Table 1.

Genes and Funtional Polymorphisms Involved in Natural Variation for Different Traits and Species

				Functional Nucleotide Polymorphism		Allelic Dysfunction
Plant Species	Locus/Gene	Phenotypic Effects	Molecular Function	Gene Position	Mutation		References
A. thaliana	DOG1	Seed dormancy, sugar sensing	Unknown	Promoter	Unknown	ME	Bentsink et al. (2006)
Thale cress	FRI	Flowering	Unknown	Promoter, coding	Ins, Del, nonsense Subs	TP, ME	Johanson et al. (2000); Shindo et al. (2005)
	FRL1	Flowering	FRI-like	Coding	Nonsense Subs	TP	Schläppi (2006)
	FRL2	Flowering	FRI-like	Coding	Missense Subs	AP	Schläppi (2006)
	FLC	Flowering	MADS TF	Intron, coding	TE insertion, nonsense Subs	ME, TP	Michaels et al. (2003); Werner et al. (2005a)
	FLW1/FLM	Flowering	MADS TF	Promoter + coding	Gene Del	Null expression	Werner et al. (2005b)
	ART1/HUA2	Flowering, shoot morphology	RNA processing factor	Coding	Nonsense and missense Subs	TP, AP	Doyle et al. (2005); Wang et al. (2007)
	EDI/CRY2	Flowering, seedling growth, fruit size	Photoreceptor	Coding	Missense Subs	AP	El-Assal et al. (2001, 2004)
	PHYD	Flowering, seedling growth	Photoreceptor	Coding	Del	TP	Aukerman et al. (1997)
	PHYC	Flowering, seedling growth	Photoreceptor	Coding	Nonsense Subs	TP	Balasubramanian et al. (2006)
	PHYA	Seedling growth	Photoreceptor	Coding	Missense Subs	AP	Maloof et al. (2001)
	PHYB	Seedling growth	Photoreceptor	Coding	Missense Subs	AP	Filiault et al. (2008)
	TZP/Light5	Seedling growth	Zn knuckle protein	Coding	Ins	TP	Loudet et al. (2008)
	CAL	Flower morphology	MADS TF	Coding	Missense Subs	AP	Kempin et al. (1995)
	IIL1	Leaf morphology	Leu biosynthesis enzyme	Intron	Ins, Del	ME	Sureshkumar et al. (2009)
	GL1	Trichome formation	Myb TF	Coding	Del	ME	Hauser et al. (2001)
	PUB8	Self-incompatibility	U box protein	Promoter	Unknown	ME	Liu et al. (2007)
	MUM2	Seed mucilage	Galactosidase	Coding	Del	ME	Macquet et al. (2007)
	BRX	Root growth	Novel TF	Coding	Nonsense Subs	TP	Mouchel et al. (2004)
	LPR1	Root growth response to P	Multicopper oxidase	Promoter	Del	ME	Svistoonoff et al. (2007)
	INV	Sugar composition, root growth	Invertase	Unknown	Unknown	Unknown	Sergeeva et al. (2006)
	Small effect QTL	Biomass accumulation	Protein kinase	Unknown	Unknown	Unknown	Kroyman and Mitchell-Olds (2005)
	DM1	Hybrid incompatibility, disease resistance	NB-LRR proteins	Promoter + coding	Nonsense Subs, Del	AP	Bomblies et al. (2007)
	QTL3	Hybrid incompatibility, disease resistance	NB-LRR proteins	Unknown	Unknown	Unknown	Alcázar et al. (2009)
	LD1. 1	Genetic incompatiblity, embryogenesis	His biosynthesis enzyme	Promoter, coding	Nonsense Subs	ME, TP	Bikard et al. (2009)
	LD1.5	Genetic incompatiblity, embryogenesis	His biosynthesis enzyme	Promoter + coding	Gene Del	Null expression	Bikard et al. (2009)
	APR2	Sulfate accumulation	Sulfate reductase	Coding	Nonsense Subs	AP	Loudet et al. (2007)
	MOT1	Mo accumulation	Sulfate transporter	Promoter	Del	ME	Baxter et al. (2008)
	HMA5	Cu toxicity	Cu ATPase transporter	Coding	Missense Subs	AP	Kobayashi et al. (2008)
	HKT1	Na accumulation	Na+ transporter	Promoter	Del	ME	Rus et al. (2006)
A. lyrata	FRI	Flowering	FRI-like	Coding	Indel	AP	Kuittinen et al. (2008)
B. rapa	BrFLC1	Flowering	MADS TF	Unknown	Unknown	Unknown	Kole et al. (2001)
Turnip	BrFLC2	Flowering	MADS TF	Unknown	Unknown	Unknown	Schranz et al. (2002)
S. lycopersicum	SUN	Fruit shape	IQ67 domain protein	Coding + promotor	Gene duplication	ME	Xiao et al. (2008)
Tomato	OVATE	Fruit shape	Nuclear protein	Coding	Nonsense Subs	TP	Cong et al. (2002)
	FAS	Fruit shape	Yabby TF	Intron	Ins	ME	Cong et al. (2008)
	Fw2.2	Fruit size	Cell cycle control	Promoter	Subs, indel	ME	Frary et al. (2000)
	Sw4. 1	Seed size	Transporter	Unknown	Unknown	Unknown	Orsi and Tanksley (2009)
	Brix9-2-5/LIN5	Fruit sugar content	Invertase	Coding	Missense Subs	AP	Fridman et al. (2004)
	Cnr	Fruit ripening	SBP TF	Promoter	DNA methylation	ME	Manning et al. (2006)
Pisum sativum	LF/PsTFL1c	Flowering	TFL1-like protein	Promoter, coding	Gene Del	Null expression	Foucher et al. (2003)
Pea	R	Seed composition and morphology	Starch branching enzyme	Coding	TE insertion	TP, ME	Bhattacharyya et al. (1990)
Lynaria vulgaris	Lcyc	Flower simetry	TCP TF	Promoter + coding	DNA methylation	ME	Cubas et al. (1999)
Toadflax
T. aestivum	VRN1	Flowering	AP1-like MADS TF	Promoter, intron	Del, Ins	ME	Yan et al. (2003)
Bread wheat	VRN3	Flowering	FT-like protein	Promoter	TE insertion	ME	Yan et al. (2006)
	Q	Seed free-thressing	AP2-like TF	Coding	Missense Subs	AP	Simons et al. (2006)
	RhtB1, RhtD1	Plant and leaf size	GAI-like protein	Coding	Nonsense Subs	TP	Peng et al. (1999)
	Gpc-B1/NAM-B1	Senescence; Zn, Fe, and protein content	NAC TF	Coding	Del, gen Del	TP	Uauy et al. (2006)
Triticum monococum	VRN1	Flowering	AP1-like MADS TF	Promoter	Del	ME	Yan et al. (2003)
Einkorn wheat	VRN2	Flowering	CCT domain protein	Promoter, coding	Missense Subs	AP	Yan et al. (2004a)
H. vulgare	VRN2	Flowering	CCT domain protein	Promoter + coding	Gene Del	Null expression	Yan et al. (2004a)
Barley	VRN3	Flowering	FT-like protein	Intron	Subs	ME	Yan et al. (2006)
	Ppd1	Flowering	Response regulator	Coding	Missense Subs	AP	Turner et al. (2005)
	Nud	Seed free-threshing	ERF TF	Promoter + coding	Gene Del	Null expression	Taketa et al. (2008)
	Vrs1	Seed number, ear morphology	HD TF	Coding	Ins	TP	Komatsuda et al. (2007)
	Bot1	Boron toxicity tolerance	Boron efflux transporter	Promoter + coding	Gene duplication	ME	Sutton et al. (2007)
O. sativa	qLTG3	Germination	Unknown	Coding	Del	ME	Fujino et al. (2008)
Rice	Rc	Germination, seed color	bHLH TF	Coding	Del	TP	Sweeney et al. (2006)
	Hd1	Flowering	CO-like TF	Coding	Del, TE insertion	TP, ME	Yano et al. (2000); Doi et al. (2004)
	Hd3a	Flowering	FT-like protein	Unknown	Unknown	ME	Kojima et al. (2002)
	Hd6	Flowering	Protein kinase CK2	Coding	Nonsense Subs	TP	Takahashi et al. (2001)
	Ehd1	Flowering	Response regulator	Coding	Missense Subs	AP	Doi et al. (2004)
	Ghd7	Flowering, plant height, seed yield	CCT domain protein	Coding	Gene Del, nonsense Subs	Null expression	Xue et al. (2008)
	sh4	Shattering	Myb TF	Coding	Missense Subs	AP	Li et al. (2006)
	qSH1	Shattering	HD TF	Promoter	Missense Subs	ME	Konishi et al. (2006)
	qSW5	Seed size	Unknown	Coding, promoter	Del	ME	Shomura et al. (2008)
	GW2	Seed size	RING protein	Coding	Del	TP	Song et al. (2007)
	GS3	Seed size	Unknown	Coding	Missense Subs	TP	Fan et al. (2006)
	Gn1a	Seed number	CK oxidase/dehydrogenase	Promoter	Del	ME	Ashikari et al. (2005)
	Wx	Seed starch composition	Starch biosynthesis enzyme	Intron	Splice site Subs	TP	Isshiki et al. (1998)
	SKC1	Salt tolerance	HKT transporter	Coding	Missense Subs	AP	Ren et al. (2005)
Z. mays	Vgt1	Flowering	AP2-like TF	Promoter enhancer	TE insertion, indel	ME	Salvi et al. (2007)
Maize	tb 1	Inflorescence architecture	TCP TF	Promoter enhancer	Unknown	ME	Doebley et al. (1997)
	tga1	Seed morphology	SBP TF	Coding	Missense Subs	AP	Wang et al. (2005)
	Wx	Starch composition	Starch biosynthesis enzyme	Promoter, intron, coding	TE insertion	ME	Varagona et al. (1992)

TF: Transcription factor; TE: Transposable element; Subs: substitution; Ins: insertion; Del: deletion; TP: truncated protein; AP: altered protein; ME: Misexpression