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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
CIPK01 OsCIPK01
CIPK1
OsCIPK1
OsSnRK3.3
SnRK3.3
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 1 CBL-interacting protein kinase 1
Sucrose nonfermenting-1-related protein kinase 3.3
 1 Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Biochemical character
Character as QTL - Yield and productivity
 GO:0009409 - response to cold
GO:0004674 - protein serine/threonine kinase activity
GO:0005524 - ATP binding
GO:0004713 - protein tyrosine kinase activity
GO:0030307 - positive regulation of cell growth
GO:0009740 - gibberellic acid mediated signaling
GO:0009413 - response to flooding
GO:0009651 - response to salt stress
GO:0030145 - manganese ion binding
GO:0006468 - protein amino acid phosphorylation
GO:0007165 - signal transduction
GO:0009414 - response to water deprivation
 TO:0000303 - cold tolerance
TO:0000382 - 1000-seed weight
TO:0000432 - temperature response trait
TO:0020033 - glume length
TO:0020034 - glume width
TO:0000734 - grain length
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000396 - grain yield
TO:0000391 - seed size
TO:0000397 - grain size
TO:0000590 - grain weight
TO:0000114 - flooding related trait
 PO:0025034 - leaf
Os01g0292200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g18800.3
LOC_Os01g18800.4
LOC_Os01g18800.1
LOC_Os01g18800.2
LOC_Os01g18800.5
MADS51 OsMADS51
OsMADS65
MADS65
qHd1
DLN36
OsDLN36
 MADS BOX GENE 51 MADS box gene51
DLN repressor 36
DLN motif protein 36
 1 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Seed - Morphological traits
Character as QTL - Plant growth activity
Other
Tolerance and resistance - Disease resistance
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009408 - response to heat
GO:0050832 - defense response to fungus
GO:0009409 - response to cold
GO:0043565 - sequence-specific DNA binding
 TO:0000396 - grain yield
TO:0000259 - heat tolerance
TO:0000432 - temperature response trait
TO:0000137 - days to heading
TO:0002616 - flowering time
TO:0000449 - grain yield per plant
TO:0000152 - panicle number
TO:0000455 - seed set percent
TO:0000329 - tillering ability
TO:0000357 - growth and development trait
TO:0000074 - blast disease
TO:0000590 - grain weight
TO:0000303 - cold tolerance
 Os01g0922800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g69850.1
YUCCA4 OsYUCCA4
OsYUC4
YUC4
YUCCA6
OsYUCCA6
 YUCCA-LIKE GENE 4 (YUCCA-like gene)
 1 Tolerance and resistance - Stress tolerance
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Embryo
Tolerance and resistance - Disease resistance
Biochemical character
 GO:0051707 - response to other organism
GO:0042594 - response to starvation
GO:0009793 - embryonic development ending in seed dormancy
GO:0009408 - response to heat
GO:0004499 - flavin-containing monooxygenase activity
GO:0009851 - auxin biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0048653 - anther development
GO:0009901 - anther dehiscence
GO:0051607 - defense response to virus
 TO:0002672 - auxin content
TO:0000657 - spikelet anatomy and morphology trait
TO:0000148 - viral disease resistance
TO:0000259 - heat tolerance
TO:0000620 - embryo development trait
TO:0000615 - abscisic acid sensitivity
TO:0000189 - embryoless
 PO:0001035 - G anther dehiscence stage
PO:0009066 - anther
PO:0007631 - plant embryo stage
PO:0001004 - anther development stage
Os01g0224700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g12490.1
YUCCA6 OsYUCCA6
OsYUC6
YUC6
 YUCCA-LIKE GENE 6 (YUCCA-like gene)
 7 Biochemical character
Seed - Morphological traits - Embryo
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0010262 - somatic embryogenesis
GO:0009629 - response to gravity
GO:0004499 - flavin-containing monooxygenase activity
GO:0051607 - defense response to virus
GO:0009851 - auxin biosynthetic process
GO:0009266 - response to temperature stimulus
 TO:0002672 - auxin content
TO:0002693 - gravity response trait
TO:0000432 - temperature response trait
TO:0000020 - black streak dwarf virus resistance
 PO:0000423 - plant zygote
PO:0020148 - shoot apical meristem
PO:0025275 - procambium
PO:0005020 - vascular bundle
PO:0025127 - primordium
Os07g0437000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g25540.1
YUCCA7 OsYUCCA7
OsYUC7
OsYUC5
YUC5
YUC7
 YUCCA-LIKE GENE 7 (YUCCA-like gene)
 4 Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Morphological traits - Embryo
 GO:0046686 - response to cadmium ion
GO:0010262 - somatic embryogenesis
GO:0009629 - response to gravity
GO:0004499 - flavin-containing monooxygenase activity
GO:0009851 - auxin biosynthetic process
 TO:0002693 - gravity response trait
 PO:0000423 - plant zygote
PO:0009005 - root
Os04g0128900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g03980.1
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
CDPK31 OsCDPK31
OsCPK31
CPK31
 CALCIUM-DEPENDENT PROTEIN KINASE 31 calcium-dependent protein kinase
 Biochemical character
Seed - Morphological traits - Endosperm
Seed
 GO:0010431 - seed maturation
GO:0010857 - calcium-dependent protein kinase activity
GO:0043036 - starch grain
GO:0031000 - response to caffeine
 TO:0002661 - seed maturation
 PO:0007633 - endosperm development stage
PO:0009001 - fruit
-
SSIVB OsSSIVb
SSIV-2
OsSSIV-2
SSIVb
SSIV-2
SSIV2
OsSSIV2
 SOLUBLE STARCH SYNTHASE IVB SOLUBLE STARCH SYNTHASE IV-2
 5 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
 GO:0009269 - response to desiccation
GO:0009011 - starch synthase activity
GO:0009507 - chloroplast
GO:0005978 - glycogen biosynthetic process
GO:0009960 - endosperm development
GO:0009501 - amyloplast
GO:0019252 - starch biosynthetic process
 TO:0000394 - drought related trait
 PO:0025034 - leaf
PO:0009089 - endosperm
PO:0007633 - endosperm development stage
Os05g0533600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g45720.4
LOC_Os05g45720.3
LOC_Os05g45720.2
LOC_Os05g45720.1
SBE4 RBE4
OsSBE4
BEIIa
QEIIb
BEIIA
OsBEIIa
 STARCH BRANCHING ENZYME 4 Q-enzyme IIb
starch branching enzyme IIb
Starch branching enzyme IIa
 4 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
 GO:0005982 - starch metabolic process
GO:0019252 - starch biosynthetic process
GO:0003844 - 1,4-alpha-glucan branching enzyme activity
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0005976 - polysaccharide metabolic process
GO:0009501 - amyloplast
GO:0009568 - amyloplast starch grain
 TO:0000099 - sugary endosperm
TO:0000097 - amylopectin content
TO:0000162 - seed quality
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0000489 - carbohydrate composition related trait
 PO:0025034 - leaf
Os04g0409200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g33460.1
GHD7 Ghd2
Ghd7
OsGhd7
OsCCT26
OsCMF8
OsI
Ghd7/Hd4
Hd4
EH7-1/Hd4
Ghd7-0a
EH7-1
EH7/Ghd7
EH7
OsEH7
GLW7.1
OsGLW7.1
 HEADING DATE 7 heading date 7
"Grain number
plant height
and heading date7"
"GRAIN NUMBER
PLANT HEIGHT AND HEADING DATE 7"
CCT domain-containing gene 26
CCT (CO, CO-LIKE and TOC1) domain protein 26
CCT domain protein 26
CCT MOTIF FAMILY (CMF) gene 8
Early heading 7
"Grain Length
Width and Weight 7.1"
Grain height date 7
 7 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Heterochrony
Seed - Physiological traits
Vegetative organ - Culm
Seed - Physiological traits - Storage substances
Seed - Physiological traits - Taste
 GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009648 - photoperiodism
GO:0005985 - sucrose metabolic process
GO:0042128 - nitrate assimilation
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0045848 - positive regulation of nitrogen utilization
GO:0006521 - regulation of cellular amino acid metabolic process
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0008643 - carbohydrate transport
GO:0048573 - photoperiodism, flowering
GO:0051781 - positive regulation of cell division
GO:0009416 - response to light stimulus
GO:0009740 - gibberellic acid mediated signaling
GO:0010229 - inflorescence development
GO:0007623 - circadian rhythm
GO:0030307 - positive regulation of cell growth
GO:0006109 - regulation of carbohydrate metabolic process
GO:0015770 - sucrose transport
GO:0006808 - regulation of nitrogen utilization
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0010109 - regulation of photosynthesis
GO:0009744 - response to sucrose stimulus
GO:0009745 - sucrose mediated signaling
 TO:0000621 - inflorescence development trait
TO:0000397 - grain size
TO:0000382 - 1000-seed weight
TO:0000734 - grain length
TO:0002653 - endosperm storage protein content
TO:0000590 - grain weight
TO:0002675 - gibberellic acid content
TO:0000266 - chalky endosperm
TO:0000469 - days to maturity
TO:0000456 - spikelet number
TO:0000229 - photoperiod sensitivity
TO:0000207 - plant height
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000050 - inflorescence branching
TO:0002759 - grain number
TO:0000011 - nitrogen sensitivity
TO:0000196 - amylose content
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0000152 - panicle number
TO:0000696 - starch content
TO:0000107 - endosperm storage protein-1 content
TO:0000109 - endosperm storage protein-2 content
TO:0000137 - days to heading
TO:0000019 - seedling height
TO:0000211 - gel consistency
TO:0002616 - flowering time
TO:0000710 - globulin protein content
TO:0000449 - grain yield per plant
TO:0000352 - plant dry weight
TO:0002680 - albumin content
TO:0000357 - growth and development trait
 PO:0001083 - inflorescence development stage
Os07g0261200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g15770.1
GIF1 gif1
CIN2
OsCIN2
OsGIF1
WB1
OsWB1
GIF1/OsCIN2
 GRAIN INCOMPLETE FILLING 1 grain incomplete filling 1
"Beta-fructofuranosidase
insoluble isoenzyme 2"
Sucrose hydrolase 2
Invertase 2
Cell wall beta-fructosidase 2
cell-wall invertase 2
White Belly 1
 4 Seed - Morphological traits
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Seed - Physiological traits - Taste
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Morphological traits - Endosperm
 GO:0005987 - sucrose catabolic process
GO:0016787 - hydrolase activity
GO:0048046 - apoplast
GO:0051707 - response to other organism
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0005986 - sucrose biosynthetic process
GO:0004564 - beta-fructofuranosidase activity
GO:0004575 - sucrose alpha-glucosidase activity
GO:0005618 - cell wall
GO:0005975 - carbohydrate metabolic process
GO:0009960 - endosperm development
 TO:0000696 - starch content
TO:0000734 - grain length
TO:0000097 - amylopectin content
TO:0000382 - 1000-seed weight
TO:0000447 - filled grain number
TO:0000456 - spikelet number
TO:0000328 - sucrose content
TO:0000391 - seed size
TO:0000455 - seed set percent
TO:0000300 - glucose content
TO:0000311 - invertase activity
TO:0000221 - glume color
TO:0002656 - starch grain shape
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000162 - seed quality
TO:0000396 - grain yield
TO:0000397 - grain size
TO:0006005 - fructose content
TO:0000592 - 1000-dehulled grain weight
TO:0000196 - amylose content
TO:0000590 - grain weight
TO:0002661 - seed maturation
TO:0000266 - chalky endosperm
TO:0000575 - endosperm related trait
TO:0000487 - endosperm color
 PO:0005019 - carpel vascular system
PO:0009089 - endosperm
PO:0009084 - pericarp
PO:0007633 - endosperm development stage
PO:0006326 - inflorescence internode
PO:0000025 - root tip
Os04g0413500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g33740.1
YUCCA9 OsYUCCA9
OsYUC9
YUC9
 YUCCA-LIKE GENE 9 (YUCCA-like gene)
 1 Seed - Morphological traits - Embryo
Seed - Morphological traits - Endosperm
Seed - Physiological traits - Storage substances
Biochemical character
 GO:0048316 - seed development
GO:0010262 - somatic embryogenesis
GO:0009851 - auxin biosynthetic process
GO:0004499 - flavin-containing monooxygenase activity
 TO:0002672 - auxin content
TO:0000653 - seed development trait
TO:0000266 - chalky endosperm
 PO:0009089 - endosperm
PO:0000423 - plant zygote
PO:0009006 - shoot system
PO:0009005 - root
PO:0009009 - plant embryo
PO:0009047 - stem
PO:0001170 - seed development stage
PO:0009049 - inflorescence
Os01g0273800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g16714.1
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
RL9 rl9
SLL1/RL9
SLL1
OsSLL1
OsADD1
ADD1
AH2
OsAH2
CL1
OsCL1
OsKAN1
KAN1
 ROLLED LEAF 9 SHALLOT-LIKE1
SHALLOT-LIKE 1
ROLLED LEAF9
anther dehiscence defected 1
abnormal hull 2
curling leaf 1
KANADI1
OsKANADI1
 9 Coloration - Chlorophyll
Other
Character as QTL - Plant growth activity
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
Reproductive organ - Inflorescence
Vegetative organ - Root
Reproductive organ - Spikelet, flower, glume, awn
Character as QTL - Grain quality
Character as QTL - Yield and productivity
Reproductive organ - panicle
Seed - Morphological traits
Vegetative organ - Culm
 GO:0009685 - gibberellin metabolic process
GO:0045487 - gibberellin catabolic process
GO:0006351 - transcription, DNA-dependent
GO:0009739 - response to gibberellin stimulus
GO:0009957 - epidermal cell fate specification
GO:0051510 - regulation of unidimensional cell growth
GO:0080006 - internode patterning
GO:0048364 - root development
GO:0003677 - DNA binding
GO:0003682 - chromatin binding
GO:0005634 - nucleus
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0006355 - regulation of transcription, DNA-dependent
GO:0048366 - leaf development
GO:0009555 - pollen development
GO:0010229 - inflorescence development
GO:0012501 - programmed cell death
GO:0042127 - regulation of cell proliferation
GO:0030154 - cell differentiation
GO:0048653 - anther development
GO:0048437 - floral organ development
GO:0001558 - regulation of cell growth
GO:0010088 - phloem development
GO:0010158 - abaxial cell fate specification
GO:0048316 - seed development
 TO:0000085 - leaf rolling
TO:0000397 - grain size
TO:0006022 - floral organ development trait
TO:0000587 - endosperm quality
TO:0000474 - glume opening
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000207 - plant height
TO:0000421 - pollen fertility
TO:0001006 - adventitious root number
TO:0000165 - panicle exsertion
TO:0000495 - chlorophyll content
TO:0000227 - root length
TO:0002681 - leaf curling
TO:0001012 - lateral root length
TO:0000019 - seedling height
TO:0000657 - spikelet anatomy and morphology trait
TO:0002689 - leaf sheath length
TO:0000072 - awn length
TO:0000166 - gibberellic acid sensitivity
TO:0002675 - gibberellic acid content
TO:0000145 - internode length
TO:0000449 - grain yield per plant
TO:0000653 - seed development trait
TO:0000211 - gel consistency
TO:0000598 - protein content
TO:0000196 - amylose content
TO:0000455 - seed set percent
TO:0000734 - grain length
TO:0000040 - panicle length
TO:0000152 - panicle number
TO:0000382 - 1000-seed weight
TO:0000326 - leaf color
TO:0001027 - net photosynthetic rate
TO:0000135 - leaf length
TO:0000295 - chlorophyll-b content
TO:0002757 - flag leaf length
TO:0000370 - leaf width
TO:0000316 - photosynthetic ability
TO:0000462 - gelatinization temperature
TO:0000656 - root development trait
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0000053 - pollen sterility
TO:0000391 - seed size
TO:0000655 - leaf development trait
 PO:0001170 - seed development stage
PO:0025034 - leaf
PO:0009051 - spikelet
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0025426 - phloem development stage
PO:0000017 - vascular leaf primordium
PO:0020148 - shoot apical meristem
PO:0009049 - inflorescence
PO:0001007 - pollen development stage
PO:0009005 - root
PO:0020141 - stem node
PO:0001004 - anther development stage
PO:0025585 - floral organ formation stage
PO:0007520 - root development stage
PO:0020142 - stem internode
PO:0000293 - guard cell
PO:0006019 - leaf abaxial epidermis
PO:0001050 - leaf development stage
Os09g0395300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g23200.1
AGPL2 OsAGPL2
osagpl2
APL2
OsAPL2
AGPiso
sh2
Sh2
GIF2
GAS1
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 2 sativa ADP-glucose pyrophosphorylase large subunit 2
ADP-glucose Pyrophosphorylase large subunit 2
AGPase large subunit 2
AGPase large unit 2
ADP-glucose pyrophosphorylase subunit SH2
GRAIN INCOMPLETE FILLING 2
 1 Seed - Morphological traits - Endosperm
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Storage substances
 GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0009058 - biosynthetic process
GO:0010035 - response to inorganic substance
GO:0009269 - response to desiccation
GO:0005829 - cytosol
GO:0009536 - plastid
GO:0016779 - nucleotidyltransferase activity
GO:0005978 - glycogen biosynthetic process
GO:0009651 - response to salt stress
GO:0048316 - seed development
GO:0010431 - seed maturation
GO:0010581 - regulation of starch biosynthetic process
GO:0019252 - starch biosynthetic process
 TO:0000162 - seed quality
TO:0000382 - 1000-seed weight
TO:0000394 - drought related trait
TO:0002661 - seed maturation
TO:0000653 - seed development trait
TO:0000480 - nutrient sensitivity
TO:0000104 - floury endosperm
TO:0000696 - starch content
TO:0000100 - shrunken endosperm
TO:0000396 - grain yield
TO:0006001 - salt tolerance
TO:0000590 - grain weight
 PO:0009089 - endosperm
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
PO:0009010 - seed
PO:0007022 - seed imbibition stage
PO:0009001 - fruit
Os01g0633100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g44220.7
LOC_Os01g44220.6
LOC_Os01g44220.5
LOC_Os01g44220.1
LOC_Os01g44220.2
LOC_Os01g44220.3
LOC_Os01g44220.4
AGPL4 OsAGPL4
APL4
OsAPL4
OsSTA193
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 4 sativa ADP-glucose pyrophosphorylase large subunit 4
ADP-glucose Pyrophosphorylase large subunit 4
AGPase large subunit 4
AGPase large unit 4
 7 Seed - Morphological traits - Endosperm
Seed - Physiological traits - Storage substances
Reproductive organ - Spikelet, flower, glume, awn
Biochemical character
 GO:0016779 - nucleotidyltransferase activity
GO:0019252 - starch biosynthetic process
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0009058 - biosynthetic process
GO:0009536 - plastid
 TO:0000106 - male sterility type
TO:0000696 - starch content
 PO:0009066 - anther
PO:0009089 - endosperm
Os07g0243200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g13980.1
AGPS2 OsAGPS2a
AGPS2A
AGPS2B
OsAGPS2
osagps2
APS2
APS2a
APS2b
AGPS2a
APGS2b
OsAGPS2b
AGPP
GAS8
OsAPS2
OsAPS2a
OsAPS2b
 ADP-GLUCOSE PYROPHOSPHORYLASE SMALL SUBUNIT 2 sativa ADP-glucose pyrophosphorylase small subunit 2a
sativa ADP-glucose pyrophosphorylase small subunit 2
ADP-glucose Pyrophosphorylase small subunit 2
AGPase small subunit 2
ADP-glucose pyrophosphorylase small subunit 2a
ADP-glucose pyrophosphorylase 51kD subunit
ADP-glucose pyrophosphorylase small unit 2
ADP-glucose pyrophosphorylase small subunit 2b
 8 Seed - Morphological traits - Endosperm
Character as QTL - Yield and productivity
Seed - Physiological traits - Storage substances
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0009408 - response to heat
GO:0010035 - response to inorganic substance
GO:0009269 - response to desiccation
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0005982 - starch metabolic process
GO:0005829 - cytosol
GO:0019252 - starch biosynthetic process
GO:0005524 - ATP binding
GO:0009501 - amyloplast
GO:0009507 - chloroplast
GO:0009536 - plastid
GO:0009415 - response to water
GO:0000003 - reproduction
GO:0009651 - response to salt stress
GO:0009791 - post-embryonic development
GO:0005978 - glycogen biosynthetic process
 TO:0000394 - drought related trait
TO:0000011 - nitrogen sensitivity
TO:0000480 - nutrient sensitivity
TO:0000237 - water stress trait
TO:0000100 - shrunken endosperm
TO:0000333 - sugar content
TO:0002661 - seed maturation
TO:0000259 - heat tolerance
TO:0000696 - starch content
TO:0000382 - 1000-seed weight
TO:0006001 - salt tolerance
 PO:0025034 - leaf
PO:0007022 - seed imbibition stage
PO:0009010 - seed
PO:0009089 - endosperm
PO:0007632 - seed maturation stage
Os08g0345800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g25734.2
LOC_Os08g25734.1
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
AGO17 OsAGO17
 ARGONAUTE 17 Protein argonaute 17
 2 Character as QTL - Yield and productivity
Seed - Physiological traits - Storage substances
Other
Seed - Morphological traits
Reproductive organ - panicle
Vegetative organ - Culm
 GO:0003676 - nucleic acid binding
GO:0005739 - mitochondrion
GO:0031047 - gene silencing by RNA
GO:0051512 - positive regulation of unidimensional cell growth
GO:0005634 - nucleus
 TO:0000592 - 1000-dehulled grain weight
TO:0000397 - grain size
TO:0000455 - seed set percent
TO:0000266 - chalky endosperm
TO:0000456 - spikelet number
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000657 - spikelet anatomy and morphology trait
TO:0000590 - grain weight
TO:0000576 - stem length
TO:0000051 - stem strength
TO:0000449 - grain yield per plant
TO:0000734 - grain length
TO:0000040 - panicle length
TO:0000339 - stem thickness
TO:0000145 - internode length
 PO:0020141 - stem node
Os02g0169400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07310.1
AGO2 OsAGO2
 ARGONAUTE 2 sativa Argonaute 2
Protein argonaute 2
ARGONAUTE2
 4 Tolerance and resistance - Stress tolerance
Other
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Coloration - Chlorophyll
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
 GO:0009409 - response to cold
GO:0009658 - chloroplast organization
GO:0003676 - nucleic acid binding
GO:0043067 - regulation of programmed cell death
GO:0051607 - defense response to virus
GO:0031047 - gene silencing by RNA
GO:0046466 - membrane lipid catabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0009690 - cytokinin metabolic process
GO:0048316 - seed development
GO:0009651 - response to salt stress
GO:0050687 - negative regulation of defense response to virus
GO:0006306 - DNA methylation
GO:0010150 - leaf senescence
 TO:0000734 - grain length
TO:0000455 - seed set percent
TO:0000615 - abscisic acid sensitivity
TO:0002660 - cytokinin content
TO:0000249 - leaf senescence
TO:0006001 - salt tolerance
TO:0002715 - chloroplast development trait
TO:0000495 - chlorophyll content
TO:0000020 - black streak dwarf virus resistance
TO:0000326 - leaf color
TO:0001015 - photosynthetic rate
TO:0000269 - 100-seed weight
TO:0000605 - hydrogen peroxide content
TO:0000449 - grain yield per plant
TO:0000396 - grain yield
TO:0000316 - photosynthetic ability
TO:0000303 - cold tolerance
 Os04g0615700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g52540.1
AGPL1 OsAGPL1
OsAPL1
APL1
OsAGPL3
AGPL3
OsAGPSL3
AGPSL3
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1 sativa ADP-glucose pyrophosphorylase large subunit 1
ADP-glucose Pyrophosphorylase large subunit 1
AGPase large subunit 1
ADP-glucose pyrophosphorylase large subunit 3
AGPase large unit 3
 3 Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
Biochemical character
Vegetative organ - Culm
Seed - Morphological traits - Endosperm
 GO:0009629 - response to gravity
GO:0005978 - glycogen biosynthetic process
GO:0009058 - biosynthetic process
GO:0019252 - starch biosynthetic process
GO:0016779 - nucleotidyltransferase activity
GO:0009959 - negative gravitropism
GO:0009536 - plastid
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
 TO:0000696 - starch content
TO:0002693 - gravity response trait
TO:0000567 - tiller angle
 PO:0025034 - leaf
Os03g0735000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g52460.1
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
F3'H OsF3'H
OsCYP75B3
CYP75B3
OsF3'H10
F3'H10
OsCYP71P3
CYP71P3
 FLAVONOID 3'-HYDROXYLASE sativa flavonoid 3'-hydroxylase
Flavanone 3'-hydroxylase
P-450 75B3
Cytochrome P450 75B3
flavonoid 3'-monooxygenase
flavonoid 3'-hydroxylase 10
 10 Tolerance and resistance - Disease resistance
Tolerance and resistance - Insect resistance
Coloration - Anthocyanin
Biochemical character
Seed
Seed - Morphological traits
Tolerance and resistance - Stress tolerance
 GO:0002213 - defense response to insect
GO:0050832 - defense response to fungus
GO:0004497 - monooxygenase activity
GO:0005506 - iron ion binding
GO:0016021 - integral to membrane
GO:0005634 - nucleus
GO:0016020 - membrane
GO:0009718 - anthocyanin biosynthetic process
GO:0045486 - naringenin 3-dioxygenase activity
GO:0009753 - response to jasmonic acid stimulus
GO:0009408 - response to heat
GO:0048316 - seed development
GO:0020037 - heme binding
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0009813 - flavonoid biosynthetic process
 TO:0000259 - heat tolerance
TO:0000071 - anthocyanin content
TO:0000424 - brown planthopper resistance
TO:0000172 - jasmonic acid sensitivity
TO:0000653 - seed development trait
TO:0000074 - blast disease
 PO:0001170 - seed development stage
Os10g0320100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g17260.1
LOX1 OsLOX1
OsLOX5
 LIPOXYGENASE 1 lipoxygenase 1
Probable lipoxygenase 4
lipoxygenase 5
 3 Seed - Morphological traits - Embryo
Biochemical character
Seed - Physiological traits
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
 GO:0009611 - response to wounding
GO:0009266 - response to temperature stimulus
GO:0009793 - embryonic development ending in seed dormancy
GO:0006521 - regulation of cellular amino acid metabolic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0019216 - regulation of lipid metabolic process
GO:0006629 - lipid metabolic process
GO:0005506 - iron ion binding
GO:0016165 - lipoxygenase activity
GO:0031408 - oxylipin biosynthetic process
GO:0055114 - oxidation reduction
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0006979 - response to oxidative stress
 TO:0000196 - amylose content
TO:0006001 - salt tolerance
TO:0005001 - linoleic acid content
TO:0000435 - seed longevity
TO:0002657 - oxidative stress
TO:0000432 - temperature response trait
TO:0000620 - embryo development trait
TO:0000276 - drought tolerance
TO:0000345 - seed viability
TO:0000696 - starch content
TO:0000162 - seed quality
TO:0000211 - gel consistency
 PO:0007631 - plant embryo stage
Os03g0700700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g49380.3
LOC_Os03g49380.2
LOC_Os03g49380.1
CKX1 OsCKX1
 CYTOKININ OXIDASE/DEHYDROGENASE 1 cytokinin oxidase 1
 1 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Biochemical character
Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
 GO:0042594 - response to starvation
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0009725 - response to hormone stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0009823 - cytokinin catabolic process
GO:0009793 - embryonic development ending in seed dormancy
GO:0019139 - cytokinin dehydrogenase activity
 TO:0000167 - cytokinin sensitivity
TO:0000011 - nitrogen sensitivity
TO:0002660 - cytokinin content
TO:0000163 - auxin sensitivity
TO:0000401 - plant growth hormone sensitivity
TO:0000620 - embryo development trait
TO:0000266 - chalky endosperm
 PO:0007631 - plant embryo stage
PO:0009005 - root
Os01g0187600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g09260.1
CKX4 OsCKX4
ckx4
OsSCRM
OsSCRM2
SCRM
SCRM2
 CYTOKININ OXIDASE/DEHYDROGENASE 4 Putative cytokinin dehydrogenase 4
cytokinin oxidase 4
 1 Character as QTL - Grain quality
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Biochemical character
 GO:0009725 - response to hormone stimulus
GO:0019139 - cytokinin dehydrogenase activity
GO:0048364 - root development
GO:0009736 - cytokinin mediated signaling
GO:0042594 - response to starvation
GO:0009735 - response to cytokinin stimulus
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0032940 - secretion by cell
GO:0009733 - response to auxin stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009734 - auxin mediated signaling pathway
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0022900 - electron transport chain
GO:0016491 - oxidoreductase activity
GO:0051607 - defense response to virus
GO:0009823 - cytokinin catabolic process
 TO:0000227 - root length
TO:0000346 - tiller number
TO:0000456 - spikelet number
TO:0000401 - plant growth hormone sensitivity
TO:0006032 - panicle size
TO:0000734 - grain length
TO:0000402 - grain width
TO:0002660 - cytokinin content
TO:0000656 - root development trait
TO:0000011 - nitrogen sensitivity
TO:0000207 - plant height
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000148 - viral disease resistance
TO:0000019 - seedling height
TO:0000020 - black streak dwarf virus resistance
TO:0000382 - 1000-seed weight
TO:0000172 - jasmonic acid sensitivity
TO:0002685 - crown root number
TO:0000449 - grain yield per plant
TO:0000430 - germination rate
TO:0000455 - seed set percent
 PO:0009105 - inflorescence branch meristem
PO:0009005 - root
PO:0007520 - root development stage
PO:0025034 - leaf
Os01g0940000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g71310.1
CKX7 OsCKX7
 CYTOKININ OXIDASE/DEHYDROGENASE 7 cytokinin oxidase 7
 2 Biochemical character
Reproductive organ - panicle
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
 GO:0019139 - cytokinin dehydrogenase activity
GO:0050660 - FAD binding
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0005615 - extracellular space
GO:0050832 - defense response to fungus
GO:0009823 - cytokinin catabolic process
 TO:0000734 - grain length
TO:0000255 - sheath blight disease resistance
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000402 - grain width
TO:0000266 - chalky endosperm
TO:0000455 - seed set percent
 PO:0020104 - leaf sheath
Os02g0220100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g12780.1
CKX8 OsCKX8
 CYTOKININ OXIDASE/DEHYDROGENASE 8 cytokinin oxidase 8
 4 Reproductive organ - Panicle, Mode of branching
Seed - Morphological traits - Grain shape
Biochemical character
 GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0050660 - FAD binding
GO:0009690 - cytokinin metabolic process
GO:0019139 - cytokinin dehydrogenase activity
GO:0009735 - response to cytokinin stimulus
 TO:0000167 - cytokinin sensitivity
TO:0000557 - secondary branch number
TO:0000382 - 1000-seed weight
TO:0002660 - cytokinin content
TO:0002759 - grain number
TO:0000734 - grain length
 Os04g0523500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g44230.1
REG1 RICE EMBRYO GLOBULIN-1 PROTEIN Seed - Morphological traits - Embryo
 GO:0019825 - oxygen binding
GO:0020037 - heme binding
GO:0015671 - oxygen transport
GO:0009790 - embryonic development
 -
REG2 REG-2
 RICE EMBRYO GLOBULIN-2 PROTEIN Seed - Morphological traits - Embryo
Seed - Physiological traits - Storage substances
 GO:0020037 - heme binding
GO:0019825 - oxygen binding
GO:0015671 - oxygen transport
GO:0009790 - embryonic development
 TO:0002653 - endosperm storage protein content
 -
HOX29 Oshox29
OsHox29
OSHB5
HB5
 HOMEOBOX GENE 29 rice homeobox gene 29
Homeobox-leucine zipper protein HOX29
Homeodomain transcription factor HOX29
HD-ZIP protein HOX29
HOMEODOMAIN CONTAINING PROTEIN 5
 1 Other
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000397 - grain size
 Os01g0200300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g10320.1
HAP2I OsHAP2I
NF-YA
CBF-B
NF-YA8
OsNF-YA8
OsEnS-136
NFYA8
 HAP2 SUBUNIT OF CCAAT-BOX BINDING COMPLEX NUCLEAR FACTOR-Y subunit A8
NUCLEAR FACTOR-Y subunit NF-YA8
NF-YA transcription factor 8
endosperm-specific gene 136
NF-YA subunit 8
NF-YA family 8
 10 Character as QTL - Yield and productivity
Other
Seed - Morphological traits - Endosperm
Seed - Morphological traits - Grain shape
Character as QTL - Grain quality
Tolerance and resistance - Disease resistance
 GO:0010167 - response to nitrate
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009753 - response to jasmonic acid stimulus
GO:0051607 - defense response to virus
GO:0043565 - sequence-specific DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005634 - nucleus
GO:0005737 - cytoplasm
GO:0006350 - transcription
 TO:0000148 - viral disease resistance
TO:0000598 - protein content
TO:0000011 - nitrogen sensitivity
TO:0000172 - jasmonic acid sensitivity
TO:0000266 - chalky endosperm
TO:0000696 - starch content
 PO:0009089 - endosperm
Os10g0397900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g25850.1
HAP3D OsHAP3D
OsEnS-83
OsNF-YB9
NF-YB9
NFYB9
OsLEC1A
LEC1A
 HAP3D SUBUNIT OF CCAAT-BOX BINDING COMPLEX HAP3 subunit D
LEC1-type 3 subunit protein-D
endosperm-specific gene 83
NUCLEAR FACTOR-Y subunit B9
NUCLEAR FACTOR-Y subunit NF-YB9
HAP3 SUBUNIT D
NF-YB subunit 9
NF-YB family 9
 6 Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Other
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0042127 - regulation of cell proliferation
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009790 - embryonic development
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0005737 - cytoplasm
GO:0009845 - seed germination
 TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000266 - chalky endosperm
TO:0000391 - seed size
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0020033 - glume length
TO:0000487 - endosperm color
TO:0000575 - endosperm related trait
TO:0000064 - embryo related trait
TO:0000485 - sterility related trait
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0000276 - drought tolerance
TO:0000211 - gel consistency
TO:0000162 - seed quality
TO:0000222 - head rice
TO:0000207 - plant height
TO:0000382 - 1000-seed weight
TO:0000346 - tiller number
TO:0000639 - seed fertility
TO:0000421 - pollen fertility
 PO:0001170 - seed development stage
PO:0009009 - plant embryo
PO:0009089 - endosperm
PO:0020094 - plant egg cell
PO:0000003 - whole plant
PO:0009010 - seed
Os06g0285200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g17480.1
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
HAP5A OsHAP5A
NF-YC
CBF-C
OsNF-YC1
Os-NF-YC1
NF-YC1
NFYC1
OsNF-YC4-2
NF-YC4-2
 HAP5A SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C1 subunit
Nuclear factor Y C subunit 1
NUCLEAR FACTOR-Y subunit C1
NUCLEAR FACTOR-Y subunit NF-YC1
NF-YC subunit 1
NF-YC family 1
 2 Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
Other
 GO:0008284 - positive regulation of cell proliferation
GO:0005634 - nucleus
GO:0050688 - regulation of defense response to virus
GO:0009414 - response to water deprivation
GO:0009737 - response to abscisic acid stimulus
GO:0009651 - response to salt stress
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
GO:0006350 - transcription
GO:0051607 - defense response to virus
GO:0080050 - regulation of seed development
GO:0030307 - positive regulation of cell growth
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000919 - grain weight
TO:0000653 - seed development trait
TO:0000615 - abscisic acid sensitivity
TO:0006001 - salt tolerance
TO:0000137 - days to heading
TO:0000590 - grain weight
TO:0000276 - drought tolerance
TO:0000397 - grain size
TO:0000148 - viral disease resistance
TO:0000391 - seed size
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000382 - 1000-seed weight
TO:0000399 - grain thickness
TO:0000975 - grain width
TO:0001034 - relative plant height
TO:0000402 - grain width
 PO:0009049 - inflorescence
PO:0001170 - seed development stage
Os02g0170500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07450.1
LOC_Os02g07450.2
DEP1 OsDEP1
EP
qPE9-1
DN1
DEP1/DN1/qPE9-1
qNGR9
qDEP1
RGG4/DEP1/DN1/qPE9-1/OsGGC3
RGG4
OsDN1
OsGGC3
GGC3
 DENSE AND ERECT PANICLE 1 dense and erect panicle 1
erect-pose panicle
DENSE PANICLE 1
DENSE AND ERECT PANICLE1
DENSE AND ERECT PANICLES 1
G gamma subunit DEP1
Heterotrimeric G Protein gamma4 Subunit
 9 Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Vegetative organ - Root
Reproductive organ - Panicle, Mode of branching
Vegetative organ - Culm
Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
 GO:0035330 - regulation of hippo signaling cascade
GO:0010729 - positive regulation of hydrogen peroxide biosynthetic process
GO:0010618 - aerenchyma formation
GO:0010229 - inflorescence development
GO:0051171 - regulation of nitrogen compound metabolic process
GO:0043068 - positive regulation of programmed cell death
GO:0005882 - intermediate filament
GO:0005886 - plasma membrane
GO:0009414 - response to water deprivation
GO:0009409 - response to cold
GO:0009651 - response to salt stress
GO:0048573 - photoperiodism, flowering
GO:0005634 - nucleus
GO:0007186 - G-protein coupled receptor protein signaling pathway
 TO:0000207 - plant height
TO:0000152 - panicle number
TO:0000397 - grain size
TO:0000456 - spikelet number
TO:0000734 - grain length
TO:0000276 - drought tolerance
TO:0000303 - cold tolerance
TO:0000050 - inflorescence branching
TO:0002731 - grain length to width ratio
TO:0006001 - salt tolerance
TO:0000455 - seed set percent
TO:0002759 - grain number
TO:0000396 - grain yield
TO:0000382 - 1000-seed weight
TO:0000605 - hydrogen peroxide content
TO:0000137 - days to heading
TO:0000043 - root anatomy and morphology trait
TO:0000621 - inflorescence development trait
TO:0000625 - spikelet density
TO:0000040 - panicle length
 Os09g0441900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g26999.1
LOC_Os09g26999.3
LOC_Os09g26999.2
DLT dlt
OsGRAS32
OsDLT
OsDLT1
DTL1
OsGRAS-32
OsGRAS32
GRAS-32
GRAS32
SMOS2/DLT
SMOS2
OsSMOS2
OsGS6
GS6
DLT/GS6/SMOS2
 DWARF AND LOW-TILLERING GRAS protein 32
SMALL ORGAN SIZE 2
 6 Vegetative organ - Root
Character as QTL - Plant growth activity
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
Reproductive organ - Heading date
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
Seed - Morphological traits
 GO:0010422 - regulation of brassinosteroid biosynthetic process
GO:0080006 - internode patterning
GO:0009742 - brassinosteroid mediated signaling
GO:0009741 - response to brassinosteroid stimulus
GO:0009734 - auxin mediated signaling pathway
GO:0010229 - inflorescence development
GO:0007275 - multicellular organismal development
GO:0051302 - regulation of cell division
GO:0008283 - cell proliferation
GO:0000226 - microtubule cytoskeleton organization
GO:0016131 - brassinosteroid metabolic process
GO:0005634 - nucleus
GO:0009755 - hormone-mediated signaling
GO:0010928 - regulation of auxin mediated signaling pathway
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006351 - transcription, DNA-dependent
 TO:0002616 - flowering time
TO:0000326 - leaf color
TO:0002637 - leaf size
TO:0000040 - panicle length
TO:0002688 - leaf lamina joint bending
TO:0000346 - tiller number
TO:0000011 - nitrogen sensitivity
TO:0002677 - brassinosteroid sensitivity
TO:0000152 - panicle number
TO:0000227 - root length
TO:0000145 - internode length
TO:0000621 - inflorescence development trait
TO:0000357 - growth and development trait
TO:0002676 - brassinosteroid content
TO:0001035 - stem width
TO:0000206 - leaf angle
TO:0000397 - grain size
TO:0002684 - plant cell size
TO:0000329 - tillering ability
TO:0002601 - stamen size
TO:0002602 - pistil size
TO:0000019 - seedling height
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000576 - stem length
 PO:0001083 - inflorescence development stage
Os06g0127800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g03710.1
MIR159A miR159a
osa-miR159a
osa-MIR159a
OsmiR159a
OsmiR159a.2
miR159a.2
OsmiR159a.1
miR159a.1
osa-miR159a.1
osa-miR159a.2
 MICRORNA159A 1 Tolerance and resistance - Insect resistance
Seed - Morphological traits
Vegetative organ - Culm
Seed - Physiological traits - Storage substances
Character as QTL - Yield and productivity
Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Pollination, fertilization, fertility
Other
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
 GO:0009409 - response to cold
GO:0035195 - gene silencing by miRNA
GO:0050832 - defense response to fungus
GO:0002213 - defense response to insect
GO:0016442 - RNA-induced silencing complex
GO:0035068 - micro-ribonucleoprotein complex
GO:0048443 - stamen development
GO:0009555 - pollen development
GO:0006379 - mRNA cleavage
GO:0048316 - seed development
 TO:0000187 - anther color
TO:0000653 - seed development trait
TO:0000207 - plant height
TO:0000485 - sterility related trait
TO:0000303 - cold tolerance
TO:0000447 - filled grain number
TO:0000424 - brown planthopper resistance
TO:0000342 - panicle axis angle
TO:0000371 - yield trait
TO:0000053 - pollen sterility
TO:0000074 - blast disease
TO:0000696 - starch content
TO:0006032 - panicle size
TO:0000734 - grain length
 PO:0001170 - seed development stage
PO:0001007 - pollen development stage
Os01g0507000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g32259.1
C3H33 OsC3H33
OsTZF5
TZF5
OsCCCH-Zn-5
CCCH-Zn-5
OsC3H36
C3H36
 ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 33 Zinc finger CCCH domain-containing protein 33
Tandem zinc finger protein 5
CCCH Zinc Finger Family Gene 36
 5 Seed - Morphological traits - Grain shape
Other
Tolerance and resistance - Stress tolerance
 GO:0030912 - response to deep water
GO:0009651 - response to salt stress
GO:0003677 - DNA binding
GO:0008270 - zinc ion binding
GO:0005737 - cytoplasm
GO:0009753 - response to jasmonic acid stimulus
GO:0009409 - response to cold
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
 TO:0000172 - jasmonic acid sensitivity
TO:0000276 - drought tolerance
TO:0000524 - submergence tolerance
TO:0000382 - 1000-seed weight
TO:0000402 - grain width
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000357 - growth and development trait
TO:0000615 - abscisic acid sensitivity
TO:0001016 - relative chlorophyll content
TO:0000136 - relative water content
TO:0000396 - grain yield
 PO:0008037 - seedling
PO:0025034 - leaf
PO:0009046 - flower
PO:0009010 - seed
PO:0009047 - stem
PO:0009005 - root
PO:0009049 - inflorescence
Os05g0128200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g03760.1
LIC OsC3H46
C3H46
OsLIC
OsFLA6
FLA6
OsC3H52
C3H52
 LEAF AND TILLER ANGLE INCREASED CONTROLLER Zinc finger CCCH domain-containing protein 46
LEAF and TILLER ANGLE INCREASED CONTROLLER
Flag leaf angle 6
CCCH Zinc Finger Family Gene 52
 6 Other
Reproductive organ - panicle
Character as QTL - Yield and productivity
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
 GO:0009742 - brassinosteroid mediated signaling
GO:0003677 - DNA binding
GO:0008270 - zinc ion binding
GO:0005634 - nucleus
GO:0009741 - response to brassinosteroid stimulus
GO:0005737 - cytoplasm
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005739 - mitochondrion
 TO:0000547 - primary branch number
TO:0000445 - seed number
TO:0002688 - leaf lamina joint bending
TO:0000207 - plant height
TO:0000124 - flag leaf angle
TO:0000449 - grain yield per plant
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000206 - leaf angle
TO:0002677 - brassinosteroid sensitivity
TO:0000040 - panicle length
TO:0000396 - grain yield
TO:0000397 - grain size
TO:0000402 - grain width
TO:0000567 - tiller angle
 Os06g0704300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g49080.1
KNAT7 HOS66
HB365
OsKNAT7
 KNOTTED ARABIDOPSIS THALIANA 7 HOMEOBOX ORYZA SATIVA 66
Homeobox protein knotted-1-like 3
Homeobox protein HOS66
KNOTTED ARABIDOPSIS THALIANA7
KNOX ARABIDOPSIS THALIANA7
 3 Tolerance and resistance - Stress tolerance
Other
Reproductive organ - Inflorescence
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
 GO:0030244 - cellulose biosynthetic process
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009834 - secondary cell wall biogenesis
GO:0052386 - cell wall thickening
GO:0003700 - transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0080006 - internode patterning
GO:0010229 - inflorescence development
GO:0009664 - plant-type cell wall organization
GO:0001558 - regulation of cell growth
GO:0009809 - lignin biosynthetic process
GO:0030308 - negative regulation of cell growth
GO:0005634 - nucleus
 TO:0000068 - lodging incidence
TO:0000051 - stem strength
TO:0000621 - inflorescence development trait
TO:0000731 - lignin content
TO:0000397 - grain size
 PO:0001083 - inflorescence development stage
Os03g0123500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g03164.3
LOC_Os03g03164.2
LOC_Os03g03164.1
GAMYBL2 OsGAMYBL2
Os2R_MYB40
2R_MYB40
MYB2-45
OsMYB2-45
 GAMYB-LIKE 2 R2R3-MYB Transcription Factor 40
R2R3-MYB transcription factor 2-45
 3 Other
Seed - Morphological traits - Grain shape
Tolerance and resistance - Insect resistance
Character as QTL - Yield and productivity
Character as QTL - Plant growth activity
 GO:0009742 - brassinosteroid mediated signaling
GO:0005634 - nucleus
GO:0002213 - defense response to insect
GO:0010476 - gibberellin-mediated signaling
GO:0009908 - flower development
 TO:0000357 - growth and development trait
TO:0000424 - brown planthopper resistance
TO:0000397 - grain size
 Os03g0578900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g38210.1
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
NADP-ME2 OscytME1
OsNADP-ME2-3
NADP-ME2-3
 NADP-MALIC ENZYME 2 cytosolic NADP malic enzyme 1
 1 Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Grain shape
Biochemical character
Vegetative organ - Culm
Reproductive organ - panicle
Tolerance and resistance - Disease resistance
 GO:0009740 - gibberellic acid mediated signaling
GO:0042866 - pyruvate biosynthetic process
GO:0006108 - malate metabolic process
GO:0009739 - response to gibberellin stimulus
GO:0055114 - oxidation reduction
GO:0046872 - metal ion binding
GO:0051287 - NAD or NADH binding
GO:0009507 - chloroplast
GO:0009626 - plant-type hypersensitive response
GO:0004473 - malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity
GO:0005829 - cytosol
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0050832 - defense response to fungus
 TO:0000166 - gibberellic acid sensitivity
TO:0000447 - filled grain number
TO:0000145 - internode length
TO:0000382 - 1000-seed weight
TO:0000734 - grain length
TO:0000397 - grain size
TO:0000152 - panicle number
TO:0000040 - panicle length
TO:0000207 - plant height
TO:0000455 - seed set percent
TO:0002675 - gibberellic acid content
TO:0000074 - blast disease
 Os01g0723400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g52500.1
LOC_Os01g52500.2
LOC_Os01g52500.3
LOC_Os01g52500.4
LOC_Os01g52500.5
EP2 ep2
EP2/DEP2/SRS1
SRS1/DEP2
DEP2
SRS1
OsSRS1
CL7(t)
OsRELA
RELA
SUG1
OsSUG1
 ERECT PANICLE 2 erect panical 2
Erect panicle2
erect panicle2-1
erect panicle2-2
dense and erect panicle 2
small and round seed 1
cleistogamy 7
cleistogamy gene on chromosome 7
regulator of leaf angle
suppressor of GS2AA 1
 7 Tolerance and resistance - Disease resistance
Character as QTL - Plant growth activity
Seed - Morphological traits - Grain shape
Vegetative organ - Leaf
Character as QTL - Yield and productivity
Reproductive organ - Panicle, Mode of branching
 GO:0050777 - negative regulation of immune response
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0032491 - detection of molecule of fungal origin
GO:0002679 - respiratory burst during defense response
GO:0002221 - pattern recognition receptor signaling pathway
GO:0050832 - defense response to fungus
GO:0009742 - brassinosteroid mediated signaling
GO:0005737 - cytoplasm
GO:0009741 - response to brassinosteroid stimulus
GO:0010200 - response to chitin
GO:0001558 - regulation of cell growth
GO:0009739 - response to gibberellin stimulus
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009740 - gibberellic acid mediated signaling
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0010422 - regulation of brassinosteroid biosynthetic process
 TO:0000050 - inflorescence branching
TO:0000074 - blast disease
TO:0002637 - leaf size
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000590 - grain weight
TO:0000397 - grain size
TO:0002677 - brassinosteroid sensitivity
TO:0000472 - vascular bundle number
TO:0002759 - grain number
TO:0000342 - panicle axis angle
TO:0000734 - grain length
TO:0000339 - stem thickness
TO:0000040 - panicle length
TO:0000207 - plant height
TO:0000557 - secondary branch number
TO:0000180 - spikelet fertility
TO:0000402 - grain width
TO:0000382 - 1000-seed weight
TO:0000051 - stem strength
TO:0002688 - leaf lamina joint bending
TO:0000166 - gibberellic acid sensitivity
TO:0000206 - leaf angle
TO:0002730 - grain shape
TO:0000399 - grain thickness
 PO:0009082 - spikelet floret
PO:0025034 - leaf
PO:0009037 - lemma
PO:0009049 - inflorescence
PO:0009038 - palea
PO:0001083 - inflorescence development stage
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0009005 - root
PO:0005020 - vascular bundle
Os07g0616000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g42410.1
LOX-L2 OsLOX-L2
LOX1.1
LOX L-2
LOX-2
OsLOX2
LOX2
 LIPOXYGENASE L2 Lipoxygenase 2
Lipoxygenase L-2
 3 Biochemical character
Tolerance and resistance - Insect resistance
Tolerance and resistance - Disease resistance
Character as QTL - Germination
Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
Seed - Physiological traits - Longevity
 GO:0009266 - response to temperature stimulus
GO:0010030 - positive regulation of seed germination
GO:0055114 - oxidation reduction
GO:0048364 - root development
GO:0051707 - response to other organism
GO:0050832 - defense response to fungus
GO:0016165 - lipoxygenase activity
GO:0002213 - defense response to insect
GO:0005737 - cytoplasm
GO:0009793 - embryonic development ending in seed dormancy
GO:0009816 - defense response to bacterium, incompatible interaction
GO:0005506 - iron ion binding
GO:0009753 - response to jasmonic acid stimulus
GO:0009611 - response to wounding
GO:0009507 - chloroplast
GO:0009737 - response to abscisic acid stimulus
GO:0031408 - oxylipin biosynthetic process
 TO:0000403 - leaf-folder resistance
TO:0000620 - embryo development trait
TO:0000074 - blast disease
TO:0000435 - seed longevity
TO:0000172 - jasmonic acid sensitivity
TO:0000432 - temperature response trait
 PO:0009005 - root
PO:0007631 - plant embryo stage
PO:0007057 - 0 seed germination stage
PO:0009049 - inflorescence
PO:0009047 - stem
Os03g0738600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g52860.1
EMF1 OsEMF1
 EMBRYONIC FLOWER 1 1 Seed - Morphological traits - Embryo
 GO:0048573 - photoperiodism, flowering
 -
BU1 ILI4
OsILI4
OsBU1
BU1/ILI4
OsbHLH172
bHLH172
 BRASSINOSTEROID UPREGULATED 1 BRASSINOSTEROID UPREGULATED1
Increased Leaf Inclination4
BR upregulated 1
basic helix-loop-helix protein 172
 6 Seed - Morphological traits - Grain shape
Seed - Morphological traits
Character as QTL - Plant growth activity
Reproductive organ - Pollination, fertilization, fertility
Vegetative organ - Culm
Vegetative organ - Leaf
Other
Character as QTL - Yield and productivity
 GO:0006355 - regulation of transcription, DNA-dependent
GO:0005737 - cytoplasm
GO:0009741 - response to brassinosteroid stimulus
GO:0009742 - brassinosteroid mediated signaling
GO:0046983 - protein dimerization activity
GO:0040008 - regulation of growth
GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
GO:0009723 - response to ethylene stimulus
GO:0009753 - response to jasmonic acid stimulus
 TO:0000326 - leaf color
TO:0000492 - leaf shape
TO:0000590 - grain weight
TO:0000402 - grain width
TO:0002677 - brassinosteroid sensitivity
TO:0000206 - leaf angle
TO:0000734 - grain length
TO:0000397 - grain size
TO:0000145 - internode length
TO:0000207 - plant height
TO:0000361 - stem anatomy and morphology trait
TO:0000485 - sterility related trait
TO:0000357 - growth and development trait
TO:0002688 - leaf lamina joint bending
TO:0000172 - jasmonic acid sensitivity
TO:0000173 - ethylene sensitivity
 PO:0005052 - plant callus
Os06g0226500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g12210.1
SSG SUBSTANDARD STARCH GRAIN Seed - Morphological traits - Endosperm
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/rice/oryzabase