Table 1.

Parallel or convergent orthologies (adapted from Lenser and Theissen, 2013 [18]).

trait type	phenotypic trait	crop species	orthologue phylogeny	phylogeny of domestication trait	orthologous gene(s)	gene product	potentially parallel?	references
domestication	determinate growth	tomato, soya bean, common bean	family/above family	outside the cereals	SP, Dt1, PvTFL1y	signalling protein	parallel	[1,20–23]
domestication	dwarfism	rice, barley	family	cereal-wide	OsGA20ox-2, HvGA20ox-2	metabolic enzyme	parallel	[24–26]
domestication	dwarfism	sorghum, pearl millet	family	cereal-wide	dw3, d2	transporter protein	parallel	[27,28]
domestication	dwarfism	wheat	species	species-specific, cereals	Rht-1	SH2-TF	unknown	[1]
domestication	fragrance	rice, soya bean	species/family	cereals and beyond	BADH2, GmBADH2	metabolic enzyme	parallel	[29,30]
domestication	glutinous seeds	rice, wheat, maize, foxtail millet, barley, amaranth, sorghum, broom, maize millet	species/family/above family	cereals and beyond	GBSSI, waxy	metabolic enzyme	parallel	[31–36]
domestication	grain quality	maize	species	species-specific, cereals	Opaque2	bZIP-TF	unknown	[37]
domestication	shatter resistance	sorghum, rice, maize	family	cereal-wide	Sh1, OsSh1, ZmSh1	YABBY-like TF	parallel	[38]
both	coloration	pea, potato	above family	outside the cereals	flavonoid 3′,5′-hydroxylase	metabolic enzyme	parallel	[37]
both	coloration	rice, potato	species/above family	cereals and beyond	Rd/DFR, DFR	metabolic enzyme	parallel	[39,40]
both	coloration	blood orange	species	species-specific, outside cereals	Ruby	MYB-TF	unknown	[41]
both	coloration	rice	species	species-specific, cereals	Bh4	transporter protein	unknown	[42]
both	coloration	soya bean	species	species-specific, outside cereals	R	MYB-TF	unknown	[43]
both	coloration	rice	species	species-specific, cereals	Rc	bHLH-TF	unknown	[37]
both	coloration	grapevine	species	species-specific, outside cereals	VvMYBA1-3	MYB-TF	unknown	[37]
both	flowering time	barley, pea, strawberry	above family	cereals and beyond	HvCEN, PsTFL1c, FvTFL1	signalling protein	parallel	[44–46]
both	flowering time	rice, barley, pea, lentil	family/above family	cereals and beyond	Hd17, EAM8, Mat-a, HR, LcELF3	Circadian clock	parallel	[47–50]
both	flowering time	rice, wheat, sunflower, barley	family/above family	cereals and beyond	Hd3a (Heading date 3a), VRN3/TaFT, HaFT1, HvFT	signalling protein	parallel	[51–53]
both	flowering time	sorghum, rice	family	cereal-wide	Ghd7, SbGhd7	CCT domain protein	parallel	[54,55]
both	flowering time	turnip, Brassica oleracea	family	outside the cereals	BrFLC2, BoFLC2	MADS domain TF	parallel	[56–58]
both	flowering time	barley, wheat, rye cereals	species/family	cereal-wide	VRN1, BM5, TmAP1, WAP1, LpVRN1	MADS domain TF	parallel	[59]
both	flowering time	rice, barley, wheat, sorghum, sugar beet	species/family/above family	cereals and beyond	OsPRR37, Ppd-H1, Ppd1, SbPRR37, BvBTC1	circadian clock	parallel	[60–65]
both	flowering time	rice	species	species-specific, cereals	Hd1	zinc finger TF	unknown	[37]
both	flowering time	barley, wheat, maize	species/family	cereal-wide	VRN2, ZCCT1, ZmCCT9	CCT domain protein	parallel	[66]
both	plant architecture	maize, pearl millet, barley	family	cereal-wide	tb1, Pgtb1, INT-C	TCP-TF	parallel	[67–69]
both	plant architecture	barley	species	species-specific, cereals	VRS1	homeodomain-TF	unknown	[37]
adaptation	cold tolerance	barley, wheat	family	cereal-wide	HVA1, Wrab18, Wrab19	LEA protein	parallel	[70,71]
adaptation	cold tolerance	wheat, barley	family	cereal-wide	Wcs19, Wcor14, Wcor15, Bcor14b	Cor protein	parallel	[72]
adaptation	drought tolerance	maize, Arabidopsis	above family	cereals and beyond	ZmVPP1, AVP1	H(+) pyrophosphatase	parallel	[73]
adaptation	drought tolerance	rice	species	species-specific, cereals	OsAHL1	AT-hook PPC domain	unknown	[74]
adaptation	metal tolerance	wheat, rye	family	cereal-wide	TaALMT1, ScALMT1	transporter protein	parallel	[37]
adaptation	metal tolerance	sorghum, maize	family	cereal-wide	SbMATE1, ZmMATE1	transporter protein	parallel	[37]
adaptation	pathogen resistance	wheat, rice, sorghum	family	cereal-wide	LR34	ABC transporter	parallel	[75]
adaptation	pathogen resistance	maize	species	species-specific, cereals	Rp3	NBS-LRR	unknown	[76]
adaptation	soil salinity	barley, maize, spinach	above family	cereals and beyond	HvPIP2;1, ZmPIP2-4, PM28A	Aquaporin	parallel	[77–79]
adaptation	soil salinity	rice, foxtail millet, tomato	above family	cereals and beyond	OsASR1, OsASR3, SiASR1, SlASR1	ABA stress ASR protein	parallel	[80,81]