TABLE 4.

List of genes domesticated in the past and associated metabolic pathways.

Crops	Traits	Domesticated Genes	Involvement in the metabolic pathways	References
Rice	Plant architecture	sd1	Encodes gibberellin 20-oxidase (Gibberellin pathway gene)	Spielmeyer et al., 2002
	Seed shattering	sh4	Abscisic acid response elements (ABREs) have been identified which is involved in ABA hormone signal pathways	Yan et al., 2015
		qSH1	APETALA2-like transcription factor SUPERNUMERARY BRACT (SNP) positively regulates the expression of two rice genes, qSH1 and SH5 (SNB-involved regulating pathway)	Jiang et al., 2019
	Awn	LABA1 / An-2	An-2 encodes a cytokinin synthesis enzyme that modulates awn length	Gu et al., 2015; Hua et al., 2015
		qAWNL2	N.A	Amarasinghe et al., 2020
	Seed and hull color	Rc and Rd	Involved in proanthocyanidin synthesis via the flavonoid pathway	Sweeney et al., 2006; Furukawa et al., 2007
	Seed dormancy	Sdr4	Zinc finger protein, OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway	Sugimoto et al., 2010; Chen et al., 2020
	Grain size	qSW5/GW5	GW5/ qSW5 involved in brassinosteroid signaling pathway to regulate grain width and weight (Novel nuclear protein)	Shomura et al., 2008; Weng et al., 2008; Liu et al., 2017
		Gn1a	Encodes cytokinin oxidase	Ashikari et al., 2005
Maize	Plant architecture	tb1 (teosinte branched1)	Two maize mutants, teosinte branched1 (tb1) and grassy tillers1 (gt1), have been shown affected in the regulation of auxin biosynthesis pathway	Doebley et al., 1997; Whipple et al., 2011
		br2	Gene modulates the transport of auxin	Zhang et al., 2019b
	Inflorescence architecture	ra1 (ramosa1), Tga1	RA1 involved in the ramosa pathway (Transcription factor)	Sigmon and Vollbrecht, 2010
	Grain filling	ZmSWEET4c	Hexose transporter, SWEET4c is important for the Glc to the starch biosynthesis in the endosperm during embryogenesis	Sosso et al., 2015
Wheat	Vernalization	Vrn2 (ZCCT1 and ZCCT1)	Likely to coordinate with GA, ABA, cytokinin, and JA signaling pathway	Yan et al., 2004; Deng et al., 2015
		Vrn1	Central gene in vernalization pathway similar to APETALA of Arabidopsis. Linked with GA, ABA, Cytokinin, and JA signaling pathway	Yan et al., 2003; Deng et al., 2015
	Free threshing	Q and homeologs	Involved in secondary cell wall synthesis pathways and regulation of chemical composition of glumes	Zhang Z. et al., 2020
	Plant architecture	Rht-1	Repressor of gibberellic acid pathway	Thomas, 2017
Sorghum	Plant architecture	dw3	Gene modulates the transport of auxin	Multani et al., 2003
	Grain pigmentation	Tannin1 (Tan 1)	Tan1 gene, encoding a WD40 protein, that regulate the tannin biosynthesis	Wu et al., 2012
Barley	Inflorescence architecture	Vrs2	Vrs2 expression influences the expression of genes that regulate biosynthesis and metabolism of auxin and cytokinin (Transcription factor, HD-ZIP)	Komatsuda et al., 2007; Youssef et al., 2017
	Naked (free-threshing) grains	Nud	ERF family transcription factor gene regulating a lipid biosynthesis pathway (Transcription factor)	Taketa et al., 2008
Soybean	Determinate growth habit	Dt2	Plant height of semi-determinate plants is associated with GA signaling	Zhang et al., 2019a
Tomato	Fruit size	fw2.2	Similar to human RAS, SlKLUH is the causal gene for the fw3.2 QTL and encodes a CYP450 of the 78A class	Frary et al., 2000
		SUN	Regulating auxin biosynthetic and responsive pathway	Xiao et al., 2008; Wang et al., 2019
Mustard	Flowering Time	BrFLC1	Interacts with the vernalization pathway (MADS-box transcription factor) and coordinate with gibberellic acid pathway	Yuan et al., 2009