation	Comments
1	chr2:207	66	No functional enrichment	Pyruvate	SCT1	Not realized	Hidden by the disomy, Sct1p is involved in lipid desaturation and diverges in the two strains by the size of a glutamic acid repeated sequence
2	chr2:277	47	No functional enrichment	-	Unknow	-	Hidden by the disomy
3	chr2:560	7	Daughter cell separation	Clumpness, OD, cell pop.	AMN1	Yvert et al. 2003 [34]	Impacting on cellular population estimation
4	chr3:198	20	Mating, pheromone	-	MAT	Brem et al. 2005 [35]
5	chr4:309	9	Thiamine synthesis	-	THI3	Not realized	THI3 bears two non-synonymous SNPs and a frame-shift in its coding sequence
6	chr8:20	27	Helicase	-	-	-	Disomy consequence
7	chr10:590	18	Mitochondrial protein	-	GRR1	Not realized	GRR1 has a strong cis-eQTL (LOD = 13.4) and several alteration of its coding sequence
8	chr12:667	33	Fatty acid metabolism, detoxification	-	HAP1/PDR8	Yvert et al. 2003 [34]	Genes involved in the response to oxygen (nine targets of HAP1, Additional file 5)
9	chr14:456	101	Mitochondrial protein	Succinate, Glycerol	MKT1	Smith and Kruglyak 2008 [25]	Perturbation of the mitochondrial function affect the production of metabolites
10	chr16 left-arm	50	No functional enrichment	R70	-	-	Disomy consequence
11	chr16:370	17	chr8 translocated gene	-	SSU1 translocation	Not realized	Translocation consequence

^aLocalization of the center of hotspot given in chromosome:kilo base pair.

^bNumber of total eQTL from the union of the 3 datasets.