Gene - List

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CGSNL
Gene
Symbol 		Gene symbol synonym(s) CGSNL Gene Name Gene name synonym(s) Chr. No. Trait Class Gene Ontology Trait Ontology Plant Ontology RAP ID MSU ID Mutant
Image
PSY1 OsPSY1
 PHYTOENE SYNTHASE 1 phytoene synthase 1
PSY1-like gene
 6 Coloration
Biochemical character
Tolerance and resistance - Stress tolerance
Coloration - Others
 GO:0004311 - farnesyltranstransferase activity
GO:0046905 - phytoene synthase activity
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0009416 - response to light stimulus
GO:0009507 - chloroplast
GO:0009536 - plastid
GO:0016117 - carotenoid biosynthetic process
GO:0016767 - geranylgeranyl-diphosphate geranylgeranyltransferase activity
 TO:0000075 - light sensitivity
 Os06g0729000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g51290.1
LOC_Os06g51290.2
LOC_Os06g51290.4
LOC_Os06g51290.3
PSY2 OsPSY2
 PHYTOENE SYNTHASE 2 phytoene synthase 2
 12 Coloration - Others
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0016117 - carotenoid biosynthetic process
GO:0004311 - farnesyltranstransferase activity
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0010287 - plastoglobule
GO:0005829 - cytosol
GO:0009408 - response to heat
GO:0046905 - phytoene synthase activity
GO:0009416 - response to light stimulus
GO:0009058 - biosynthetic process
GO:0009507 - chloroplast
 TO:0000075 - light sensitivity
TO:0000432 - temperature response trait
 Os12g0626400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g43130.1
ANS ANS
OsANS1
ANS1
LDOX
LDOX1
OsLDOX
OsLDOX1
 ANTHOCYANIDIN SYNTHASE anthocyanidin synthase
leucoanthocyanidin dioxygenase
 1 Coloration - Others
Seed - Morphological traits
Seed
Coloration - Anthocyanin
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0010023 - proanthocyanidin biosynthetic process
GO:0016702 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0016706 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
GO:0050589 - leucocyanidin oxygenase activity
GO:0048316 - seed development
GO:0009611 - response to wounding
GO:0005506 - iron ion binding
GO:0009416 - response to light stimulus
GO:0009813 - flavonoid biosynthetic process
GO:0009718 - anthocyanin biosynthetic process
GO:0009753 - response to jasmonic acid stimulus
GO:0009409 - response to cold
GO:0009735 - response to cytokinin stimulus
GO:0009408 - response to heat
GO:0007033 - vacuole organization
 TO:0000303 - cold tolerance
TO:0000653 - seed development trait
TO:0000168 - abiotic stress trait
TO:0000707 - pericarp color
TO:0000071 - anthocyanin content
TO:0000290 - flavonoid content
TO:0000075 - light sensitivity
TO:0000259 - heat tolerance
TO:0000167 - cytokinin sensitivity
 PO:0001170 - seed development stage
PO:0009066 - anther
PO:0007010 - whole plant fruit ripening stage
Os01g0372500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g27490.1
LPS1 SDH2
SDHB
sdhB
RPS14
rps14
sdh2-1
SDH2-RPS14
OsLPS1
OsSDH2-1
 LATE PREMATURE SENESCENCE 1 SUCCINATE:UBIQUINONE OXIDOREDUCTASE
mitochondrial succinate dehydrogenase subunit B
ribosomal protein S14
succinate dehydrogenase (iron-sulphur protein subunit)
chimeric SDH2-RPS14
 8 Reproductive organ - Pollination, fertilization, fertility
Coloration - Chlorophyll
Coloration - Others
Character as QTL - Yield and productivity
Biochemical character
Reproductive organ - panicle
Vegetative organ - Culm
Vegetative organ - Leaf
Tolerance and resistance - Stress tolerance
 GO:0006099 - tricarboxylic acid cycle
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0007005 - mitochondrion organization
GO:0009658 - chloroplast organization
GO:0009055 - electron carrier activity
GO:0000104 - succinate dehydrogenase activity
GO:0016491 - oxidoreductase activity
GO:0010150 - leaf senescence
GO:0005739 - mitochondrion
GO:0010229 - inflorescence development
 TO:0000293 - chlorophyll-a content
TO:0001015 - photosynthetic rate
TO:0000316 - photosynthetic ability
TO:0000040 - panicle length
TO:0000522 - stomatal conductance
TO:0000447 - filled grain number
TO:0002715 - chloroplast development trait
TO:0000639 - seed fertility
TO:0000621 - inflorescence development trait
TO:0000249 - leaf senescence
TO:0000396 - grain yield
TO:0000207 - plant height
TO:0000137 - days to heading
TO:0000605 - hydrogen peroxide content
TO:0000455 - seed set percent
TO:0006032 - panicle size
TO:0000496 - carotenoid content
TO:0000295 - chlorophyll-b content
 PO:0001083 - inflorescence development stage
PO:0000025 - root tip
PO:0025034 - leaf
PO:0001054 - 4 leaf senescence stage
PO:0009066 - anther
PO:0009072 - plant ovary
Os08g0120000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g02640.1
LOC_Os08g02640.2
LOC_Os08g02640.3
LOC_Os08g02640.4
LOC_Os08g02640.5
PPS OsWD40-55
OsCOP1
COP1
YEL
OsYEL
OsPPS
COP1-1
OsCOP1-1
OsRING347
RING347
 PETER PAN SYNDROME COP1 ortholog
CONSTITUTIVE PHOTOMORPHOGENIC 1
yellowish-pericarp embryo lethal
RING-type E3 ubiquitin ligase 347
 2 Seed - Morphological traits - Grain shape
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Embryo
Coloration - Others
Heterochrony
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
 GO:0010218 - response to far red light
GO:0046283 - anthocyanin metabolic process
GO:0005634 - nucleus
GO:0010119 - regulation of stomatal movement
GO:0008270 - zinc ion binding
GO:0016874 - ligase activity
GO:0009416 - response to light stimulus
GO:0009628 - response to abiotic stimulus
GO:0010228 - vegetative to reproductive phase transition
GO:0046685 - response to arsenic
GO:0009640 - photomorphogenesis
GO:0009641 - shade avoidance
GO:0048573 - photoperiodism, flowering
GO:0009637 - response to blue light
GO:0010224 - response to UV-B
GO:0006281 - DNA repair
GO:0009793 - embryonic development ending in seed dormancy
GO:0009266 - response to temperature stimulus
GO:0009962 - regulation of flavonoid biosynthetic process
 TO:0000229 - photoperiod sensitivity
TO:0000064 - embryo related trait
TO:0000601 - UV-B light sensitivity
TO:0000326 - leaf color
TO:0000675 - ferulic acid content
TO:0006006 - monosaccharide content
TO:0000397 - grain size
TO:0006007 - polysaccharide content
TO:0000137 - days to heading
TO:0000707 - pericarp color
TO:0000051 - stem strength
TO:0000430 - germination rate
TO:0000159 - blue light sensitivity
TO:0000168 - abiotic stress trait
TO:0000590 - grain weight
TO:0000075 - light sensitivity
TO:0000432 - temperature response trait
TO:0000396 - grain yield
TO:0002616 - flowering time
TO:0000130 - far red light sensitivity
TO:0000290 - flavonoid content
 Os02g0771100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g53140.1
BF Bf
 BROWN FURROWS OF HULL Brown furrows of hull
 Coloration - Others
 GO:0043473 - pigmentation
 TO:0000056 - stem color
TO:0000287 - brown rice shape
TO:0000264 - lemma and palea color
 PO:0009047 - stem
PO:0009088 - seed coat
PO:0009039 - glume
-
BHA Bha(Bh1)
Bha
Bh1
 BLACK HULL A Black hull-a
Black hull-1
 Coloration - Others
 GO:0043473 - pigmentation
 TO:0000190 - seed coat color
TO:0000264 - lemma and palea color
 PO:0009088 - seed coat
PO:0009039 - glume
-
BHB Bhb(Bh2)
Bhb
Bh2
 BLACK HULL B Black hull-b
Black hull-2
 Coloration - Others
 GO:0043473 - pigmentation
 TO:0000190 - seed coat color
TO:0000264 - lemma and palea color
 PO:0009088 - seed coat
PO:0009039 - glume
-
GF2 gf2
 GOLD FURROWS OF HULL 2 gold furrows of hull2
gold furrows of hull 2
gold furrows of hull-2
 1 Coloration - Others
 GO:0009812 - flavonoid metabolic process
 TO:0000264 - lemma and palea color
TO:0000484 - seed shape
 PO:0009088 - seed coat
-
RD Rd
DFR
OsDFR
OS-DFR
OsDFR1
DFR1
DFR-1
 RED PERICARP AND SEED COAT Red pericarp and seed coat
dihydroflavonol 4-reductase
dihydroflavonol-4-reductase
dihydroflavonol 4-reductase 1
 1 Seed - Morphological traits
Tolerance and resistance - Disease resistance
Coloration - Others
Seed
Coloration - Anthocyanin
Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Tolerance and resistance - Insect resistance
 GO:0050832 - defense response to fungus
GO:0003824 - catalytic activity
GO:0009416 - response to light stimulus
GO:0009813 - flavonoid biosynthetic process
GO:0010023 - proanthocyanidin biosynthetic process
GO:0051555 - flavonol biosynthetic process
GO:0043473 - pigmentation
GO:0009408 - response to heat
GO:0009718 - anthocyanin biosynthetic process
GO:0048316 - seed development
GO:0050662 - coenzyme binding
GO:0044237 - cellular metabolic process
GO:0002213 - defense response to insect
GO:0009812 - flavonoid metabolic process
GO:0005737 - cytoplasm
GO:0005634 - nucleus
 TO:0000071 - anthocyanin content
TO:0000326 - leaf color
TO:0000706 - hull color
TO:0000140 - apiculus color
TO:0000487 - endosperm color
TO:0000074 - blast disease
TO:0000185 - stigma color
TO:0000190 - seed coat color
TO:0000259 - heat tolerance
TO:0000486 - seed color
TO:0000707 - pericarp color
TO:0000653 - seed development trait
TO:0000075 - light sensitivity
TO:0000207 - plant height
TO:0000205 - white-backed planthopper resistance
 PO:0009073 - stigma
PO:0009089 - endosperm
PO:0006033 - paleal apiculus
PO:0009088 - seed coat
PO:0007010 - whole plant fruit ripening stage
PO:0001170 - seed development stage
Os01g0633500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g44260.1
GH2 gh2
CAD2
CAD
OsCAD2
OsGH2
 GOLD HULL AND INTERNODE 2 gold hull and internode2
gold hull and internode-2
Cinnamyl alcohol dehydrogenase 2
Sinapyl alcohol dehydrogenase
Protein GOLD HULL AND INTERNODE 2
Cinnamyl alcohol dehydrogenase
 2 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Shattering
Coloration - Others
Vegetative organ - Culm
Biochemical character
 GO:0009055 - electron carrier activity
GO:0009809 - lignin biosynthetic process
GO:0020037 - heme binding
GO:0022900 - electron transport chain
GO:0055114 - oxidation reduction
GO:0045551 - cinnamyl-alcohol dehydrogenase activity
GO:0009834 - secondary cell wall biogenesis
GO:0009642 - response to light intensity
GO:0009808 - lignin metabolic process
GO:0009411 - response to UV
GO:0042742 - defense response to bacterium
GO:0008270 - zinc ion binding
 TO:0000733 - lignin biosynthesis trait
TO:0000460 - light intensity sensitivity
TO:0002729 - fruit senescing quality trait
TO:0000160 - UV light sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000426 - internode color
TO:0000264 - lemma and palea color
TO:0000732 - lignin monomer content
TO:0000190_TO:0000426 - "seed coat color" or "internode color"
TO:0000473 - grain shattering
TO:0000051 - stem strength
TO:0000011 - nitrogen sensitivity
 PO:0000039 - shoot axis vascular system
PO:0009010 - seed
PO:0009049 - inflorescence
PO:0020104 - leaf sheath
PO:0020142 - stem internode
PO:0000036 - leaf vascular system
PO:0000003 - whole plant
PO:0009047 - stem
PO:0003011 - root vascular system
PO:0009005 - root
Os02g0187800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g09490.1
image Id ( 6725 )
GH3 gh3
 GOLD HULL AND INTERNODE 3 gold hull and internode3
gold hull and internode 3
gold hull and internode-3
 2 Coloration - Others
 TO:0000264 - lemma and palea color
TO:0000426 - internode color
TO:0000190_TO:0000426 - "seed coat color" or "internode color"
 PO:0009010 - seed
PO:0020142 - stem internode
- image Id ( 6728 )
Z3 OsZ3
z3
SIET4
OsSIET4
 ZEBRA 3 zebra3
zebra 3
zebra-3
silicon efflux transporter 4
Si efflux transporter 4
 3 Reproductive organ - Heading date
Seed - Morphological traits
Coloration - Chlorophyll
Vegetative organ - Leaf
Biochemical character
Coloration - Others
 GO:0005886 - plasma membrane
GO:0032523 - silicon efflux transmembrane transporter activity
GO:0055085 - transmembrane transport
GO:0016021 - integral to membrane
GO:0048573 - photoperiodism, flowering
GO:0015746 - citrate transport
GO:0015995 - chlorophyll biosynthetic process
GO:0007275 - multicellular organismal development
 TO:0000486 - seed color
TO:0000339 - stem thickness
TO:0000326 - leaf color
TO:0002616 - flowering time
TO:0000069 - variegated leaf
TO:0000495 - chlorophyll content
 PO:0009051 - spikelet
PO:0009047 - stem
PO:0009025 - vascular leaf
PO:0020122 - inflorescence axis
PO:0025034 - leaf
PO:0009053 - peduncle
PO:0006016 - leaf epidermis
PO:0009005 - root
PO:0020104 - leaf sheath
PO:0005004 - shoot node
PO:0006000 - caryopsis hull
PO:0006325 - inflorescence node
Os03g0147400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g05390.11
LOC_Os03g05390.10
LOC_Os03g05390.9
LOC_Os03g05390.5
LOC_Os03g05390.6
LOC_Os03g05390.7
LOC_Os03g05390.8
LOC_Os03g05390.12
LOC_Os03g05390.13
LOC_Os03g05390.1
LOC_Os03g05390.2
LOC_Os03g05390.3
LOC_Os03g05390.4
WH Wh
Hw
 WHITE HULL White hull
 4 Coloration - Others
 GO:0043473 - pigmentation
 TO:0000190 - seed coat color
TO:0000264 - lemma and palea color
 PO:0009037 - lemma
PO:0009088 - seed coat
PO:0009038 - palea
-
BHC Ph=Bhc(Po)
Bhc
Po
Ph
Bh3
PPO
Phr1
OsPhr1
BH1
OsPPO1
PPO1
 BLACK HULL C Phenol staining
polyphenol oxidase
PPO enzyme
BLACK HULL1
Phenol reaction 1
polyphenol oxidase 1
 4 Biochemical character
Coloration - Others
 GO:0043473 - pigmentation
GO:0016051 - carbohydrate biosynthetic process
 TO:0000190 - seed coat color
TO:0000264 - lemma and palea color
TO:0000062 - phenol reaction
TO:0000706 - hull color
 PO:0009088 - seed coat
PO:0009089 - endosperm
Os04g0624500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g53300.1
image Id ( 6755 )
GH1 gh1
hg
 GOLD HULL AND INTERNODE 1 gold hull and internode1
gold hull and internode 1
gold hull and internode-1
 5 Coloration - Others
 TO:0000264 - lemma and palea color
TO:0000190_TO:0000426 - "seed coat color" or "internode color"
TO:0000426 - internode color
 PO:0020142 - stem internode
PO:0009010 - seed
- image Id ( 6758 )
GF1 gf1
 GOLD FURROWS OF HULL 1 gold furrows of hull1
gold furrows of hull 1
gold furrows of hull-1
 6 Coloration - Others
 GO:0009812 - flavonoid metabolic process
 TO:0000484 - seed shape
TO:0000264 - lemma and palea color
TO:0000190 - seed coat color
 PO:0009037 - lemma
PO:0009038 - palea
PO:0009088 - seed coat
-
WP1 wp1
 WHITE PANICLE 1 white panicle1
white panicle 1
white panicle-1
 7 Coloration - Others
 GO:0015995 - chlorophyll biosynthetic process
 TO:0000264 - lemma and palea color
TO:0000495 - chlorophyll content
TO:0000077 - shoot anatomy and morphology trait
 PO:0009049 - inflorescence
-
RC Rc
OsRC
OsbHLH017
OsbHLH17
SD7-1
qSD7-1/qPC7
OsGL3C
GL3C
 BROWN PERICARP AND SEED COAT Brown pericarp and seed coat
basic/helix-loop-helix 17
basic helix loop helix 17
GLABRA3C
GLABRA 3C
 7 Coloration - Others
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Coloration - Anthocyanin
 GO:0006979 - response to oxidative stress
GO:0009812 - flavonoid metabolic process
GO:0010023 - proanthocyanidin biosynthetic process
GO:0046283 - anthocyanin metabolic process
 TO:0000605 - hydrogen peroxide content
TO:0000707 - pericarp color
TO:0000290 - flavonoid content
TO:0000190 - seed coat color
TO:0002657 - oxidative stress
TO:0000487 - endosperm color
 PO:0009089 - endosperm
PO:0009088 - seed coat
Os07g0211500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g11020.1
image Id ( 6780 )
IBF IBf
 INHIBITOR FOR BROWN FURROWS Inhibitor for brown furrows
 9 Coloration - Others
 TO:0000056 - stem color
TO:0000264 - lemma and palea color
 PO:0009039 - glume
PO:0009088 - seed coat
PO:0009047 - stem
- image Id ( 6788 )
ABA1 OsABA1
Zep1
OsAba1
Aba2
OsAba2
OsZep1
Zep
OsZep
Aba1
OsABA2
Osaba1
OsZEP-1
OsZEP
OSZEP1
ZEP1
ZEP
 ABA DEFICIENT 1 Zeaxanthin epoxidase 1
zeaxanthin epoxidase
abscisic acid-deficient 1
zeaxanthin cyclooxygenases
 4 Vegetative organ - Culm
Coloration - Others
Biochemical character
Vegetative organ - Leaf
Vegetative organ - Root
Coloration
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0016117 - carotenoid biosynthetic process
GO:0042742 - defense response to bacterium
GO:0016491 - oxidoreductase activity
GO:0051607 - defense response to virus
GO:0009266 - response to temperature stimulus
GO:0010378 - temperature compensation of the circadian clock
GO:0009738 - abscisic acid mediated signaling
GO:0010118 - stomatal movement
GO:0009651 - response to salt stress
GO:0016123 - xanthophyll biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0009536 - plastid
GO:0008152 - metabolic process
GO:0004497 - monooxygenase activity
GO:0022900 - electron transport chain
GO:0009688 - abscisic acid biosynthetic process
GO:0009540 - zeaxanthin epoxidase activity
GO:0007623 - circadian rhythm
GO:0006725 - cellular aromatic compound metabolic process
GO:0009414 - response to water deprivation
GO:0009408 - response to heat
 TO:0000619 - vivipary
TO:0000522 - stomatal conductance
TO:0000175 - bacterial blight disease resistance
TO:0000615 - abscisic acid sensitivity
TO:0000203 - bacterial leaf streak disease resistance
TO:0000135 - leaf length
TO:0000326 - leaf color
TO:0000020 - black streak dwarf virus resistance
TO:0000207 - plant height
TO:0000227 - root length
TO:0000131 - leaf water potential
TO:0000432 - temperature response trait
TO:0000478 - abscisic acid concentration
TO:0006001 - salt tolerance
TO:0000148 - viral disease resistance
TO:0002667 - abscisic acid content
TO:0000276 - drought tolerance
TO:0000259 - heat tolerance
 PO:0009006 - shoot system
PO:0009025 - vascular leaf
Os04g0448900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g37619.1
LOC_Os04g37619.2
PDA PDS1
PDS
OsPDS
Pds
OsPDA
 PHYTOENE DESATURASE "Phytoene dehydrogenase
chloroplastic/chromoplastic"
Phytoene desaturase
 3 Coloration - Others
Biochemical character
 GO:0009507 - chloroplast
GO:0009509 - chromoplast
GO:0009536 - plastid
GO:0016117 - carotenoid biosynthetic process
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0055114 - oxidation reduction
GO:0009416 - response to light stimulus
 TO:0000326 - leaf color
TO:0000075 - light sensitivity
 Os03g0184000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g08570.1
_ OsOR
OR
 _ Orange
 2 Coloration - Others
 GO:0016116 - carotenoid metabolic process
GO:0031969 - chloroplast membrane
GO:0050821 - protein stabilization
 Os02g0535000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g33149.1
ZEP1 OsZEP1
 ZEAXANTHIN EPOXIDASE 1 zeaxanthin epoxidase 1
 4 Coloration - Others
Biochemical character
 GO:0016491 - oxidoreductase activity
GO:0016117 - carotenoid biosynthetic process
 Os04g0448950 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 )
WSL1 OsPRDA1
PRDA1
OsWSL1
 WHITE SEEDLING AND LETHAL 1 white seedling and lethal 1
PEP-RELATED DEVELOPMENT ARRESTED 1
 11 Coloration - Chlorophyll
Coloration - Others
Vegetative organ - Leaf
Character as QTL - Plant growth activity
 GO:0009658 - chloroplast organization
GO:0009416 - response to light stimulus
GO:0010109 - regulation of photosynthesis
GO:0009507 - chloroplast
GO:0042793 - transcription from plastid promoter
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000496 - carotenoid content
TO:0002715 - chloroplast development trait
TO:0000075 - light sensitivity
TO:0000326 - leaf color
TO:0000293 - chlorophyll-a content
TO:0000295 - chlorophyll-b content
TO:0000357 - growth and development trait
 PO:0025034 - leaf
Os11g0425300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g23790.3
LOC_Os11g23790.2
LOC_Os11g23790.1
WLL1 OsWLL1
OsRNE
RNE
 WHITE LEAF AND LETHAL 1 RNase E
RNase E/G-Type Endoribonuclease
 8 Coloration - Chlorophyll
Biochemical character
Vegetative organ - Leaf
Coloration - Others
Character as QTL - Plant growth activity
 GO:0046872 - metal ion binding
GO:0004540 - ribonuclease activity
GO:0009507 - chloroplast
GO:0006396 - RNA processing
GO:0003723 - RNA binding
GO:0010109 - regulation of photosynthesis
GO:0006109 - regulation of carbohydrate metabolic process
GO:0090056 - regulation of chlorophyll metabolic process
GO:0015995 - chlorophyll biosynthetic process
GO:0009658 - chloroplast organization
GO:0004519 - endonuclease activity
 TO:0000496 - carotenoid content
TO:0002715 - chloroplast development trait
TO:0000357 - growth and development trait
TO:0000326 - leaf color
TO:0000293 - chlorophyll-a content
TO:0000295 - chlorophyll-b content
 PO:0020104 - leaf sheath
PO:0009049 - inflorescence
PO:0020148 - shoot apical meristem
PO:0025034 - leaf
PO:0009047 - stem
PO:0009005 - root
Os08g0323600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g23430.3
LOC_Os08g23430.2
LOC_Os08g23430.1
BH4 Bh4
OsBH4
OsATL14
ATL14
 BLACK HULL 4 Black hull 4
black husk 4
amino acid transporter-like 14
 4 Biochemical character
Coloration - Others
 GO:0016021 - integral to membrane
GO:0043473 - pigmentation
 TO:0000190 - seed coat color
TO:0000264 - lemma and palea color
 PO:0009010 - seed
Os04g0460200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g38660.1
LOC_Os04g38670.1
ERF104 DERF3
OsDERF3
OsERF#104
OsERF104
AP2/EREBP#152
AP2/EREBP152
RAP2
OsRAP2
 ETHYLENE RESPONSE FACTOR 104 drought-responsive ethylene response factor 3
drought-responsive ERF 3
ethylene response factor 104
APETALA2/ethylene-responsive element binding protein 152
 8 Coloration - Others
Other
Tolerance and resistance - Stress tolerance
 GO:0016116 - carotenoid metabolic process
GO:0009409 - response to cold
GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
GO:0003700 - transcription factor activity
GO:0009651 - response to salt stress
GO:0003677 - DNA binding
 TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
 Os08g0474000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g36920.1
YGL13 OsSIG1
SIG1
Os-SigA
OsSigA
Os Sig1
SIGA
 YELLOW-GREEN LEAF 13 Sigma factor SIG1
plastid sigma factor SIG1
sigma A
sigma factor A
yellow-green leaf 13
yellow green leaf 13
 8 Other
Coloration - Chlorophyll
Vegetative organ - Leaf
Coloration - Others
 GO:0003700 - transcription factor activity
GO:0009416 - response to light stimulus
GO:0006352 - transcription initiation
GO:0003677 - DNA binding
GO:0016987 - sigma factor activity
GO:0009658 - chloroplast organization
 TO:0002715 - chloroplast development trait
TO:0000447 - filled grain number
TO:0000293 - chlorophyll-a content
TO:0000180 - spikelet fertility
TO:0000207 - plant height
TO:0000295 - chlorophyll-b content
TO:0000496 - carotenoid content
 Os08g0163400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g06630.3
LOC_Os08g06630.1
NAC17 ONAC017
ONAC17
ONAC030
ONAC30
OsNAC111
 NAC DOMAIN-CONTAINING PROTEIN 17 NAC domain-containing protein 017
NAC domain-containing protein 17
NAC domain-containing protein 30
 11 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Other
Coloration - Others
 GO:0009609 - response to symbiotic bacterium
GO:0005634 - nucleus
GO:0009698 - phenylpropanoid metabolic process
GO:0043473 - pigmentation
GO:0003677 - DNA binding
GO:0050832 - defense response to fungus
GO:0009617 - response to bacterium
GO:0006355 - regulation of transcription, DNA-dependent
GO:0051607 - defense response to virus
GO:0030912 - response to deep water
 TO:0000386 - rice ragged stunt virus resistance
TO:0000213 - rice grassy stunt 1 and 2 virus resistance
TO:0000148 - viral disease resistance
TO:0000020 - black streak dwarf virus resistance
TO:0000074 - blast disease
TO:0000624 - allelopathic effect
 Os11g0154500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g05614.1
LYCE OsLCYe
OsLCYepsilon
LCYepsilon
epsilon-LCY
OsLYCE
OsLYC-E
LYC-E
 LYCOPENE EPSILON-CYCLASE e-ionone-forming lycopene cyclase
lycopene e-cyclase
epsilon-ionone-forming lycopene cyclase
lycopene epsilon-cyclase
 1 Tolerance and resistance - Stress tolerance
Coloration - Others
Biochemical character
 GO:0016120 - carotene biosynthetic process
GO:0009414 - response to water deprivation
GO:0016117 - carotenoid biosynthetic process
GO:0016123 - xanthophyll biosynthetic process
GO:0009416 - response to light stimulus
GO:0045435 - lycopene epsilon cyclase activity
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
 TO:0002701 - lutein content
TO:0000075 - light sensitivity
TO:0000276 - drought tolerance
 Os01g0581300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g39960.1
LCYB OsLCYbeta
OsLYCb
OsLCY
beta-OsLCY
beta-LCY
 LYCOPENE BETA-CYCLASE lycopene e-cyclase
lycopene beta-cyclase
 2 Coloration - Others
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0009408 - response to heat
GO:0045436 - lycopene beta cyclase activity
GO:0016117 - carotenoid biosynthetic process
GO:0016120 - carotene biosynthetic process
GO:0009416 - response to light stimulus
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
 TO:0000259 - heat tolerance
TO:0000075 - light sensitivity
 Os02g0190600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g09750.1
_ IBF1
OsFBX310
FBX310
OsFBX310
FBX310
 _ inhibitor for brown furrows1
F-box protein 310
F-box-type E3 ubiquitin ligase X310
 9 Coloration - Others
 Os09g0292900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g12150.1
PHS3 OsCRTISO
MHZ5
MHZ5/CRTISO
CRTISO
 PRE-HARVEST SPROUTING 3 carotenoid isomerase
Pre-harvest sprouting 3
 11 Vegetative organ - Root
Character as QTL - Plant growth activity
Biochemical character
Coloration - Others
Character as QTL - Germination
Tolerance and resistance - Stress tolerance
 GO:0060359 - response to ammonium ion
GO:0009693 - ethylene biosynthetic process
GO:0046608 - carotenoid isomerase activity
GO:0009723 - response to ethylene stimulus
GO:0009738 - abscisic acid mediated signaling
GO:0009507 - chloroplast
GO:0009873 - ethylene mediated signaling pathway
GO:0048364 - root development
GO:0016117 - carotenoid biosynthetic process
GO:0048623 - seed germination on parent plant
 TO:0000516 - relative root length
TO:0000181 - seed weight
TO:0000619 - vivipary
TO:0002667 - abscisic acid content
TO:0000207 - plant height
TO:0000578 - root fresh weight
TO:0000040 - panicle length
TO:0002699 - lycopene content
TO:0000326 - leaf color
TO:0002696 - alpha carotene content
TO:0000295 - chlorophyll-b content
TO:0000293 - chlorophyll-a content
TO:0000656 - root development trait
TO:0000173 - ethylene sensitivity
TO:0000496 - carotenoid content
TO:0000346 - tiller number
TO:0002695 - beta-carotene content
TO:0002701 - lutein content
TO:0000391 - seed size
TO:0000289 - carotene content
 PO:0007045 - coleoptile emergence stage
PO:0025034 - leaf
PO:0001031 - 4 root elongation stage
PO:0007520 - root development stage
Os11g0572700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g36440.1
PSY3 OsPSY
PSY
OsPSY3
 PHYTOENE SYNTHASE 3 phytoene synthase 3
 9 Vegetative organ - Root
Coloration - Others
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0009507 - chloroplast
GO:0016117 - carotenoid biosynthetic process
GO:0009688 - abscisic acid biosynthetic process
GO:0046905 - phytoene synthase activity
GO:0004311 - farnesyltranstransferase activity
 TO:0002667 - abscisic acid content
 Os09g0555500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g38320.1
NCED1 OsNCED1
OsCCD4a
CCD4a
 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 9-cis-epoxycarotenoid dioxygenase 1
carotenoid-cleavage dioxygenase 4a
"zeaxanthin 7
8(7',8')-cleavage dioxygenase
chromoplastic"
 2 Biochemical character
Tolerance and resistance - Stress tolerance
Coloration - Anthocyanin
Tolerance and resistance - Disease resistance
Coloration - Others
Tolerance and resistance - Insect resistance
 GO:0009409 - response to cold
GO:0042742 - defense response to bacterium
GO:0009813 - flavonoid biosynthetic process
GO:0009725 - response to hormone stimulus
GO:0006970 - response to osmotic stress
GO:0051213 - dioxygenase activity
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0009413 - response to flooding
GO:0016702 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0009688 - abscisic acid biosynthetic process
GO:0010287 - plastoglobule
GO:0009737 - response to abscisic acid stimulus
GO:0002213 - defense response to insect
GO:0009753 - response to jasmonic acid stimulus
 TO:0000289 - carotene content
TO:0000095 - osmotic response sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000424 - brown planthopper resistance
TO:0002667 - abscisic acid content
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000401 - plant growth hormone sensitivity
TO:0000496 - carotenoid content
TO:0000276 - drought tolerance
TO:0000114 - flooding related trait
TO:0000172 - jasmonic acid sensitivity
TO:0000303 - cold tolerance
TO:0000301 - xanthophyll content
 PO:0007131 - seedling development stage
PO:0008037 - seedling
PO:0025034 - leaf
PO:0009049 - inflorescence
Os02g0704000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g47510.1
NCED2 OsNCED2
OsNced2
OsCCD4b
CCD4b
OsCCD4c
CCD4c
 9-CIS-EPOXYCAROTENOID DIOXYGENASE 2 9-cis-epoxycarotenoid dioxygenase 2
carotenoid-cleavage dioxygenase 4b
 12 Vegetative organ - Culm
Vegetative organ - Root
Biochemical character
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Coloration - Chlorophyll
Character as QTL - Plant growth activity
Coloration - Others
Vegetative organ - Leaf
 GO:0009409 - response to cold
GO:0006970 - response to osmotic stress
GO:0010231 - maintenance of seed dormancy
GO:0019566 - arabinose metabolic process
GO:0009507 - chloroplast
GO:0006979 - response to oxidative stress
GO:0043289 - apocarotenoid biosynthetic process
GO:0009741 - response to brassinosteroid stimulus
GO:0009688 - abscisic acid biosynthetic process
GO:0046872 - metal ion binding
GO:0009414 - response to water deprivation
GO:0045549 - 9-cis-epoxycarotenoid dioxygenase activity
GO:0016117 - carotenoid biosynthetic process
GO:0010287 - plastoglobule
GO:0006109 - regulation of carbohydrate metabolic process
GO:0032881 - regulation of polysaccharide metabolic process
GO:0010162 - seed dormancy
GO:0016702 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0044042 - glucan metabolic process
GO:0009725 - response to hormone stimulus
GO:0019321 - pentose metabolic process
GO:0051510 - regulation of unidimensional cell growth
 TO:0000253 - seed dormancy
TO:0000207 - plant height
TO:0000576 - stem length
TO:0000495 - chlorophyll content
TO:0000095 - osmotic response sensitivity
TO:0000401 - plant growth hormone sensitivity
TO:0000326 - leaf color
TO:0002695 - beta-carotene content
TO:0000303 - cold tolerance
TO:0000301 - xanthophyll content
TO:0000289 - carotene content
TO:0000496 - carotenoid content
TO:0002677 - brassinosteroid sensitivity
TO:0002667 - abscisic acid content
TO:0000276 - drought tolerance
TO:0002657 - oxidative stress
TO:0000227 - root length
TO:0000357 - growth and development trait
 PO:0009049 - inflorescence
PO:0007010 - whole plant fruit ripening stage
PO:0009010 - seed
PO:0008037 - seedling
Os12g0435200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g24800.1
TSC1 ABCI7
OsABCI7
OsABCI7_1
OsABCI7_2
OsABCI8
ABCI8
OsABCI8.1
OsABCI8.2
OsCNL1
CNL1
OsTSC1
TSC1.1
TSC1.2
 TRANSPLANT-SENSITIVE CHLOROPLAST-DEFICIENT 1 ABC transporter superfamily ABCI subgroup member 7
chlorotic and necrotic leaf1
transplant-sensitive chloroplast-deficient 1
 11 Coloration - Chlorophyll
Coloration - Others
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
 GO:0055070 - copper ion homeostasis
GO:0009628 - response to abiotic stimulus
GO:0009536 - plastid
GO:0009507 - chloroplast
GO:0006826 - iron ion transport
GO:0009642 - response to light intensity
GO:0055065 - metal ion homeostasis
GO:0009646 - response to absence of light
GO:0006974 - response to DNA damage stimulus
GO:0046466 - membrane lipid catabolic process
GO:0015979 - photosynthesis
GO:0005524 - ATP binding
GO:0009826 - unidimensional cell growth
GO:0016887 - ATPase activity
GO:0009658 - chloroplast organization
GO:0042651 - thylakoid membrane
GO:0015995 - chlorophyll biosynthetic process
GO:0010027 - thylakoid membrane organization
GO:0070265 - necrotic cell death
GO:0055072 - iron ion homeostasis
GO:0006281 - DNA repair
GO:0006260 - DNA replication
GO:0012501 - programmed cell death
GO:0009651 - response to salt stress
GO:0009409 - response to cold
GO:0009657 - plastid organization
GO:0033013 - tetrapyrrole metabolic process
 TO:0001018 - transpiration rate
TO:0000326 - leaf color
TO:0000293 - chlorophyll-a content
TO:0000295 - chlorophyll-b content
TO:0000496 - carotenoid content
TO:0002715 - chloroplast development trait
TO:0000168 - abiotic stress trait
TO:0006001 - salt tolerance
TO:0000460 - light intensity sensitivity
TO:0000652 - leaf necrosis
TO:0000316 - photosynthetic ability
TO:0000303 - cold tolerance
TO:0001027 - net photosynthetic rate
TO:0000145 - internode length
TO:0000207 - plant height
TO:0000357 - growth and development trait
TO:0000605 - hydrogen peroxide content
 PO:0025034 - leaf
PO:0000003 - whole plant
Os11g0490800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g29850.1
LOC_Os11g29850.2
CYP97A4 CYP97A4
OsCYP97A4
 P-450 97A4 Cytochrome P450 97A4
Carotenoid beta-Ring Hydroxylase CYP97A4
 2 Coloration - Others
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0020037 - heme binding
GO:0016117 - carotenoid biosynthetic process
GO:0005506 - iron ion binding
GO:0010291 - carotene beta-ring hydroxylase activity
GO:0009055 - electron carrier activity
GO:0009507 - chloroplast
GO:0016123 - xanthophyll biosynthetic process
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
 TO:0002701 - lutein content
 Os02g0817900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g57290.1
LOC_Os02g57290.2
LOC_Os02g57290.3
LOC_Os02g57290.4
CYP97C2 OsCYP97C2
 P-450 97C2 Cytochrome P450 97C2
 10 Coloration - Others
Biochemical character
 GO:0016117 - carotenoid biosynthetic process
GO:0005506 - iron ion binding
GO:0009055 - electron carrier activity
GO:0009941 - chloroplast envelope
GO:0009974 - epsilon hydroxylase activity
GO:0020037 - heme binding
 TO:0002701 - lutein content
 Os10g0546600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g39930.2
LOC_Os10g39930.1
DJB7 OsDjB7
DjB7
 DNAJ DOMAIN PROTEIN B7 DnaJ domain protein B7
 5 Tolerance and resistance - Stress tolerance
Coloration - Others
 GO:0006950 - response to stress
GO:0006457 - protein folding
GO:0016116 - carotenoid metabolic process
 TO:0000168 - abiotic stress trait
 Os05g0562300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g48810.1
BZIP48 OsbZIP48
OsHY5
HY5
OsHY5L2
HY5L2
 b-ZIP TRANSCRIPTION FACTOR 48 b-ZIP transcription factor 48
ELONGATED HYPOCOTYL 5
 6 Vegetative organ - Culm
Coloration - Others
Tolerance and resistance - Stress tolerance
Seed - Morphological traits
Character as QTL - Grain quality
Other
Coloration - Anthocyanin
 GO:0005982 - starch metabolic process
GO:0003700 - transcription factor activity
GO:0003677 - DNA binding
GO:0005634 - nucleus
GO:0005983 - starch catabolic process
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0010224 - response to UV-B
GO:0032502 - developmental process
GO:0005985 - sucrose metabolic process
GO:0009740 - gibberellic acid mediated signaling
GO:0031542 - positive regulation of anthocyanin biosynthetic process
GO:0016116 - carotenoid metabolic process
GO:0010581 - regulation of starch biosynthetic process
 TO:0000196 - amylose content
TO:0000486 - seed color
TO:0002656 - starch grain shape
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
TO:0000222 - head rice
TO:0002658 - starch grain synthesis
TO:0000696 - starch content
TO:0000601 - UV-B light sensitivity
TO:0000071 - anthocyanin content
TO:0000266 - chalky endosperm
TO:0000374 - breakdown viscosity
TO:0000412 - setback viscosity
TO:0000162 - seed quality
 PO:0007632 - seed maturation stage
Os06g0601500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g39960.1
YGL98 OsChlD
ChlD
CHLD
OsCHLD
Ygl7
YGL3
OsvWA12
vWA12
 YELLOW-GREEN LEAF 98 magnesium chelatase subunit ChlD
magnesium-chelatase ChlD subunit
yellow-green leaf mutant 98
yellow-green leaf 7
magnesium-chelatase ChlD protein
MgCh D subunit
D-subunit of Mg-chelatase
Mg-chelatase D subunit
yellow green leaf3
yellow green leaf 3
von Willebrand factor A12
 3 Vegetative organ - Leaf
Tolerance and resistance - Disease resistance
Coloration - Chlorophyll
Biochemical character
Coloration - Others
Tolerance and resistance - Stress tolerance
 GO:0009658 - chloroplast organization
GO:0017111 - nucleoside-triphosphatase activity
GO:0015979 - photosynthesis
GO:0009507 - chloroplast
GO:0015995 - chlorophyll biosynthetic process
GO:0009637 - response to blue light
GO:0051707 - response to other organism
GO:0005524 - ATP binding
GO:0050832 - defense response to fungus
GO:0016851 - magnesium chelatase activity
GO:0042742 - defense response to bacterium
GO:0009414 - response to water deprivation
GO:0009645 - response to low light intensity stimulus
GO:0009739 - response to gibberellin stimulus
GO:0009725 - response to hormone stimulus
GO:0033014 - tetrapyrrole biosynthetic process
 TO:0000159 - blue light sensitivity
TO:0000326 - leaf color
TO:0002715 - chloroplast development trait
TO:0000166 - gibberellic acid sensitivity
TO:0000295 - chlorophyll-b content
TO:0000460 - light intensity sensitivity
TO:0000276 - drought tolerance
TO:0000203 - bacterial leaf streak disease resistance
TO:0000175 - bacterial blight disease resistance
TO:0000255 - sheath blight disease resistance
TO:0000293 - chlorophyll-a content
TO:0000401 - plant growth hormone sensitivity
TO:0000495 - chlorophyll content
 PO:0025034 - leaf
PO:0020104 - leaf sheath
Os03g0811100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g59640.1
CHI3 gh1
GH1
OsGH1
OsCHI
Cfi
CHI
OsCHI3
 CHALCONE ISOMERASE 3 gold hull and internode 1
chalcone isomerase
chalcone flavonone isomerase
chalcone-flavonone isomerase
 3 Vegetative organ - Culm
Seed
Tolerance and resistance - Insect resistance
Tolerance and resistance - Stress tolerance
Biochemical character
Vegetative organ - Leaf
Seed - Morphological traits
Coloration - Anthocyanin
Coloration - Others
 GO:0009416 - response to light stimulus
GO:0009411 - response to UV
GO:0009809 - lignin biosynthetic process
GO:0009814 - defense response, incompatible interaction
GO:0002213 - defense response to insect
GO:0009813 - flavonoid biosynthetic process
GO:0048316 - seed development
GO:0009628 - response to abiotic stimulus
GO:0045430 - chalcone isomerase activity
GO:0009718 - anthocyanin biosynthetic process
 TO:0000653 - seed development trait
TO:0000707 - pericarp color
TO:0000051 - stem strength
TO:0000071 - anthocyanin content
TO:0000160 - UV light sensitivity
TO:0000675 - ferulic acid content
TO:0000290 - flavonoid content
TO:0000733 - lignin biosynthesis trait
TO:0000731 - lignin content
TO:0000168 - abiotic stress trait
TO:0000396 - grain yield
TO:0000424 - brown planthopper resistance
TO:0000326 - leaf color
TO:0000494 - pigment content
TO:0000075 - light sensitivity
TO:0000534 - culm color
 PO:0001170 - seed development stage
PO:0009049 - inflorescence
PO:0025034 - leaf
Os03g0819600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g60509.2
LOC_Os03g60509.1
ERF133 OsERF#133
OsERF133
AP2/EREBP#065
AP2/EREBP65
OsDREB1H
DREB1H
OsDREB1m
DREB1m
 ETHYLENE RESPONSE FACTOR 133 ethylene response factor 133
APETALA2/ethylene-responsive element binding protein 65
Dehydration-responsive element-binding protein 1H
 9 Coloration - Others
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Other
 GO:0009409 - response to cold
GO:0016116 - carotenoid metabolic process
GO:0006950 - response to stress
GO:0030912 - response to deep water
GO:0009845 - seed germination
GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
GO:0003700 - transcription factor activity
GO:0009609 - response to symbiotic bacterium
GO:0003677 - DNA binding
 TO:0000303 - cold tolerance
TO:0000524 - submergence tolerance
 PO:0007022 - seed imbibition stage
Os09g0522100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g35020.1
WP2 wp2*
wp2
 WHITE PANICLE 2 white panicle-2
 Coloration - Others
 GO:0015995 - chlorophyll biosynthetic process
 TO:0000495 - chlorophyll content
TO:0000077 - shoot anatomy and morphology trait
TO:0000264 - lemma and palea color
 PO:0009049 - inflorescence
PO:0009025 - vascular leaf
-
DREB1C OsDREB1C
CBF1
ERF26
OsERF026
OsERF#026
OsERF26
AP2/EREBP#098
AP2/EREBP98
OsCBF2
CBF2
 DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 1C Dehydration-responsive element-binding protein 1C
Protein DREB1C
Protein C-repeat-binding factor 1
ethylene response factor 26
APETALA2/ethylene-responsive element binding protein 98
C-REPEAT BINDING FACTOR 1
 6 Character as QTL - Yield and productivity
Character as QTL - Plant growth activity
Other
Seed - Morphological traits - Grain shape
Coloration - Others
Tolerance and resistance - Stress tolerance
Coloration - Chlorophyll
Reproductive organ - Heading date
 GO:0042594 - response to starvation
GO:0006995 - cellular response to nitrogen starvation
GO:0009416 - response to light stimulus
GO:0009658 - chloroplast organization
GO:0009915 - phloem loading
GO:0015706 - nitrate transport
GO:0042128 - nitrate assimilation
GO:0031667 - response to nutrient levels
GO:0019740 - nitrogen utilization
GO:0048578 - positive regulation of long-day photoperiodism, flowering
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0006950 - response to stress
GO:0005634 - nucleus
GO:0006350 - transcription
GO:0009409 - response to cold
GO:0009414 - response to water deprivation
GO:0009611 - response to wounding
GO:0009737 - response to abscisic acid stimulus
GO:0009651 - response to salt stress
GO:0048573 - photoperiodism, flowering
GO:0005829 - cytosol
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009413 - response to flooding
GO:0046686 - response to cadmium ion
GO:0003700 - transcription factor activity
GO:0030912 - response to deep water
 TO:0000303 - cold tolerance
TO:0000522 - stomatal conductance
TO:0000382 - 1000-seed weight
TO:0000615 - abscisic acid sensitivity
TO:0002672 - auxin content
TO:0000357 - growth and development trait
TO:0000162 - seed quality
TO:0001017 - water use efficiency
TO:0000598 - protein content
TO:0000399 - grain thickness
TO:0000557 - secondary branch number
TO:0000114 - flooding related trait
TO:0000734 - grain length
TO:0000276 - drought tolerance
TO:0000153 - relative yield
TO:0000612 - seed density
TO:0000447 - filled grain number
TO:0000466 - carbon content
TO:0000011 - nitrogen sensitivity
TO:0000128 - harvest index
TO:0000075 - light sensitivity
TO:0000396 - grain yield
TO:0000137 - days to heading
TO:0000316 - photosynthetic ability
TO:0000524 - submergence tolerance
TO:0000496 - carotenoid content
TO:0000495 - chlorophyll content
TO:0002715 - chloroplast development trait
TO:0000696 - starch content
TO:0000328 - sucrose content
TO:0006005 - fructose content
TO:0000449 - grain yield per plant
TO:0006001 - salt tolerance
TO:0000227 - root length
 Os06g0127100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g03670.1
SET29 OsSET29
SDG749
OsSDG749
 SET PROTEIN 29 SET protein 29
 8 Coloration - Others
 GO:0016279 - protein-lysine N-methyltransferase activity
GO:0032259 - methylation
GO:0005634 - nucleus
GO:0016116 - carotenoid metabolic process
 Os08g0244400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g14660.1
DET1 OsDET1
 DE-ETIOLATED1 1 Coloration - Others
Seed - Morphological traits - Embryo
Coloration - Chlorophyll
Seed - Morphological traits - Grain shape
 GO:0031625 - ubiquitin protein ligase binding
GO:0031461 - cullin-RING ubiquitin ligase complex
GO:0032436 - positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0009416 - response to light stimulus
GO:0005634 - nucleus
GO:0007623 - circadian rhythm
GO:0009962 - regulation of flavonoid biosynthetic process
GO:0016567 - protein ubiquitination
GO:0048316 - seed development
GO:0009793 - embryonic development ending in seed dormancy
 TO:0000734 - grain length
TO:0000590 - grain weight
TO:0000075 - light sensitivity
TO:0000707 - pericarp color
TO:0000399 - grain thickness
TO:0000064 - embryo related trait
TO:0000653 - seed development trait
TO:0000290 - flavonoid content
TO:0000495 - chlorophyll content
TO:0000397 - grain size
TO:0000269 - 100-seed weight
 PO:0001170 - seed development stage
PO:0009010 - seed
PO:0025034 - leaf
PO:0020104 - leaf sheath
Os01g0104600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g01484.1
LOC_Os01g01484.2
LOC_Os01g01484.4
LOC_Os01g01484.5
DXS1 CLA1
OsDXS1
dxs1
OsDXS
DXS
OsTKL1
TKL1
 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE 1 CLA1 transketolase-like protein
1-Deoxy-D-xylulose 5-phosphate synthase 1
transketolase 1
 5 Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Biochemical character
Coloration - Others
 GO:0009570 - chloroplast stroma
GO:0015995 - chlorophyll biosynthetic process
GO:0008299 - isoprenoid biosynthetic process
GO:0016114 - terpenoid biosynthetic process
GO:0005829 - cytosol
GO:0009416 - response to light stimulus
GO:0009228 - thiamin biosynthetic process
GO:0008661 - 1-deoxy-D-xylulose-5-phosphate synthase activity
GO:0019288 - isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway
GO:0016117 - carotenoid biosynthetic process
GO:0046872 - metal ion binding
 TO:0000075 - light sensitivity
TO:0000289 - carotene content
 Os05g0408900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g33840.1
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