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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
GID1 gid1
OsGID1
Thl
Os GID1
 GIBBERELLIN INSENSITIVE DWARF1 GIBBERELLIN-INSENSITIVE DWARF1
Gibberellin receptor GID1
Gibberellin-insensitive dwarf protein 1
Protein GIBBERELLIN INSENSITIVE DWARF1
Thumbelina
GA-insensitive dwarf 1
 5 Vegetative organ - Culm
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
 GO:0004872 - receptor activity
GO:0010162 - seed dormancy
GO:0010271 - regulation of chlorophyll catabolic process
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0006109 - regulation of carbohydrate metabolic process
GO:0009740 - gibberellic acid mediated signaling
GO:0009737 - response to abscisic acid stimulus
GO:0014001 - sclerenchyma cell differentiation
GO:2000037 - regulation of stomatal complex patterning
GO:2000038 - regulation of stomatal complex development
GO:0008152 - metabolic process
GO:0005634 - nucleus
GO:0016787 - hydrolase activity
GO:0009409 - response to cold
GO:0050832 - defense response to fungus
GO:0009739 - response to gibberellin stimulus
GO:0009609 - response to symbiotic bacterium
 TO:0000566 - stomatal frequency
TO:0000286 - submergence sensitivity
TO:0000495 - chlorophyll content
TO:0000074 - blast disease
TO:0000135 - leaf length
TO:0000175 - bacterial blight disease resistance
TO:0000207 - plant height
TO:0000276 - drought tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000303 - cold tolerance
TO:0000253 - seed dormancy
TO:0000291 - carbohydrate content
TO:0000470 - vascular tissue related trait
 Os05g0407500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g33730.1
FLO27 OsbZIP58
bZIP58
OsEnS-92
OsSMF1
SMF1
OsRISBZ1
RISBZ1/bZIP58
RISBZ1
OsFLO27
 FLOURY ENDOSPERM 27 bZIP transcription factor 58
rice seed b-Zipper 1
endosperm-specific gene 92
seed maturation factor 1
rice seed basic leucine zipper 1
RICE SEED bZIP1
 7 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Grain shape
Seed - Morphological traits - Endosperm
Other
 GO:0034976 - response to endoplasmic reticulum stress
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010581 - regulation of starch biosynthetic process
GO:0009960 - endosperm development
GO:0012501 - programmed cell death
GO:0010431 - seed maturation
GO:0043565 - sequence-specific DNA binding
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0030968 - endoplasmic reticulum unfolded protein response
 TO:0002653 - endosperm storage protein content
TO:0002661 - seed maturation
TO:0000104 - floury endosperm
TO:0000432 - temperature response trait
TO:0000259 - heat tolerance
TO:0002673 - amino acid content
TO:0000590 - grain weight
TO:0000399 - grain thickness
TO:0000402 - grain width
TO:0000734 - grain length
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0002656 - starch grain shape
TO:0000100 - shrunken endosperm
TO:0000487 - endosperm color
TO:0000490 - protein composition related trait
 PO:0007057 - 0 seed germination stage
PO:0007632 - seed maturation stage
PO:0009089 - endosperm
PO:0005360 - aleurone layer
PO:0007633 - endosperm development stage
Os07g0182000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g08420.1
AMY1C Amy1A/C*(RAmy1A/C)
alpha Amy10
Amy1C
RAmy1A/C
Amy1A/C*
Amy3
RAmy1C
OsAmy1C
alphaAmy10-C
OsRAmy3A
RAmy3A
 ALPHA-AMYLASE 1C Alpha-amylase1C
Alpha-amylase 1C
Amylase-3
Alpha-amylase-1A
alpha-amylase 10-C
 2 Seed - Physiological traits - Dormancy
Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
Character as QTL - Germination
 GO:0009737 - response to abscisic acid stimulus
GO:0004556 - alpha-amylase activity
GO:0005983 - starch catabolic process
GO:0005975 - carbohydrate metabolic process
GO:0005509 - calcium ion binding
GO:0009651 - response to salt stress
GO:0009845 - seed germination
GO:0009408 - response to heat
 TO:0006001 - salt tolerance
TO:0000259 - heat tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000266 - chalky endosperm
 PO:0009010 - seed
PO:0007633 - endosperm development stage
PO:0007057 - 0 seed germination stage
Os02g0765400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g52700.1
AMY3C Amy3A/B/C*(RAmy3A/B/C)
AmyII-6
AMY1.7
Amy3C
RAmy3A/B/C
Amy3A/B/C*
Amy7
AMY3B
RAmy3C
OsAmy3B
 ALPHA-AMYLASE 3C Alpha-amylase3C
Alpha-amylase isozyme 3C precursor
Alpha-amylase isozyme 3C
Amylase-7
Alpha-amylase-3A
 9 Character as QTL - Germination
Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Dormancy
 GO:0009739 - response to gibberellin stimulus
GO:0005509 - calcium ion binding
GO:0009737 - response to abscisic acid stimulus
GO:0004556 - alpha-amylase activity
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0005987 - sucrose catabolic process
GO:0005983 - starch catabolic process
GO:0005975 - carbohydrate metabolic process
GO:0009845 - seed germination
GO:0009408 - response to heat
 TO:0000259 - heat tolerance
TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
 PO:0007057 - 0 seed germination stage
Os09g0457800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g28420.1
PT4 OsPT4
PHT1-4
OsPht1;4
PHT1-2
PHT1;4
OsPHT1;4
 PHOSPHATE TRANSPORTER 4 Probable inorganic phosphate transporter 1-4
Plant Phosphate Transporter 1;4
 4 Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
Seed - Physiological traits - Dormancy
Biochemical character
 GO:0001887 - selenium metabolic process
GO:0009609 - response to symbiotic bacterium
GO:0046685 - response to arsenic
GO:0005315 - inorganic phosphate transmembrane transporter activity
GO:0005886 - plasma membrane
GO:0009790 - embryonic development
GO:0006817 - phosphate transport
GO:0009845 - seed germination
GO:0015293 - symporter activity
GO:0009737 - response to abscisic acid stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0016020 - membrane
GO:0009739 - response to gibberellin stimulus
GO:0016021 - integral to membrane
GO:0046688 - response to copper ion
GO:0042594 - response to starvation
GO:0055085 - transmembrane transport
GO:0016036 - cellular response to phosphate starvation
GO:0010269 - response to selenium ion
 TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000021 - copper sensitivity
TO:0000102 - phosphorus sensitivity
 PO:0007633 - endosperm development stage
PO:0009009 - plant embryo
PO:0007057 - 0 seed germination stage
PO:0020103 - flag leaf
PO:0001170 - seed development stage
PO:0007631 - plant embryo stage
PO:0007632 - seed maturation stage
Os04g0186400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g10750.4
LOC_Os04g10750.1
LOC_Os04g10750.2
LOC_Os04g10750.3
ABI5 OsABI5
OsbZIP10
OsABF1
OREB1
OsABI5-1
OsABI5-2
OsOREB1
OREB1
 ABA INSENSITIVE 5 ABA Insensitive 5
bZIP-type transcription factor ABI5
bZIP transcription factors OsABI5
bZIP transcription factor 10
Abscisic acid insensitive 5
 1 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
Reproductive organ - Pollination, fertilization, fertility - Male sterility
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Character as QTL - Germination
Character as QTL - Grain quality
Character as QTL - Yield and productivity
 GO:0009725 - response to hormone stimulus
GO:0010029 - regulation of seed germination
GO:0010162 - seed dormancy
GO:0045449 - regulation of transcription
GO:0009787 - regulation of abscisic acid mediated signaling
GO:0010581 - regulation of starch biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0045454 - cell redox homeostasis
GO:0005982 - starch metabolic process
GO:0006995 - cellular response to nitrogen starvation
GO:0005985 - sucrose metabolic process
GO:0009753 - response to jasmonic acid stimulus
GO:0010187 - negative regulation of seed germination
GO:0042744 - hydrogen peroxide catabolic process
GO:0009409 - response to cold
GO:0046345 - abscisic acid catabolic process
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009651 - response to salt stress
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0031667 - response to nutrient levels
GO:0010152 - pollen maturation
GO:0003700 - transcription factor activity
GO:0009845 - seed germination
GO:0042594 - response to starvation
GO:0009739 - response to gibberellin stimulus
GO:0009733 - response to auxin stimulus
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0019740 - nitrogen utilization
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0030187 - melatonin biosynthetic process
 TO:0000615 - abscisic acid sensitivity
TO:0000303 - cold tolerance
TO:0000276 - drought tolerance
TO:0000250 - vigor related trait
TO:0000401 - plant growth hormone sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000430 - germination rate
TO:0000696 - starch content
TO:0000196 - amylose content
TO:0000097 - amylopectin content
TO:0000382 - 1000-seed weight
TO:0002658 - starch grain synthesis
TO:0002656 - starch grain shape
TO:0000266 - chalky endosperm
TO:0000399 - grain thickness
TO:0000590 - grain weight
TO:0000134 - alkali digestion
TO:0002667 - abscisic acid content
TO:0000011 - nitrogen sensitivity
TO:0000396 - grain yield
TO:0000172 - jasmonic acid sensitivity
TO:0000053 - pollen sterility
TO:0000253 - seed dormancy
TO:0002672 - auxin content
TO:0000604 - fat and essential oil content
TO:0002653 - endosperm storage protein content
TO:0000300 - glucose content
TO:0000455 - seed set percent
TO:0000040 - panicle length
TO:0000462 - gelatinization temperature
TO:0000211 - gel consistency
TO:0000487 - endosperm color
TO:0000162 - seed quality
TO:0000166 - gibberellic acid sensitivity
TO:0000163 - auxin sensitivity
TO:0000919 - grain weight
TO:0000397 - grain size
TO:0000483 - germinability at low temperature
TO:0000420 - fertility related trait
TO:0000429 - salt sensitivity
 PO:0009049 - inflorescence
PO:0007057 - 0 seed germination stage
PO:0020091 - obsolete microgametophyte
PO:0025500 - whole plant fruit development stage
PO:0009010 - seed
Os01g0859300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g64000.1
LOC_Os01g64000.2
LOC_Os01g64000.3
LEC1 OsHAP3E
HAP3E
OsLEC1/OsHAP3E
OsLEC1
LEC1
OsNF-YB7
NF-YB7
NFYB7
L1L
OsLEC1B
LEC1B
 LEAFY COTYLEDON 1 HAP3 subunit E
LEC1-type 3 subunit protein-E
leafy cotyledon 1
NUCLEAR FACTOR-Y subunit B7
NUCLEAR FACTOR-Y subunit NF-YB7
LEC1-LIKE
LEAFY COTYLEDON1-LIKE
HAP3 SUBUNIT E
NF-YB subunit 7
NF-YB family 7
LEAFY COTYLEDON1
 2 Coloration - Chlorophyll
Character as QTL - Germination
Reproductive organ - Heading date
Seed - Morphological traits - Embryo
Tolerance and resistance - Stress tolerance
Other
Seed - Physiological traits - Dormancy
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0009790 - embryonic development
GO:0010109 - regulation of photosynthesis
GO:0048700 - acquisition of desiccation tolerance
GO:0010099 - regulation of photomorphogenesis
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0010187 - negative regulation of seed germination
GO:0009269 - response to desiccation
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010431 - seed maturation
GO:0048316 - seed development
GO:0015995 - chlorophyll biosynthetic process
GO:0009734 - auxin mediated signaling pathway
GO:0043565 - sequence-specific DNA binding
GO:0009740 - gibberellic acid mediated signaling
GO:0009733 - response to auxin stimulus
GO:0008284 - positive regulation of cell proliferation
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0009738 - abscisic acid mediated signaling
GO:0015979 - photosynthesis
GO:0009845 - seed germination
 TO:0000430 - germination rate
TO:0000428 - callus induction
TO:0000397 - grain size
TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000163 - auxin sensitivity
TO:0000620 - embryo development trait
TO:0000391 - seed size
TO:0002661 - seed maturation
TO:0000276 - drought tolerance
TO:0000485 - sterility related trait
TO:0000064 - embryo related trait
TO:0000495 - chlorophyll content
TO:0000207 - plant height
TO:0000488 - seed composition based quality trait
 PO:0001170 - seed development stage
PO:0007057 - 0 seed germination stage
PO:0007631 - plant embryo stage
PO:0009010 - seed
PO:0020110 - scutellum
PO:0005421 - parenchyma
PO:0009009 - plant embryo
PO:0005052 - plant callus
PO:0007632 - seed maturation stage
Os02g0725700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g49370.1
LOC_Os02g49370.2
HAP3K OsHAP3K/OsNF-YB1
OsHAP3K
OsNF-YB1
NF-YB1
nf-yb1
OsLEC1
OsNF-YB-1
NFYB1
OsEnS-41
 HAP3K SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear transcription factor Y subunit B-1
CCAAT-binding transcription factor subunit NF-YB1
leafy cotyledon 1
endosperm-specific gene 41
Nuclear Factor YB1
NUCLEAR FACTOR-Y subunit B1
NUCLEAR FACTOR-Y subunit NF-YB1
NF-YB subunit 1
NF-YB family 1
 2 Seed - Morphological traits - Grain shape
Seed - Morphological traits - Endosperm
Seed - Physiological traits - Dormancy
Seed - Physiological traits - Storage substances
Seed - Morphological traits
Other
Character as QTL - Germination
Character as QTL - Grain quality
Tolerance and resistance - Stress tolerance
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0048623 - seed germination on parent plant
GO:0010162 - seed dormancy
GO:0009737 - response to abscisic acid stimulus
GO:0010600 - regulation of auxin biosynthetic process
GO:0043565 - sequence-specific DNA binding
GO:0008283 - cell proliferation
GO:0009960 - endosperm development
GO:0009738 - abscisic acid mediated signaling
GO:0010431 - seed maturation
GO:0045449 - regulation of transcription
GO:0005829 - cytosol
GO:0009651 - response to salt stress
GO:0005737 - cytoplasm
 TO:0000734 - grain length
TO:0000184 - seed anatomy and morphology trait
TO:0000408 - hot paste viscosity
TO:0000409 - peak viscosity
TO:0000653 - seed development trait
TO:0000162 - seed quality
TO:0000266 - chalky endosperm
TO:0000397 - grain size
TO:0000196 - amylose content
TO:0000379 - cool paste viscosity
TO:0000391 - seed size
TO:0000619 - vivipary
TO:0000399 - grain thickness
TO:0002661 - seed maturation
TO:0002672 - auxin content
TO:0000396 - grain yield
TO:0000696 - starch content
TO:0000604 - fat and essential oil content
TO:0000462 - gelatinization temperature
TO:0000211 - gel consistency
TO:0000382 - 1000-seed weight
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000253 - seed dormancy
 PO:0007633 - endosperm development stage
PO:0009089 - endosperm
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
PO:0006220 - central endosperm
PO:0005360 - aleurone layer
Os02g0725900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g49410.1
HAP5F OsHAP5F
NF-YC
CBF-C
OsNF-YC5
Os-NF-YC5
NF-YC5
NFYC5
 HAP5F SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C5 subunit
Nuclear factor Y C subunit 5
NUCLEAR FACTOR-Y subunit C5
NUCLEAR FACTOR-Y subunit NF-YC5
NF-YC subunit 5
NF-YC family 5
 8 Other
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
Character as QTL - Germination
 GO:0006979 - response to oxidative stress
GO:0010116 - positive regulation of abscisic acid biosynthetic process
GO:0009738 - abscisic acid mediated signaling
GO:0009414 - response to water deprivation
GO:0009651 - response to salt stress
GO:0010187 - negative regulation of seed germination
GO:0043565 - sequence-specific DNA binding
GO:0009845 - seed germination
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0009753 - response to jasmonic acid stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0016602 - CCAAT-binding factor complex
GO:0046345 - abscisic acid catabolic process
GO:0010730 - negative regulation of hydrogen peroxide biosynthetic process
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0042744 - hydrogen peroxide catabolic process
GO:0010162 - seed dormancy
 TO:0000172 - jasmonic acid sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000019 - seedling height
TO:0000276 - drought tolerance
TO:0002667 - abscisic acid content
TO:0000615 - abscisic acid sensitivity
TO:0000430 - germination rate
TO:0000280 - seedling vigor
TO:0000653 - seed development trait
TO:0002657 - oxidative stress
TO:0006001 - salt tolerance
TO:0000253 - seed dormancy
 PO:0007057 - 0 seed germination stage
Os08g0206500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g10560.1
PIP1;3 OsPIP1;3. PIP1.3
PIP1-3
RWC3
RWC-3
OsPIP1-3
 PLASMA MEMBRANE INTRINSIC PROTEIN 1;3 Aquaporin PIP 1.3
Aquaporin PIP 1-3
Plasma membrane intrinsic protein 1-3
Water channel protein RWC3
Aquaporin RWC3
 2 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Seed - Physiological traits - Dormancy
Tolerance and resistance - Disease resistance
 GO:0006950 - response to stress
GO:0042128 - nitrate assimilation
GO:0009409 - response to cold
GO:0009414 - response to water deprivation
GO:0042542 - response to hydrogen peroxide
GO:0006970 - response to osmotic stress
GO:0010036 - response to boron
GO:0046713 - boron transport
GO:0005215 - transporter activity
GO:0005886 - plasma membrane
GO:0006833 - water transport
GO:0009651 - response to salt stress
GO:0016020 - membrane
GO:0006810 - transport
GO:0042742 - defense response to bacterium
GO:0015250 - water channel activity
GO:0016021 - integral to membrane
GO:0055085 - transmembrane transport
GO:0009737 - response to abscisic acid stimulus
 TO:0000615 - abscisic acid sensitivity
TO:0000276 - drought tolerance
TO:0001027 - net photosynthetic rate
TO:0000357 - growth and development trait
TO:0000018 - boron sensitivity
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000442 - plant fresh weight
TO:0000175 - bacterial blight disease resistance
TO:0000457 - total biomass yield
TO:0000207 - plant height
TO:0000241 - leaf number
TO:0000352 - plant dry weight
TO:0000095 - osmotic response sensitivity
TO:0001017 - water use efficiency
 PO:0025034 - leaf
PO:0009005 - root
PO:0005059 - root endodermis
Os02g0823100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g57720.1
PIP2;2 OsPIP2;2
PIP2-2
OsPIP2-3
OsPIP2.1
PIP2.1
 PLASMA MEMBRANE INTRINSIC PROTEIN 2;2 Probable aquaporin PIP2-2
Plasma membrane intrinsic protein 2-2
 2 Tolerance and resistance - Disease resistance
Reproductive organ - Spikelet, flower, glume, awn
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0005215 - transporter activity
GO:0045089 - positive regulation of innate immune response
GO:0002237 - response to molecule of bacterial origin
GO:0006833 - water transport
GO:0005886 - plasma membrane
GO:0016021 - integral to membrane
GO:0043410 - positive regulation of MAPKKK cascade
GO:0050832 - defense response to fungus
GO:0006970 - response to osmotic stress
GO:0009409 - response to cold
GO:0009414 - response to water deprivation
GO:0007623 - circadian rhythm
GO:0042742 - defense response to bacterium
GO:0034021 - response to silicon dioxide
GO:0009737 - response to abscisic acid stimulus
GO:0009651 - response to salt stress
GO:0055085 - transmembrane transport
GO:0046686 - response to cadmium ion
GO:0042542 - response to hydrogen peroxide
GO:0030104 - water homeostasis
 TO:0000276 - drought tolerance
TO:0000074 - blast disease
TO:0002616 - flowering time
TO:0000615 - abscisic acid sensitivity
TO:0000203 - bacterial leaf streak disease resistance
TO:0006001 - salt tolerance
TO:0000175 - bacterial blight disease resistance
TO:0006002 - proline content
TO:0000303 - cold tolerance
TO:0000095 - osmotic response sensitivity
 PO:0007616 - flowering stage
PO:0025034 - leaf
Os02g0629200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g41860.2
LOC_Os02g41860.1
LOC_Os02g41860.4
LOC_Os02g41860.3
BT1-1 OsBT1-1
OsEnS-29
OsBT1
OsBt1
BT1
Bt1
OsBt1-1
shr3
OsBT1-2
BT1-2
 BRITTLE 1-1 Brittle-1-1
endosperm-specific gene 29
BRITTLE1
shrunken3
 2 Seed - Physiological traits - Dormancy
Seed - Physiological traits - Storage substances
Biochemical character
Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Endosperm
 GO:0009408 - response to heat
GO:0010431 - seed maturation
GO:0003735 - structural constituent of ribosome
GO:0006412 - translation
GO:0010581 - regulation of starch biosynthetic process
GO:0015711 - organic anion transport
GO:0005982 - starch metabolic process
GO:0055085 - transmembrane transport
GO:0033097 - amyloplast membrane
GO:0019252 - starch biosynthetic process
GO:0009660 - amyloplast organization
GO:0010162 - seed dormancy
GO:0005975 - carbohydrate metabolic process
GO:0016021 - integral to membrane
GO:0010021 - amylopectin biosynthetic process
GO:0022891 - substrate-specific transmembrane transporter activity
 TO:0000382 - 1000-seed weight
TO:0000259 - heat tolerance
TO:0000196 - amylose content
TO:0002658 - starch grain synthesis
TO:0000487 - endosperm color
TO:0000696 - starch content
TO:0000100 - shrunken endosperm
TO:0002661 - seed maturation
TO:0000253 - seed dormancy
 PO:0009089 - endosperm
PO:0007632 - seed maturation stage
Os02g0202400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g10800.3
LOC_Os02g10800.2
LOC_Os02g10800.1
SDR4 Sdr4
OsSdr4
OsSdr4-n
OsSdr4-k
OsSdr4L
Sdr4L
 SEED DORMANCY 4 Sdr4-like
 7 Character as QTL - Germination
Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
GO:0009738 - abscisic acid mediated signaling
GO:0048623 - seed germination on parent plant
GO:0010162 - seed dormancy
 TO:0000619 - vivipary
TO:0000615 - abscisic acid sensitivity
TO:0000253 - seed dormancy
 PO:0009010 - seed
Os07g0585700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g39700.1
MKK3 OsMKK3
OsMAPKK3
MAPKK3
OsMEK8a
MEK8a
OsMEK3
MEK3
 MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 MAPK kinase 3
 6 Tolerance and resistance - Insect resistance
Biochemical character
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
 GO:0005737 - cytoplasm
GO:0009733 - response to auxin stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0048623 - seed germination on parent plant
GO:0005634 - nucleus
GO:0042742 - defense response to bacterium
GO:0009787 - regulation of abscisic acid mediated signaling
GO:0042542 - response to hydrogen peroxide
GO:0009739 - response to gibberellin stimulus
GO:2000033 - regulation of seed dormancy
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0002213 - defense response to insect
 TO:0000424 - brown planthopper resistance
TO:0000253 - seed dormancy
TO:0000619 - vivipary
TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000163 - auxin sensitivity
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000175 - bacterial blight disease resistance
 PO:0009006 - shoot system
PO:0025034 - leaf
PO:0009049 - inflorescence
Os06g0473200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g27890.4
LOC_Os06g27890.3
LOC_Os06g27890.2
LOC_Os06g27890.1
FIE1 OsFIE1
OsWD40-154
OsEnS-116
OsFIE1/OsWD40-154
WD40-154
OsPcG6
PcG6
 FERTILIZATION-INDEPENDENT ENDOSPERM 1 FERTILIZATION-INDEPENDENT ENDOSPERM1
Fertilization-Independent Endosperm 1
dwarf and flower aberrant mutant
endosperm-specific gene 116
Polycomb group protein 6
 8 Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Physiological traits - Dormancy
Vegetative organ - Culm
Seed - Morphological traits
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Reproductive organ - Spikelet, flower, glume, awn
 GO:0010342 - cellularization of endosperm
GO:0010373 - negative regulation of gibberellin biosynthetic process
GO:0051782 - negative regulation of cell division
GO:0000003 - reproduction
GO:0009651 - response to salt stress
GO:0048598 - embryonic morphogenesis
GO:0010187 - negative regulation of seed germination
GO:0010380 - regulation of chlorophyll biosynthetic process
GO:0009409 - response to cold
GO:0043078 - polar nucleus
GO:0009960 - endosperm development
GO:0010162 - seed dormancy
GO:0019216 - regulation of lipid metabolic process
GO:0048316 - seed development
GO:0009790 - embryonic development
GO:0016571 - histone methylation
GO:0006349 - genetic imprinting
GO:0043470 - regulation of carbohydrate catabolic process
GO:0048623 - seed germination on parent plant
 TO:0002667 - abscisic acid content
TO:0002673 - amino acid content
TO:0000653 - seed development trait
TO:0002675 - gibberellic acid content
TO:0000391 - seed size
TO:0000291 - carbohydrate content
TO:0000107 - endosperm storage protein-1 content
TO:0002653 - endosperm storage protein content
TO:0006001 - salt tolerance
TO:0000455 - seed set percent
TO:0002680 - albumin content
TO:0000710 - globulin protein content
TO:0000465 - mineral and ion content related trait
TO:0000281 - metabolite content related trait
TO:0000604 - fat and essential oil content
TO:0000253 - seed dormancy
TO:0000619 - vivipary
TO:0000064 - embryo related trait
 PO:0007633 - endosperm development stage
PO:0020056 - tegmen
PO:0020090 - embryo sac central cell
PO:0009089 - endosperm
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
Os08g0137250 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g04290.1
WFP OsSPL14
SPL14
IPA1
WFP/IPA1
OsSPL14/WFP/IPA1
OsIPA1
IPA1/OsSPL14
 WEALTHY FARMER'S PANICLE IDEAL PLANT ARCHITECTURE 1
Ideal Plant Architecture 1
Ideal Plant Architecture1
Squamosa promoter-binding-like protein 14
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14
Squamosa promoter binding protein like-14
IDEAL PLANT ARCHITECTURE1
 8 Seed
Character as QTL - Yield and productivity
Vegetative organ - Culm
Vegetative organ - Leaf
Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Vegetative organ - Root
Character as QTL - Germination
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Reproductive organ - Panicle, Mode of branching
Seed - Physiological traits - Dormancy
Character as QTL - Plant growth activity
Tolerance and resistance - Disease resistance
 GO:0003677 - DNA binding
GO:0010187 - negative regulation of seed germination
GO:0009740 - gibberellic acid mediated signaling
GO:0005634 - nucleus
GO:0048366 - leaf development
GO:0010116 - positive regulation of abscisic acid biosynthetic process
GO:0045449 - regulation of transcription
GO:0009960 - endosperm development
GO:0048623 - seed germination on parent plant
GO:0010231 - maintenance of seed dormancy
GO:0009607 - response to biotic stimulus
GO:0006350 - transcription
GO:0008270 - zinc ion binding
GO:0048506 - regulation of timing of meristematic phase transition
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009651 - response to salt stress
GO:0010081 - regulation of inflorescence meristem growth
GO:0009755 - hormone-mediated signaling
GO:0010432 - bract development
GO:0005982 - starch metabolic process
GO:0009409 - response to cold
GO:0060359 - response to ammonium ion
GO:0009736 - cytokinin mediated signaling
GO:0050832 - defense response to fungus
GO:0009626 - plant-type hypersensitive response
GO:0010050 - vegetative phase change
GO:0010162 - seed dormancy
GO:0048316 - seed development
GO:0045487 - gibberellin catabolic process
GO:0042742 - defense response to bacterium
GO:0048364 - root development
GO:0010229 - inflorescence development
 TO:0002759 - grain number
TO:0006001 - salt tolerance
TO:0000340 - total soluble sugar content
TO:0002637 - leaf size
TO:0000653 - seed development trait
TO:0000621 - inflorescence development trait
TO:0002689 - leaf sheath length
TO:0002675 - gibberellic acid content
TO:0000017 - anatomy and morphology related trait
TO:0000396 - grain yield
TO:0000329 - tillering ability
TO:0000166 - gibberellic acid sensitivity
TO:0000586 - seminal root length
TO:0000050 - inflorescence branching
TO:0000346 - tiller number
TO:0002685 - crown root number
TO:0000011 - nitrogen sensitivity
TO:0000152 - panicle number
TO:0000455 - seed set percent
TO:0000357 - growth and development trait
TO:0000135 - leaf length
TO:0000619 - vivipary
TO:0000179 - biotic stress trait
TO:0000253 - seed dormancy
TO:0000227 - root length
TO:0000656 - root development trait
TO:0000266 - chalky endosperm
TO:0000162 - seed quality
TO:0000696 - starch content
TO:0002653 - endosperm storage protein content
TO:0000447 - filled grain number
TO:0000547 - primary branch number
TO:0000303 - cold tolerance
TO:0000222 - head rice
TO:0000104 - floury endosperm
TO:0000487 - endosperm color
TO:0000109 - endosperm storage protein-2 content
TO:0000175 - bacterial blight disease resistance
TO:0000107 - endosperm storage protein-1 content
TO:0000456 - spikelet number
TO:0000074 - blast disease
 PO:0001170 - seed development stage
PO:0025034 - leaf
PO:0025487 - bract primordium
PO:0007057 - 0 seed germination stage
PO:0001083 - inflorescence development stage
PO:0007520 - root development stage
Os08g0509600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g39890.1
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
GLUA3 Glua3*
GLUA-3
GT22
GT3
Glu21
GluA-3
OsEnS-47
EnS-47
GLU3
 GLUTELIN SUBFAMILY A3 FROM WILD RICE SPECIES Glutelin subfamily A3 from wild rice species
Glutelin type-A 3 precursor
Glutelin type-A 3
Glutelin type-A 3 acidic chain
Glutelin type-A 3 basic chain
Rice glutelin-21
glutelin-21
endosperm-specific gene 47
glutelin 3
 3 Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Seed - Physiological traits - Storage substances
 GO:0009845 - seed germination
GO:0009737 - response to abscisic acid stimulus
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0045735 - nutrient reservoir activity
GO:0009415 - response to water
GO:0009651 - response to salt stress
GO:0009791 - post-embryonic development
GO:0000003 - reproduction
GO:0048316 - seed development
 TO:0006001 - salt tolerance
TO:0000490 - protein composition related trait
TO:0000237 - water stress trait
TO:0000653 - seed development trait
TO:0000615 - abscisic acid sensitivity
 PO:0009010 - seed
PO:0001170 - seed development stage
PO:0007057 - 0 seed germination stage
PO:0007022 - seed imbibition stage
Os03g0427300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g31360.1
SDRA Sdra (Sd)
Sdra
Sdua
Sdr6
 SEED DORMANCY A Seed dormancy-a
Seed dormancy-6
 Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
 TO:0000253 - seed dormancy
 PO:0009010 - seed
-
SDRB Sdrb
Sdub
Sdr7
 SEED DORMANCY B Seed dormancy-b
Seed dormancy-7
 Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
 TO:0000253 - seed dormancy
 PO:0009010 - seed
-
SG Sg
 PERMEABILITY OF TESTA TO WATER Permeability of testa to water
 Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
 TO:0000253 - seed dormancy
 PO:0009010 - seed
-
WX1 wx (Wx(am))
Wx
WX-B
GBSS-I
GBSS
OsGBSSI
GBSS1
OsGBSS1
GBSSI
GSS
OsWx
 GLUTINOUS ENDOSPERM glutinous endosperm
waxy
Waxy
WAXY
"Granule-bound starch synthase 1
chloroplastic/amyloplastic"
Granule-bound starch synthase I
UDP-glycogen synthase
"Granule-bound starch synthase
chloroplast precursor"
glycogen [starch] synthase
Granule-bound glycogen synthase
UDPG-glycogen transglucosylase
uridine diphosphoglucose-glycogen glucosyltransferase
glycogen [starch] synthetase
Granule-bound glycogen [starch] synthase
UDPG-glycogen synthetase
granule bound starch synthase I
granule-bound starch synthase 1
granule-bound starch synthase I
 6 Seed - Physiological traits - Dormancy
Biochemical character
Character as QTL - Grain quality
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
 GO:0009501 - amyloplast
GO:0009408 - response to heat
GO:0019252 - starch biosynthetic process
GO:0009415 - response to water
GO:0009651 - response to salt stress
GO:0010229 - inflorescence development
GO:0009536 - plastid
GO:0009507 - chloroplast
GO:0005982 - starch metabolic process
GO:0009011 - starch synthase activity
GO:0009413 - response to flooding
GO:0048316 - seed development
GO:0009845 - seed germination
GO:0004373 - glycogen (starch) synthase activity
GO:0009568 - amyloplast starch grain
GO:0033840 - NDP-glucose-starch glucosyltransferase activity
 TO:0000653 - seed development trait
TO:0000211 - gel consistency
TO:0000396 - grain yield
TO:0002694 - fruit flavor trait
TO:0000382 - 1000-seed weight
TO:0000266 - chalky endosperm
TO:0000696 - starch content
TO:0000011 - nitrogen sensitivity
TO:0000259 - heat tolerance
TO:0000621 - inflorescence development trait
TO:0000286 - submergence sensitivity
TO:0006001 - salt tolerance
TO:0000237 - water stress trait
TO:0000162 - seed quality
TO:0000196 - amylose content
TO:0000098 - glutinous endosperm
 PO:0001170 - seed development stage
PO:0009010 - seed
PO:0007057 - 0 seed germination stage
PO:0007632 - seed maturation stage
PO:0001083 - inflorescence development stage
PO:0009089 - endosperm
PO:0007022 - seed imbibition stage
Os06g0133000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g04200.4
LOC_Os06g04200.3
LOC_Os06g04200.1
LOC_Os06g04200.2
image Id ( 6770 )
G1 g1 (lng)
lng
g1
ELE
Os ELE
OsG1
G1/ELE
LSL2
OsLSL2
 LONG STERILE LEMMAS 1 long sterile lemmas1
long sterile lemmas 1
long sterile lemmas-1
elongated empty glume
long sterile lemma/glume1
long sterile lemma 2
 7 Seed - Morphological traits - Grain shape
Seed - Physiological traits - Dormancy
Reproductive organ - Spikelet, flower, glume, awn
 GO:0006355 - regulation of transcription, DNA-dependent
GO:0048437 - floral organ development
GO:0009299 - mRNA transcription
GO:0009908 - flower development
GO:0003677 - DNA binding
GO:0005634 - nucleus
GO:0048449 - floral organ formation
GO:0010029 - regulation of seed germination
GO:0009416 - response to light stimulus
GO:0009909 - regulation of flower development
 TO:0000382 - 1000-seed weight
TO:0002726 - sterile lemma shape
TO:0000391 - seed size
TO:0000397 - grain size
TO:0000657 - spikelet anatomy and morphology trait
TO:0000430 - germination rate
TO:0000240 - sterile lemma length
TO:0000622 - flower development trait
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0020033 - glume length
TO:0002660 - cytokinin content
TO:0002675 - gibberellic acid content
TO:0002672 - auxin content
TO:0000557 - secondary branch number
 PO:0009037 - lemma
PO:0001083 - inflorescence development stage
PO:0001170 - seed development stage
PO:0009038 - palea
PO:0007615 - flower development stage
PO:0009039 - glume
PO:0009049 - inflorescence
PO:0001047 - lemma development stage
Os07g0139300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g04670.1
image Id ( 6778 )
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 )
RIV1 riv1*
 RICE VIVIPARY 1 rice vivipary-1
 Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
 -
RIV2 riv2*
 RICE VIVIPARY 2 rice vivipary-2
 Seed - Physiological traits - Dormancy
 GO:0009845 - seed germination
 -
qSD-4-1(t) (qSD4) qSD-4-1(t) (qSD4)
 seed dormancy (QTL)-4-1(t) seed dormancy (QTL)-4-1(t)
 4 Seed - Physiological traits - Dormancy
 -
qSD-7-2(t) (qSD7-1) qSD-7-2(t) (qSD7-1)
 seed dormancy (QTL)-7-2(t) seed dormancy (QTL)-7-2(t)
 7 Seed - Physiological traits - Dormancy
 -
qSD-7-3(t) (qSD7-2) qSD-7-3(t) (qSD7-2)
 seed dormancy (QTL)-7-3(t) seed dormancy (QTL)-7-3(t)
 7 Seed - Physiological traits - Dormancy
 -
qSD-8-1(t) (qSD8) qSD-8-1(t) (qSD8)
 seed dormancy (QTL)-8-1(t) seed dormancy (QTL)-8-1(t)
 8 Seed - Physiological traits - Dormancy
 -
qSD-12-1(t) (qSD12) qSD-12-1(t) (qSD12)
 seed dormancy (QTL)-12-1(t) seed dormancy (QTL)-12-1(t)
 12 Seed - Physiological traits - Dormancy
 -
EXPB3 OsEXPB3
osaEXPb1.10
EXPb1.10
 BETA-EXPANSIN 3 Expansin-B3
Beta-expansin-3
 10 Vegetative organ - Culm
Biochemical character
Seed - Physiological traits - Dormancy
 GO:0005576 - extracellular region
GO:0007047 - cell wall organization
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0019898 - extrinsic to membrane
GO:0019953 - sexual reproduction
GO:0005618 - cell wall
 TO:0000207 - plant height
 Os10g0555900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g40720.1
OSK1 osk1
SnRK1A
OsSnRK1A
OsSNRK1a
SnRK1A/OSK1
SnRK1a
OsSnRK1.2
SnRK1.2
OsSnRK1alphaA
SnRK1alphaA
 PROTEIN KINASE 1 protein kinase 1
SnRK1A protein kinase
sucrose non-fermenting-1 related protein kinase 1a
SNF1-Related Protein Kinase 1A
 5 Character as QTL - Germination
Seed - Physiological traits - Dormancy
Tolerance and resistance - Disease resistance
Character as QTL - Plant growth activity
Seed
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
Reproductive organ - Pollination, fertilization, fertility
Vegetative organ - Root
Vegetative organ - Culm
 GO:0009409 - response to cold
GO:0017148 - negative regulation of translation
GO:0022414 - reproductive process
GO:0042594 - response to starvation
GO:0005524 - ATP binding
GO:0009845 - seed germination
GO:0010030 - positive regulation of seed germination
GO:0007165 - signal transduction
GO:0009863 - salicylic acid mediated signaling pathway
GO:0050832 - defense response to fungus
GO:0009607 - response to biotic stimulus
GO:0002679 - respiratory burst during defense response
GO:0002253 - activation of immune response
GO:0009646 - response to absence of light
GO:0033500 - carbohydrate homeostasis
GO:0010336 - gibberellic acid homeostasis
GO:0009737 - response to abscisic acid stimulus
GO:0009628 - response to abiotic stimulus
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009743 - response to carbohydrate stimulus
GO:0005634 - nucleus
GO:0042742 - defense response to bacterium
GO:0080094 - response to trehalose-6-phosphate stimulus
GO:0080141 - regulation of jasmonic acid biosynthetic process
GO:0045926 - negative regulation of growth
GO:0052544 - callose deposition in cell wall during defense response
GO:0051093 - negative regulation of developmental process
GO:0043617 - cellular response to sucrose starvation
GO:0005737 - cytoplasm
GO:0031667 - response to nutrient levels
GO:0002238 - response to molecule of fungal origin
GO:0006468 - protein amino acid phosphorylation
GO:0008643 - carbohydrate transport
GO:0009651 - response to salt stress
GO:0007623 - circadian rhythm
GO:0009685 - gibberellin metabolic process
GO:0004674 - protein serine/threonine kinase activity
GO:2000028 - regulation of photoperiodism, flowering
GO:0051511 - negative regulation of unidimensional cell growth
GO:0010200 - response to chitin
GO:0010182 - sugar mediated signaling
GO:0010431 - seed maturation
GO:0048316 - seed development
 TO:0000456 - spikelet number
TO:0001015 - photosynthetic rate
TO:0006003 - oligosaccharide content
TO:0000291 - carbohydrate content
TO:0000328 - sucrose content
TO:0000397 - grain size
TO:0000001 - carbon sensitivity
TO:0000371 - yield trait
TO:0000653 - seed development trait
TO:0000457 - total biomass yield
TO:0000396 - grain yield
TO:0000227 - root length
TO:0000137 - days to heading
TO:0000571 - shoot fresh weight
TO:0000552 - shoot dry weight
TO:0000168 - abiotic stress trait
TO:0000280 - seedling vigor
TO:0000420 - fertility related trait
TO:0000455 - seed set percent
TO:0000357 - growth and development trait
TO:0000576 - stem length
TO:0000179 - biotic stress trait
TO:0000460 - light intensity sensitivity
TO:0002664 - leaf yellowing tolerance
TO:0002668 - jasmonic acid content
TO:0000636 - relative shoot dry weight
TO:0000327 - biomass yield
TO:0000480 - nutrient sensitivity
TO:0000356 - brown spot disease resistance
TO:0002675 - gibberellic acid content
TO:0000145 - internode length
TO:0000253 - seed dormancy
TO:0000153 - relative yield
TO:0006001 - salt tolerance
TO:0000430 - germination rate
TO:0002661 - seed maturation
TO:0000074 - blast disease
TO:0000207 - plant height
TO:0000346 - tiller number
TO:0000447 - filled grain number
TO:0002616 - flowering time
TO:0000366 - reproductive growth time
TO:0000255 - sheath blight disease resistance
TO:0000175 - bacterial blight disease resistance
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
 PO:0005052 - plant callus
PO:0009049 - inflorescence
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
PO:0025034 - leaf
PO:0025082 - reproductive shoot system
Os05g0530500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g45420.1
LOC_Os05g45420.3
LOC_Os05g45420.2
TIL1 NAC2
OsNAC2
ONAC004
ONAC4
ONAC034
ONAC34
ONAC058
ONAC58
OMTN2
Ostil1
OsNAC2/ONAC004
OsORE1.2
DLN113
OsDLN113
 TILLERING 1 NAC domain-containing protein 004
NAC domain-containing protein 4
NAC domain-containing protein 34
NAC domain-containing protein 58
miR164-targeted NAC2
Oryza miR164-targeted NAC2
Oryza sativa tillering1
ORESARA 1.2
DLN repressor 113
DLN motif protein 113
 4 Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Character as QTL - Germination
Vegetative organ - Leaf
Seed - Physiological traits - Dormancy
Other
Reproductive organ - Heading date
Vegetative organ - Root
Vegetative organ - Culm
 GO:0080036 - regulation of cytokinin mediated signaling
GO:0006979 - response to oxidative stress
GO:0080142 - regulation of salicylic acid biosynthetic process
GO:0010446 - response to alkalinity
GO:0042742 - defense response to bacterium
GO:0009738 - abscisic acid mediated signaling
GO:0006970 - response to osmotic stress
GO:0009735 - response to cytokinin stimulus
GO:0010150 - leaf senescence
GO:0010730 - negative regulation of hydrogen peroxide biosynthetic process
GO:0009651 - response to salt stress
GO:0003677 - DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0048573 - photoperiodism, flowering
GO:0009740 - gibberellic acid mediated signaling
GO:0009863 - salicylic acid mediated signaling pathway
GO:0009414 - response to water deprivation
GO:0048364 - root development
GO:0006350 - transcription
GO:0009737 - response to abscisic acid stimulus
GO:0005634 - nucleus
GO:0010942 - positive regulation of cell death
GO:0006309 - DNA fragmentation involved in apoptosis
GO:0009733 - response to auxin stimulus
GO:0010928 - regulation of auxin mediated signaling pathway
GO:0050777 - negative regulation of immune response
GO:0009788 - negative regulation of abscisic acid mediated signaling
GO:0009723 - response to ethylene stimulus
GO:0009751 - response to salicylic acid stimulus
GO:0045449 - regulation of transcription
GO:0010365 - positive regulation of ethylene biosynthetic process
GO:0010187 - negative regulation of seed germination
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0010029 - regulation of seed germination
 TO:0000656 - root development trait
TO:0000396 - grain yield
TO:0002759 - grain number
TO:0000040 - panicle length
TO:0000430 - germination rate
TO:0001016 - relative chlorophyll content
TO:0000136 - relative water content
TO:0002657 - oxidative stress
TO:0000481 - alkali sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000276 - drought tolerance
TO:0000207 - plant height
TO:0002639 - shoot branching
TO:0000249 - leaf senescence
TO:0000450 - grain yield per panicle
TO:0000017 - anatomy and morphology related trait
TO:0000567 - tiller angle
TO:0000227 - root length
TO:0002685 - crown root number
TO:0002660 - cytokinin content
TO:0000167 - cytokinin sensitivity
TO:0000163 - auxin sensitivity
TO:0000095 - osmotic response sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000346 - tiller number
TO:0000145 - internode length
TO:0000166 - gibberellic acid sensitivity
TO:0002667 - abscisic acid content
TO:0000615 - abscisic acid sensitivity
TO:0000173 - ethylene sensitivity
TO:0006001 - salt tolerance
TO:0002616 - flowering time
TO:0002768 - spikelet length
 PO:0000025 - root tip
PO:0001054 - 4 leaf senescence stage
PO:0000043 - crown root
PO:0005029 - root primordium
PO:0020121 - lateral root
PO:0007057 - 0 seed germination stage
PO:0007045 - coleoptile emergence stage
Os04g0460600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g38720.1
SNG OsTubA1
TubA1
OS-TubA3
TubA3
OsTUBA3
OsSNG
 SMALL AND NOTCHED GRAIN Tubulin alpha-1 chain
Tubulin alpha-1
Small and notched grain
 7 Seed - Physiological traits - Dormancy
Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Grain quality
 GO:0009266 - response to temperature stimulus
GO:0009845 - seed germination
GO:0016049 - cell growth
GO:0010229 - inflorescence development
GO:0048316 - seed development
GO:0007020 - microtubule nucleation
GO:0003924 - GTPase activity
GO:0005198 - structural molecule activity
GO:0007018 - microtubule-based movement
GO:0046688 - response to copper ion
GO:0005200 - structural constituent of cytoskeleton
GO:0007017 - microtubule-based process
GO:0005737 - cytoplasm
GO:0035265 - organ growth
GO:0005874 - microtubule
GO:0005525 - GTP binding
GO:0000226 - microtubule cytoskeleton organization
GO:0046785 - microtubule polymerization
GO:0001558 - regulation of cell growth
GO:0051258 - protein polymerization
 TO:0000447 - filled grain number
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0002730 - grain shape
TO:0000653 - seed development trait
TO:0000432 - temperature response trait
TO:0000021 - copper sensitivity
TO:0000621 - inflorescence development trait
TO:0000734 - grain length
TO:0000399 - grain thickness
TO:0000547 - primary branch number
TO:0000402 - grain width
TO:0000207 - plant height
TO:0000382 - 1000-seed weight
TO:0000266 - chalky endosperm
TO:0000222 - head rice
TO:0020033 - glume length
 PO:0025034 - leaf
PO:0001170 - seed development stage
PO:0009082 - spikelet floret
PO:0007057 - 0 seed germination stage
PO:0009010 - seed
PO:0001083 - inflorescence development stage
PO:0009047 - stem
Os07g0574800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g38730.1
MAPK4 OsMAPK4
OsMAP2
OsMSRMK3
OsMPK4
OsMPK7
MAP2
MSRMK3
MPK4
MPK7
MAPK7
OsMAPK7
 MITOGEN-ACTIVATED PROTEIN KINASE 4 Mitogen-activated protein kinase 4
MAP kinase 4
Multiple stress-responsive MAP kinase 3
 6 Tolerance and resistance - Disease resistance
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0009409 - response to cold
GO:0009411 - response to UV
GO:0009737 - response to abscisic acid stimulus
GO:0009787 - regulation of abscisic acid mediated signaling
GO:0005634 - nucleus
GO:0042742 - defense response to bacterium
GO:0042542 - response to hydrogen peroxide
GO:0005737 - cytoplasm
GO:0009723 - response to ethylene stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009751 - response to salicylic acid stimulus
GO:0009611 - response to wounding
GO:0009814 - defense response, incompatible interaction
GO:0002213 - defense response to insect
GO:2000033 - regulation of seed dormancy
GO:0009739 - response to gibberellin stimulus
GO:0005524 - ATP binding
GO:0006468 - protein amino acid phosphorylation
GO:0006950 - response to stress
GO:0004707 - MAP kinase activity
 TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000160 - UV light sensitivity
TO:0000424 - brown planthopper resistance
TO:0000175 - bacterial blight disease resistance
TO:0000172 - jasmonic acid sensitivity
TO:0000173 - ethylene sensitivity
TO:0000253 - seed dormancy
TO:0000303 - cold tolerance
 PO:0009049 - inflorescence
PO:0009006 - shoot system
Os06g0699400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g48590.2
LOC_Os06g48590.1
AMY3D Amy3D/E*(RAmy3D/E)
alpha Amy3
AmyII-4
AMY1.3
Amy3D
Amy3D/E*
RAmy3D/E
Amy3D_E
Amy8
aAmy3
RAmy3D
OsAmy3D
alphaAmy3
OsRamy3D
 ALPHA-AMYLASE 3D Alpha-amylase3D
Alpha-amylase isozyme 3D precursor
Alpha-amylase isozyme 3D
Alpha-amylase-3D
Amylase-8
 8 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Character as QTL - Grain quality
Seed - Physiological traits - Dormancy
 GO:0001666 - response to hypoxia
GO:0009409 - response to cold
GO:0010182 - sugar mediated signaling
GO:0004556 - alpha-amylase activity
GO:0005509 - calcium ion binding
GO:0005983 - starch catabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0009413 - response to flooding
GO:0033500 - carbohydrate homeostasis
GO:0045927 - positive regulation of growth
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0009873 - ethylene mediated signaling pathway
GO:0009723 - response to ethylene stimulus
GO:0009408 - response to heat
GO:0005987 - sucrose catabolic process
 TO:0000280 - seedling vigor
TO:0000449 - grain yield per plant
TO:0000015 - oxygen sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000266 - chalky endosperm
TO:0000259 - heat tolerance
TO:0000303 - cold tolerance
TO:0000173 - ethylene sensitivity
TO:0000253 - seed dormancy
TO:0000168 - abiotic stress trait
TO:0000432 - temperature response trait
TO:0000114 - flooding related trait
 PO:0009010 - seed
PO:0001170 - seed development stage
Os08g0473900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g36910.3
LOC_Os08g36910.2
LOC_Os08g36910.1
AMY3E Amy3D/E*(RAmy3D/E)
alpha Amy8
alphaAmy8
AmyII-3
AMY1.4
Amy3E
Amy3D/E*
RAmy3D/E
Amy9
RAmy3E
alphaAmy8-C
AMY3E/AMY1.4
OsAmy3E
OsRamy3E
RAmy3E
 ALPHA-AMYLASE 3E Alpha-amylase3E
Alpha-amylase isozyme 3E precursor
Alpha-amylase isozyme 3E
Alpha-amylase-3E
Amylase-9
Alpha-amylase-3D
 8 Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Longevity
Character as QTL - Grain quality
Vegetative organ - Culm
Biochemical character
Character as QTL - Germination
 GO:0009737 - response to abscisic acid stimulus
GO:0005987 - sucrose catabolic process
GO:0010182 - sugar mediated signaling
GO:0010212 - response to ionizing radiation
GO:0009651 - response to salt stress
GO:0001666 - response to hypoxia
GO:0009270 - response to humidity
GO:0009408 - response to heat
GO:0009739 - response to gibberellin stimulus
GO:0009409 - response to cold
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0051775 - response to redox state
GO:0080006 - internode patterning
GO:0004556 - alpha-amylase activity
GO:0005509 - calcium ion binding
GO:0005975 - carbohydrate metabolic process
GO:0009845 - seed germination
GO:0005983 - starch catabolic process
 TO:0000161 - radiation response trait
TO:0000166 - gibberellic acid sensitivity
TO:0000259 - heat tolerance
TO:0000266 - chalky endosperm
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000441 - humidity related trait
TO:0006001 - salt tolerance
TO:0000435 - seed longevity
TO:0000250 - vigor related trait
TO:0000345 - seed viability
TO:0000015 - oxygen sensitivity
TO:0010001 - percent germination
TO:0000544 - mesocotyl length
 PO:0007057 - 0 seed germination stage
PO:0001170 - seed development stage
PO:0009010 - seed
Os08g0473600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g36900.1
LOC_Os08g36900.2
PHS8 ISA1
OsISA1
ISA
OsISA
PHS8/ISA1
OsPHS8
ISA I
OsISA I
ISAI
OsISAI
 PRE-HARVEST SPROUTING 8 isoamylase 1
isoamylase1
sugary-1
pre-harvest sprouting 8
 8 Biochemical character
Seed - Morphological traits - Endosperm
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Grain shape
 GO:0019156 - isoamylase activity
GO:0009269 - response to desiccation
GO:0009737 - response to abscisic acid stimulus
GO:0009738 - abscisic acid mediated signaling
GO:0005980 - glycogen catabolic process
GO:0010581 - regulation of starch biosynthetic process
GO:0009960 - endosperm development
GO:0019252 - starch biosynthetic process
GO:0010021 - amylopectin biosynthetic process
GO:0010029 - regulation of seed germination
GO:0010231 - maintenance of seed dormancy
GO:0048623 - seed germination on parent plant
GO:0043169 - cation binding
 TO:0000394 - drought related trait
TO:0000099 - sugary endosperm
TO:0002658 - starch grain synthesis
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0000615 - abscisic acid sensitivity
TO:0000011 - nitrogen sensitivity
 PO:0007633 - endosperm development stage
PO:0007632 - seed maturation stage
Os08g0520900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g40930.1
LCG1 SLRL2
OsSLRL2
OsGRAS-30
OsGRAS30
GRAS-30
GRAS30
OsLCG1
 LESS CHALK GRAIN 1 SLR1-like2
GRAS protein 30
SLENDER RICE LIKE 2
Less Chalk Grain1
 5 Character as QTL - Germination
Seed - Physiological traits - Dormancy
Tolerance and resistance - Disease resistance
Vegetative organ - Leaf
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Physiological traits - Taste
Vegetative organ - Culm
Other
 GO:0010162 - seed dormancy
GO:0009740 - gibberellic acid mediated signaling
GO:0006350 - transcription
GO:0009738 - abscisic acid mediated signaling
GO:0010029 - regulation of seed germination
GO:0046890 - regulation of lipid biosynthetic process
GO:0010581 - regulation of starch biosynthetic process
GO:0032885 - regulation of polysaccharide biosynthetic process
GO:0016020 - membrane
GO:0045449 - regulation of transcription
GO:0009737 - response to abscisic acid stimulus
GO:0010468 - regulation of gene expression
GO:0005634 - nucleus
GO:0003677 - DNA binding
GO:0048623 - seed germination on parent plant
GO:0050832 - defense response to fungus
 TO:0000162 - seed quality
TO:0002653 - endosperm storage protein content
TO:0000615 - abscisic acid sensitivity
TO:0002694 - fruit flavor trait
TO:0000074 - blast disease
TO:0000097 - amylopectin content
TO:0002758 - flag leaf lamina width
TO:0000196 - amylose content
TO:0000207 - plant height
TO:0000211 - gel consistency
TO:0000412 - setback viscosity
TO:0000696 - starch content
TO:0000266 - chalky endosperm
TO:0000253 - seed dormancy
TO:0000409 - peak viscosity
TO:0000619 - vivipary
TO:0002656 - starch grain shape
TO:0002658 - starch grain synthesis
TO:0000374 - breakdown viscosity
TO:0000557 - secondary branch number
TO:0000604 - fat and essential oil content
 PO:0009010 - seed
PO:0001170 - seed development stage
PO:0009084 - pericarp
Os05g0574900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g49930.1
ABA8OX1 OsABA8OX1
CYP707A5
OsCYP707A5
ABA8ox1
OsABA8ox1
OsABA8'OH1
ABA8'OH1
 ABA-8'-HYDROXYLASE 1 Abscisic acid 8'-hydroxylase 1
ABA 8'-hydroxylase 1 ; Cytochrome P450 707A5
ABA 8'-hydroxylase1
 2 Biochemical character
Character as QTL - Germination
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
 GO:0010167 - response to nitrate
GO:0009651 - response to salt stress
GO:0007263 - nitric oxide mediated signal transduction
GO:0009414 - response to water deprivation
GO:0046345 - abscisic acid catabolic process
GO:0055114 - oxidation reduction
GO:0032940 - secretion by cell
GO:0005783 - endoplasmic reticulum
GO:0009055 - electron carrier activity
GO:0010295 - (+)-abscisic acid 8'-hydroxylase activity
GO:0016021 - integral to membrane
GO:0030912 - response to deep water
GO:0020037 - heme binding
GO:0009409 - response to cold
GO:0006950 - response to stress
GO:0009737 - response to abscisic acid stimulus
GO:0016491 - oxidoreductase activity
GO:0022900 - electron transport chain
GO:0042742 - defense response to bacterium
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0010029 - regulation of seed germination
GO:0009413 - response to flooding
 TO:0000478 - abscisic acid concentration
TO:0000276 - drought tolerance
TO:0000175 - bacterial blight disease resistance
TO:0000259 - heat tolerance
TO:0002667 - abscisic acid content
TO:0000524 - submergence tolerance
TO:0000103 - deepwater stress
TO:0000430 - germination rate
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000286 - submergence sensitivity
TO:0006001 - salt tolerance
 PO:0007045 - coleoptile emergence stage
PO:0009006 - shoot system
PO:0007057 - 0 seed germination stage
Os02g0703600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g47470.3
LOC_Os02g47470.2
LOC_Os02g47470.1
ABA8OX2 OsABA8OX2
OsABA8ox2
CYP707A6
OsCYP707A6
OsAba-ox2
OsABA8ox2
OsABA8OH2
ABA8OH2
ABA8'-OH2
OsABA8'ox2
ABA8'ox2
OsABAX2
ABAX2
OsABA8'OH2
ABA8'OH2
 ABA-8'-HYDROXYLASE 2 Abscisic acid 8'-hydroxylase 2
ABA 8'-hydroxylase 2
Cytochrome P450 707A6
 8 Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Dormancy
Character as QTL - Germination
 GO:0046345 - abscisic acid catabolic process
GO:0009414 - response to water deprivation
GO:0009609 - response to symbiotic bacterium
GO:0010295 - (+)-abscisic acid 8'-hydroxylase activity
GO:0016021 - integral to membrane
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0020037 - heme binding
GO:0055114 - oxidation reduction
GO:0009055 - electron carrier activity
GO:0009415 - response to water
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0009739 - response to gibberellin stimulus
 TO:0000259 - heat tolerance
TO:0000031 - silicon sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000276 - drought tolerance
TO:0000237 - water stress trait
 PO:0007057 - 0 seed germination stage
Os08g0472800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g36860.1
ABA8OX3 OsABA8OX3
OsABA8ox3
CYP707A7
OsCYP707A7
OsAba-ox3
OsABA8ox3
OsABA8'ox3
ABA8'ox3
OsABAX3
ABAX3
OsABA8'OH3
ABA8'OH3
 ABA-8'-HYDROXYLASE 3 Abscisic acid 8'-hydroxylase 3
ABA 8'-hydroxylase 3
Cytochrome P450 707A7
 9 Character as QTL - Germination
Tolerance and resistance - Disease resistance
Biochemical character
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
 GO:0010353 - response to trehalose stimulus
GO:0010231 - maintenance of seed dormancy
GO:0010162 - seed dormancy
GO:0009413 - response to flooding
GO:0009055 - electron carrier activity
GO:0010295 - (+)-abscisic acid 8'-hydroxylase activity
GO:0009845 - seed germination
GO:0009414 - response to water deprivation
GO:0016021 - integral to membrane
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0020037 - heme binding
GO:0046345 - abscisic acid catabolic process
GO:0055114 - oxidation reduction
GO:0051607 - defense response to virus
GO:0009408 - response to heat
GO:0060359 - response to ammonium ion
GO:0048364 - root development
 TO:0000656 - root development trait
TO:0000276 - drought tolerance
TO:0002667 - abscisic acid content
TO:0000148 - viral disease resistance
TO:0000578 - root fresh weight
TO:0000524 - submergence tolerance
TO:0000020 - black streak dwarf virus resistance
TO:0000253 - seed dormancy
TO:0000516 - relative root length
TO:0000259 - heat tolerance
 PO:0007057 - 0 seed germination stage
PO:0007520 - root development stage
PO:0007022 - seed imbibition stage
Os09g0457100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g28390.1
NCED2 OSNCED2
OsNCED2
OsNCED5
NCED5
 9-CIS-EPOXYCAROTENOID DIOXYGENASE 2 9-cis-epoxycarotenoid dioxygenase 2
 12 Character as QTL - Germination
Seed - Physiological traits - Dormancy
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0009507 - chloroplast
GO:0009753 - response to jasmonic acid stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
GO:0009413 - response to flooding
GO:0045549 - 9-cis-epoxycarotenoid dioxygenase activity
GO:0001666 - response to hypoxia
GO:0009409 - response to cold
GO:0009845 - seed germination
GO:0009688 - abscisic acid biosynthetic process
GO:0016702 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
 TO:0000615 - abscisic acid sensitivity
TO:0000015 - oxygen sensitivity
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000172 - jasmonic acid sensitivity
TO:0000114 - flooding related trait
TO:0002667 - abscisic acid content
 PO:0007616 - flowering stage
PO:0009010 - seed
PO:0007057 - 0 seed germination stage
Os12g0617400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g42280.1
NCED3 OSNCED3
OsNCED-3
OsNCED3
OsNCED3a
NCED3a
OsNCED4
NCED4
OsNECD2
OsNCED2b
NCED2b
 9-CIS-EPOXYCAROTENOID DIOXYGENASE 3 9-cis-epoxycarotenoid dioxygenase 3
 7 Vegetative organ - Culm
Vegetative organ - Leaf
Biochemical character
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Seed - Physiological traits - Dormancy
Character as QTL - Germination
 GO:0051707 - response to other organism
GO:0009409 - response to cold
GO:0009414 - response to water deprivation
GO:0009413 - response to flooding
GO:0009507 - chloroplast
GO:0009749 - response to glucose stimulus
GO:0009688 - abscisic acid biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0042742 - defense response to bacterium
GO:0009651 - response to salt stress
GO:0009753 - response to jasmonic acid stimulus
GO:0010029 - regulation of seed germination
GO:0001666 - response to hypoxia
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0045549 - 9-cis-epoxycarotenoid dioxygenase activity
 TO:0000172 - jasmonic acid sensitivity
TO:0006001 - salt tolerance
TO:0000492 - leaf shape
TO:0000175 - bacterial blight disease resistance
TO:0000207 - plant height
TO:0000276 - drought tolerance
TO:0000615 - abscisic acid sensitivity
TO:0002667 - abscisic acid content
TO:0000015 - oxygen sensitivity
TO:0000259 - heat tolerance
TO:0000114 - flooding related trait
TO:0000303 - cold tolerance
 PO:0009010 - seed
PO:0008037 - seedling
PO:0009006 - shoot system
PO:0007022 - seed imbibition stage
PO:0007616 - flowering stage
PO:0007057 - 0 seed germination stage
PO:0007632 - seed maturation stage
Os07g0154100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g05940.1
MATE19 OsMATE19
 MULTIDRUG AND TOXIC COMPOUND EXTRUSION 19 multidrug and toxic compound extrusion 19
multi-antimicrobial extrusion protein 19
 4 Biochemical character
Seed - Physiological traits - Dormancy
 GO:0042910 - xenobiotic transporter activity
GO:0022857 - transmembrane transporter activity
GO:0015297 - antiporter activity
GO:0010162 - seed dormancy
GO:0016020 - membrane
 TO:0000253 - seed dormancy
 Os04g0571600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 )
ERF29 OsERF#029
OsERF029
OsERF29
DERF4
OsDERF4
AP2/EREBP#161
AP2/EREBP161
OsDREB1I
DREB1I
OsDREB1G
DREB1G
 ETHYLENE RESPONSE FACTOR 29 drought-responsive ethylene response factor 4
drought-responsive ERF 4
ethylene response factor 29
APETALA2/ethylene-responsive element binding protein 161
Dehydration-responsive element-binding protein 1I
 8 Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
 GO:0005634 - nucleus
GO:0003677 - DNA binding
GO:0006950 - response to stress
GO:0009845 - seed germination
GO:0009414 - response to water deprivation
GO:0003700 - transcription factor activity
GO:0006351 - transcription, DNA-dependent
 TO:0000276 - drought tolerance
 PO:0007022 - seed imbibition stage
Os08g0545500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g43210.1
ACO4 OsACO4
 AMINOCYCLOPROPANE-1-CARBOXYLIC ACID OXIDASE 4 ACC oxidase 4
1-Aminocyclopropane-1-carboxylate oxidase 4
 11 Biochemical character
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
 GO:0010446 - response to alkalinity
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:0009753 - response to jasmonic acid stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0010162 - seed dormancy
GO:0009693 - ethylene biosynthetic process
 TO:0000172 - jasmonic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000253 - seed dormancy
TO:0000481 - alkali sensitivity
 PO:0009089 - endosperm
PO:0009005 - root
PO:0009009 - plant embryo
Os11g0186900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g08380.1
GA2OX6 OsGA2ox6
 GIBBERELLIN 2-OXIDASE 6 GA 2-oxidase 6
 4 Character as QTL - Germination
Biochemical character
Vegetative organ - Culm
Seed - Physiological traits - Dormancy
Tolerance and resistance - Stress tolerance
 GO:0010162 - seed dormancy
GO:0045487 - gibberellin catabolic process
GO:0009739 - response to gibberellin stimulus
GO:0048623 - seed germination on parent plant
GO:0010231 - maintenance of seed dormancy
GO:0009685 - gibberellin metabolic process
GO:0009409 - response to cold
GO:0009651 - response to salt stress
 TO:0000253 - seed dormancy
TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
TO:0000619 - vivipary
TO:0000145 - internode length
TO:0000166 - gibberellic acid sensitivity
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
 PO:0020141 - stem node
PO:0008039 - stem base
PO:0009066 - anther
PO:0009051 - spikelet
Os04g0522500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g44150.1
GA2OX8 OsGA2ox8
 GIBBERELLIN 2-OXIDASE 8 gibberellin 2-beta-dioxygenase 8
 5 Biochemical character
Seed - Physiological traits - Dormancy
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
 GO:0005634 - nucleus
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0009409 - response to cold
GO:0009737 - response to abscisic acid stimulus
GO:0006979 - response to oxidative stress
GO:0031540 - regulation of anthocyanin biosynthetic process
GO:0080141 - regulation of jasmonic acid biosynthetic process
GO:0009962 - regulation of flavonoid biosynthetic process
GO:0005737 - cytoplasm
GO:0009733 - response to auxin stimulus
GO:0006970 - response to osmotic stress
GO:0009685 - gibberellin metabolic process
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0016020 - membrane
GO:0009739 - response to gibberellin stimulus
GO:0034059 - response to anoxia
GO:0010336 - gibberellic acid homeostasis
GO:0009845 - seed germination
GO:0045487 - gibberellin catabolic process
GO:0048364 - root development
GO:0009753 - response to jasmonic acid stimulus
GO:0009651 - response to salt stress
 TO:0000227 - root length
TO:0000303 - cold tolerance
TO:0000340 - total soluble sugar content
TO:0000329 - tillering ability
TO:0002657 - oxidative stress
TO:0000011 - nitrogen sensitivity
TO:0000207 - plant height
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000095 - osmotic response sensitivity
TO:0000163 - auxin sensitivity
TO:0000152 - panicle number
TO:0002675 - gibberellic acid content
TO:0000656 - root development trait
TO:0000172 - jasmonic acid sensitivity
TO:0000576 - stem length
TO:0000396 - grain yield
 PO:0007057 - 0 seed germination stage
PO:0007520 - root development stage
PO:0009006 - shoot system
PO:0009005 - root
Os05g0560900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g48700.1
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/rice/oryzabase