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Gene	Trait	Mutation	Taxon B	Taxonomic Status	Evidence	Main Reference	Gephe ID	UniProtKB	Trait Category	Mutation Details	Taxon A	Taxon B	Edit Gene-GePhe	Taxon B	Status
Cf-2.1 and Cf-2.2	Pathogen resistance (leaf mold fungus ; root parasitic nematode)	Gene Loss, Deletion N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Dixon MS; Jones DA; Keddie JS ; et al. (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat[...] 2 Additional References Dixon MS; Hatzixanthis K; Jones DA (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucin[...] Lozano-Torres JL; Wilbers RH; Gawronski P (2012) Dual disease resistance mediated by the immune receptor Cf-2 in tomato requires a common virulence t[...]	GP00000180	Q41398	Physiology	loss of the two genes Cf-2.1 and Cf-2.2 (see Dixon et al. 1998) in cultivated tomato - resistance re-acquired from related species N	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	Cf-2.1 and Cf-2.2	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
Cf-4/9	Pathogen resistance	Gene Loss, Complex Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Parniske M; Hammond-Kosack KE; Golstein C ; et al. (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes[...]	GP00000181	Cf-4A Q7DLS4	Physiology	partial loss of two gene coding regions located in tandem; resulting in a chimeric gene	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	Cf-4/9	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
CLV3	Fruit size	Cis-regulatory, Inversion	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Xu C; Liberatore KL; MacAlister CA ; et al. (2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato.	GP00001565	CLV3 Q9XF04	Morphology	A 294 kb inversion with a breakpoint 1 kb upstream of CLV3	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	CLV3	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
phytochrome A-associated F-box protein	Circadian rhythm (phase)	Coding, Deletion	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Müller NA; Wijnen CL; Srinivasan A ; et al. (2016) Domestication selected for deceleration of the circadian clock in cultivated tomato.	GP00001287	101247753 K4CV85	Physiology	3bp deletion in CDS causing a 'K (lysine) loss in the highly conserved C terminus of EID1	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	phytochrome A-associated F-box protein	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
SELF PRUNING 5G (SP5G)	Flowering time	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Soyk S; Müller NA; Park SJ ; et al. (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato.	GP00001564	SP5G Q84XK9	Physiology	several candidate SNPs and structural variants	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	SELF PRUNING 5G (SP5G)	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
SUN	Fruit shape	Gene Amplification, Complex Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Xiao H; Jiang N; Schaffner E ; et al. (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit.	GP00001084	100147716 B1N669	Morphology	Gene duplication	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	SUN	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator

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