Table 4.

Major important genes tagged and mapped with molecular markers in rice for abiotic stress, quality, physiology and hybrid traits in recent years

Trait	Gene	RAP-DB	Encoded product	Gene function	Reference
Abiotic resistance	OsTPP1	Os02g0661100	Trehalose-6-phosphate phosphatase	Tolerance to salt and cold	Ge et al. (2008)
	OCPI1	Os01g0615100	Chymotrypsin inhibitor	Tolerance to drought	Huang et al. (2007)
	LTN1	Os05g0557700	Ubiquitin–conjugating domain protein	Signal of Pi starvation	Hu et al. (2011)
	OsLEA3-1	Os05g0542500	Late embryogenesis abundant protein	Tolerance to drought	Xiao et al. (2007)
	OsPht1	Os10g0444700	Phosphate transporter	Absorption and transport of Pi	Jia et al. (2011)
	OsSKIPa	Os02g0759800	Unknown	Tolerance to drought	Hou et al. (2009)
	LOX3	Os03g0700400	Lipoxygenase	Tolerance to various stress	Liu et al. (2008a)
	OsCOIN	Os01g0104100	Zinc finger protein	Tolerance to salt, cold and drought	Liu et al. (2007b)
	OsHAL3	Os06g0199500	Halotolerance protein	Tolerance to salt	Sun et al. (2009)
	SKC1	Os01g0307500	Na+-selective transporter	Tolerance to salt	Ren et al. (2005)
	SNAC2	Os01g0884300	Nuclear protein	Tolerance to salt and cold	Hu et al. (2008)
Quality	OsVPE1	Os04g0537900	Vacuolar processing enzyme	Maturity of gluten	Wang et al. (2009b)
	RSR1	Os05g0121600	Unknown	Regulating starch synthesis of seeds	Fu and Xue (2010)
	OsRab5a	Os12g0631100	Small GTPase	Transporting storage protein	Wang et al. (2010b)
	ALK	Os06g0229800	Soluble starch synthases	Regulating gel temperature	Gao et al. (2003)
	qGC-6(wx)	Os06g0133000	Granule-bound starch synthase	Regulating amylase content	Su et al. (2011)
	OsBADH2/fgr	Os08g0424500	Betaine aldehyde dehydrogenase	Fragrance	Chen et al. (2008)
Physiology	Phr1	Os04g0624500	Polyphenol oxidase	Browning seeds	Yu et al. (2008)
	OsMST6	Os07g0559700	Monosaccharide transporter	Regulating grain filling	Wang et al. (2008)
	SLL1	Os09g0395300	KANADI Transcription Factor	Regulating leaf morphology	Zhang et al. (2009)
	LC2	Os02g0152500	Unknown	Regulating leaf angle and flowering	Wang et al. (2013)
	Roc5	Os02g0674800	Leu-chain-like protein	Regulating leaf morphology	Zou et al. (2011)
	NLS1	Os11g0249000	Typical CC-NB-LRR domain protein	Resistance to pathogens	Tang et al. (2011)
	SL1	Os01g0129200	Z-finger domain protein	Regulating rice floral development	Xiao et al. (2009)
	NRL1/OsCSLD4	Os12g0555600	Cellulose synthase	Cell-wall synthesis and plant growth	Yoshikawa et al. (2013)
Physiology	OsRAA1	Os01g0257300	12 kDa small G protein	Regulating root growth	Han et al. (2008)
	WOX11	Os07g0684900	Unknown	Regulating root growth	Zhao et al. (2009)
	OsC6	Os11g0582500	Lipid transfer protein	Involving in anthers development	Zhang et al. (2010b)
	OsPSS1	Os04g0573000	Pi-transport protein	Involving in Pi balance of leaves	Wang et al. (2012a)
	PTC1	Os09g0449000	PHD-Finger Protein	Involving in anthers development	Li et al. (2011a, b)
	OsJAG	Os01g0129200	C2H2 Z-finger domain protein	Involving in floral development	Duan et al. (2010)
	CYP704B2	Os03g0168600	Cytochrome P450	Regulating anther and pollen formation	Li et al. (2010b)
	OsMST4	Os03g0218400	Monosaccharide transporter	Regulating sugar distribution	Wang et al. (2007)
	OsYABBY4	Os02g0643200	YABBY-domain protein	Expressing in vascular tissues	Liu et al. (2007a)
	SDG714	Os01g0927000	Histone H3K9 methyl-transferase	Regulating leaf morphology	Ding et al. (2007a)
	OsAGO7	Os03g0449200	Argonaute (AGO) protein	Regulating leaf morphology	Shi et al. (2007)
	RID1	Os10g0419200	Cys2/His2 type z-finger transcription factor	Regulating reproductive growth	Wu et al. (2008a)
	S5	Os06g0213100	Aspartic protease	Regulating reproductive isolation	Ji et al. (2012)
	Sa	Os01g0578700	Small ubiquitin-like modifier E3 ligase-like protein/F-box protein	Regulating male sterility	Long et al. (2008)
	EUI1	Os05g0482400	Cytochrome P450 monooxygenase CYP714D1	Hybrid rice pollination	Zhang et al. (2008)
	OsUgp1	Os09g0553200	UDP-glucose pyrophosphorylase	Male fertility	Chen et al. (2007)
	CSA	Os01g0274800	R2R3-type MYB transcription factor	Mutation causing sensitive male sterility	Zhang et al. (2013a)
	orfH79	Mitochondria	Cytotoxic peptide	Regulating in HL-CMS	Peng et al. (2010)
	COX11	Os03g0718600	Nuclear-encoded mitochondrial protein	Interacting with WA352	Luo et al. (2013)
	WA352	Mitochondria	Unknown	Regulating in WA-CMS
	Rf5/Rf1	Os10g0497300	PPR protein	Restoring fertility of BT-CMS	Hu et al. (2012)