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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
GH3-8 OsGH3-8
OsMGH3
OsGH3.8
GH3.8
OsGH3-2
 GRETCHEN HAGEN 3 GENE 8 Gretchen Hagen 3 protein 8
 7 Vegetative organ - Culm
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Disease resistance
Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
 GO:0009863 - salicylic acid mediated signaling pathway
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009852 - auxin catabolic process
GO:0006955 - immune response
GO:0010279 - indole-3-acetic acid amido synthetase activity
GO:0016874 - ligase activity
GO:0009651 - response to salt stress
GO:0051607 - defense response to virus
GO:0009908 - flower development
 TO:0000172 - jasmonic acid sensitivity
TO:0000207 - plant height
TO:0000622 - flower development trait
TO:0000401 - plant growth hormone sensitivity
TO:0000346 - tiller number
TO:0006001 - salt tolerance
TO:0000020 - black streak dwarf virus resistance
TO:0002672 - auxin content
 PO:0009066 - anther
PO:0005052 - plant callus
PO:0008037 - seedling
PO:0009010 - seed
PO:0009049 - inflorescence
PO:0007615 - flower development stage
Os07g0592600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g40290.1
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
NH1 OsNH1
OsNPR1
OsNPR1/NH1
NPR1
OsPR2
PR2
DLN5
OsDLN5
OsBTBA1
BTBA1
 NPR1 HOMOLOG 1 NPR1-like 1
NPR1 homologue 1
nonexpresser of PR genes 1
Arabidopsis NPR1 homolog 1
non-expressor of pathogenesis-related gene 1
Arabidopsis NPR1 homologue 1
pathogenesis-related gene 2
nonexpressor of PR genes 1
Nonexpressor of Pathogenesis-Related Genes1
NONEXPRESSOR OF PATHOGENESIS-RELATED1 HOMOLOG1
NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1
non-expressor pathogenesis-related 1
NONEXPRESSOR OF PR1
DLN repressor 5
DLN motif protein 5
BTB-type E3 ubiquitin ligase A1
 1 Tolerance and resistance - Insect resistance
Vegetative organ - Culm
Tolerance and resistance - Lesion mimic
Character as QTL - Yield and productivity
Vegetative organ - Root
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0010200 - response to chitin
GO:0009734 - auxin mediated signaling pathway
GO:0008219 - cell death
GO:0051607 - defense response to virus
GO:0005829 - cytosol
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009609 - response to symbiotic bacterium
GO:0006952 - defense response
GO:0048364 - root development
GO:0010942 - positive regulation of cell death
GO:0006950 - response to stress
GO:0031348 - negative regulation of defense response
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0009625 - response to insect
GO:0016563 - transcription activator activity
GO:0009863 - salicylic acid mediated signaling pathway
GO:0002237 - response to molecule of bacterial origin
GO:0042742 - defense response to bacterium
GO:0009737 - response to abscisic acid stimulus
GO:0005634 - nucleus
GO:0002213 - defense response to insect
GO:0009814 - defense response, incompatible interaction
GO:0002215 - defense response to nematode
GO:0010112 - regulation of systemic acquired resistance
GO:0050832 - defense response to fungus
GO:0009682 - induced systemic resistance
GO:0009408 - response to heat
GO:0009611 - response to wounding
GO:0009627 - systemic acquired resistance
 TO:0000424 - brown planthopper resistance
TO:0000172 - jasmonic acid sensitivity
TO:0000346 - tiller number
TO:0000255 - sheath blight disease resistance
TO:0000074 - blast disease
TO:0000181 - seed weight
TO:0000207 - plant height
TO:0000615 - abscisic acid sensitivity
TO:0000112 - disease resistance
TO:0000401 - plant growth hormone sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000384 - nematode damage resistance
TO:0000656 - root development trait
TO:0000445 - seed number
TO:0000148 - viral disease resistance
TO:0000163 - auxin sensitivity
TO:0000063 - mimic response
 PO:0007089 - stem elongation stage
PO:0007520 - root development stage
Os01g0194300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g09800.1
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
CIPK17 OsCIPK17
OsSnRK3.14
SnRK3.14
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 17 CBL-interacting protein kinase 17
Sucrose nonfermenting-1-related protein kinase 3.14
 5 Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Vegetative organ - Root
Tolerance and resistance - Disease resistance
Character as QTL - Plant growth activity
Character as QTL - Germination
Biochemical character
 GO:0046686 - response to cadmium ion
GO:0009414 - response to water deprivation
GO:0009409 - response to cold
GO:0004674 - protein serine/threonine kinase activity
GO:0007165 - signal transduction
GO:0006952 - defense response
GO:0005737 - cytoplasm
GO:0009408 - response to heat
GO:0010187 - negative regulation of seed germination
GO:0009651 - response to salt stress
GO:0006468 - protein amino acid phosphorylation
GO:0005524 - ATP binding
GO:0030145 - manganese ion binding
 TO:0000112 - disease resistance
TO:0000259 - heat tolerance
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000303 - cold tolerance
TO:0000352 - plant dry weight
TO:0000578 - root fresh weight
TO:0000227 - root length
TO:0000207 - plant height
 PO:0009005 - root
Os05g0136200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g04550.1
SDT miR156h
OsmiR156h
osmiR156h
osa-miR156h
osa-MIR156hosa-miR156h-3p osa-miR156h-5p
 SEMIDWARF AND HIGH-TILLERING micro RNA 156h
microRNA156h
osa-miRNA156h
semidwarf and high-tillering
 6 Tolerance and resistance - Stress tolerance
Other
Character as QTL - Yield and productivity
Vegetative organ - Culm
Tolerance and resistance - Disease resistance
 GO:0007623 - circadian rhythm
GO:0050832 - defense response to fungus
GO:0006379 - mRNA cleavage
GO:0016442 - RNA-induced silencing complex
GO:0035068 - micro-ribonucleoprotein complex
GO:0035195 - gene silencing by miRNA
 TO:0000050 - inflorescence branching
TO:0000074 - blast disease
TO:0000207 - plant height
TO:0000329 - tillering ability
TO:0000068 - lodging incidence
TO:0000346 - tiller number
TO:0000396 - grain yield
 PO:0000009 - cultured plant callus
PO:0009005 - root
PO:0009025 - vascular leaf
PO:0009049 - inflorescence
-
YAB5 OsYAB5
OsYAB3
YAB3
TOB1
OsTOB1
 YABBY 5 Protein YABBY 5
TONGARI-BOUSHI1
TONGARI-BOUSHI 1
 4 Other
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
Vegetative organ - Culm
 GO:0051510 - regulation of unidimensional cell growth
GO:0009685 - gibberellin metabolic process
GO:0045487 - gibberellin catabolic process
GO:0080006 - internode patterning
GO:0009408 - response to heat
GO:0010073 - meristem maintenance
GO:0048437 - floral organ development
GO:0010229 - inflorescence development
GO:0009739 - response to gibberellin stimulus
GO:0005634 - nucleus
GO:0030154 - cell differentiation
GO:0046872 - metal ion binding
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0048366 - leaf development
GO:0009908 - flower development
 TO:0000655 - leaf development trait
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
TO:0000145 - internode length
TO:0002689 - leaf sheath length
TO:0000072 - awn length
TO:0000019 - seedling height
TO:0000165 - panicle exsertion
TO:0000040 - panicle length
TO:0000166 - gibberellic acid sensitivity
TO:0000622 - flower development trait
TO:0000259 - heat tolerance
TO:0000657 - spikelet anatomy and morphology trait
TO:0002600 - flower organ size
TO:0006038 - floral organ number
TO:0000621 - inflorescence development trait
 PO:0001083 - inflorescence development stage
PO:0000017 - vascular leaf primordium
PO:0020104 - leaf sheath
PO:0009051 - spikelet
PO:0025487 - bract primordium
PO:0007615 - flower development stage
PO:0025034 - leaf
PO:0001050 - leaf development stage
PO:0025477 - floral organ primordium
Os04g0536300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g45330.1
NOE1 CATC
OsCat
OsCatC
OsCATC
OsNOE1
noe1
catC
OsCATC
CAT3
OsCAT3
LLM9428
OsLLM9428
 NITRIC OXIDE EXCESS 1 catalase C
catalase isozyme C
nitric oxide excess1
large lesion mimic mutant 9428
 3 Biochemical character
Vegetative organ - Leaf
Character as QTL - Plant growth activity
Seed - Physiological traits - Shattering
Tolerance and resistance - Disease resistance
Vegetative organ - Culm
Tolerance and resistance - Lesion mimic
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
 GO:0010939 - regulation of necrotic cell death
GO:0009725 - response to hormone stimulus
GO:0042744 - hydrogen peroxide catabolic process
GO:0005982 - starch metabolic process
GO:0009409 - response to cold
GO:0050832 - defense response to fungus
GO:0009414 - response to water deprivation
GO:0009642 - response to light intensity
GO:0033484 - nitric oxide homeostasis
GO:0010229 - inflorescence development
GO:0031348 - negative regulation of defense response
GO:0042548 - regulation of photosynthesis, light reaction
GO:0005634 - nucleus
GO:0004096 - catalase activity
GO:0006979 - response to oxidative stress
GO:0042742 - defense response to bacterium
GO:0020037 - heme binding
GO:0009404 - toxin metabolic process
GO:0043067 - regulation of programmed cell death
GO:0009651 - response to salt stress
GO:0005739 - mitochondrion
GO:0006801 - superoxide metabolic process
GO:0010150 - leaf senescence
GO:0050777 - negative regulation of immune response
GO:0009737 - response to abscisic acid stimulus
GO:0009408 - response to heat
GO:0005777 - peroxisome
GO:0045454 - cell redox homeostasis
GO:0009416 - response to light stimulus
 TO:0000346 - tiller number
TO:0000207 - plant height
TO:0000074 - blast disease
TO:0000382 - 1000-seed weight
TO:0000175 - bacterial blight disease resistance
TO:0000303 - cold tolerance
TO:0000249 - leaf senescence
TO:0006001 - salt tolerance
TO:0000259 - heat tolerance
TO:0002657 - oxidative stress
TO:0000605 - hydrogen peroxide content
TO:0000063 - mimic response
TO:0000455 - seed set percent
TO:0000326 - leaf color
TO:0000019 - seedling height
TO:0002637 - leaf size
TO:0000460 - light intensity sensitivity
TO:0000075 - light sensitivity
TO:0000357 - growth and development trait
TO:0002662 - leaf rolling tolerance
TO:0000621 - inflorescence development trait
TO:0000276 - drought tolerance
TO:0000473 - grain shattering
TO:0000615 - abscisic acid sensitivity
TO:0000152 - panicle number
TO:0000401 - plant growth hormone sensitivity
TO:0000447 - filled grain number
 PO:0001054 - 4 leaf senescence stage
PO:0025034 - leaf
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0001083 - inflorescence development stage
Os03g0131200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g03910.1
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
AHP1 OHP1
HPt
OsAHP1
Hpt2
Ohp1
OsHP2
HP2
OsHpt2
OsHPt2
OsHP02
 HISTIDINE CONTAINING PHOSPHOTRANSMITTER 1 histidine containing phosphotransmitter
authentic His-containing phosphotransfer protein 1
Authentic Histidine Phosphotransfer protein 1
 8 Reproductive organ - Pollination, fertilization, fertility
Biochemical character
Vegetative organ - Leaf
Vegetative organ - Culm
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
 GO:0009723 - response to ethylene stimulus
GO:0004871 - signal transducer activity
GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0009736 - cytokinin mediated signaling
GO:0009735 - response to cytokinin stimulus
 TO:0000420 - fertility related trait
TO:0000173 - ethylene sensitivity
TO:0000227 - root length
TO:0006001 - salt tolerance
TO:0000095 - osmotic response sensitivity
TO:0000656 - root development trait
TO:0000167 - cytokinin sensitivity
TO:0000346 - tiller number
TO:0000249 - leaf senescence
TO:0000207 - plant height
 PO:0000230 - inflorescence meristem
PO:0020148 - shoot apical meristem
Os08g0557700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g44350.1
AHP2 OHP2
HPt
OsAHP2 Hpt3
Ohp2
OsHP1
HP1
OsHpt3
OsHP01
 HISTIDINE CONTAINING PHOSPHOTRANSMITTER 2 histidine containing phosphotransmitter
authentic His-containing phosphotransfer protein 2
histidine phosphotransfer protein 2
 9 Vegetative organ - Culm
Vegetative organ - Leaf
Biochemical character
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility
Vegetative organ - Root
 GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0004871 - signal transducer activity
GO:0009723 - response to ethylene stimulus
GO:0009735 - response to cytokinin stimulus
GO:0009736 - cytokinin mediated signaling
 TO:0000420 - fertility related trait
TO:0000249 - leaf senescence
TO:0000095 - osmotic response sensitivity
TO:0000656 - root development trait
TO:0000173 - ethylene sensitivity
TO:0000227 - root length
TO:0000346 - tiller number
TO:0000167 - cytokinin sensitivity
TO:0000207 - plant height
TO:0006001 - salt tolerance
 PO:0000230 - inflorescence meristem
PO:0020148 - shoot apical meristem
Os09g0567400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g39400.2
LOC_Os09g39400.1
SAMDC SamDC
AdoMetDC
AdoMetDC1
OsSAMDC1
 S-ADENOSYLMETHIONINE DECARBOXYLASE S-adenosylmethionine decarboxylase
S-adenosylmethionine decarboxylase proenzyme
S-adenosylmethionine decarboxylase alpha chain
S-adenosylmethionine decarboxylase beta chain
S-adenosylmethionine decarboxylase 1
 4 Biochemical character
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
 GO:0009846 - pollen germination
GO:0009414 - response to water deprivation
GO:0004014 - adenosylmethionine decarboxylase activity
GO:0006597 - spermine biosynthetic process
GO:0008295 - spermidine biosynthetic process
GO:0009409 - response to cold
GO:0009555 - pollen development
GO:0009651 - response to salt stress
GO:0009845 - seed germination
GO:0016209 - antioxidant activity
GO:0006596 - polyamine biosynthetic process
 TO:0000207 - plant height
TO:0000346 - tiller number
TO:0000432 - temperature response trait
TO:0000276 - drought tolerance
TO:0000430 - germination rate
TO:0000449 - grain yield per plant
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000421 - pollen fertility
 Os04g0498600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g42090.1
LOC_Os04g42090.2
LOC_Os04g42090.3
LOC_Os04g42090.4
LOC_Os04g42090.5
LOC_Os04g42095.1
PT8 OsPT8
PHT1-8
OsPht1;8
Pht1;8
PHT1;8
OsPHT1;8
 PHOSPHATE TRANSPORTER 8 Probable inorganic phosphate transporter 1-8
Plant Phosphate Transporter 1;8
 10 Tolerance and resistance - Disease resistance
Biochemical character
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Vegetative organ - Root
 GO:0046688 - response to copper ion
GO:0005315 - inorganic phosphate transmembrane transporter activity
GO:0016021 - integral to membrane
GO:0055085 - transmembrane transport
GO:0048831 - regulation of shoot development
GO:0005886 - plasma membrane
GO:0002221 - pattern recognition receptor signaling pathway
GO:0009733 - response to auxin stimulus
GO:0050832 - defense response to fungus
GO:0005783 - endoplasmic reticulum
GO:0042742 - defense response to bacterium
GO:0002237 - response to molecule of bacterial origin
GO:0002238 - response to molecule of fungal origin
GO:0031348 - negative regulation of defense response
GO:0016036 - cellular response to phosphate starvation
GO:0009737 - response to abscisic acid stimulus
GO:0046685 - response to arsenic
GO:0015293 - symporter activity
GO:0006817 - phosphate transport
GO:0016020 - membrane
GO:0042594 - response to starvation
 TO:0000163 - auxin sensitivity
TO:0000102 - phosphorus sensitivity
TO:0000043 - root anatomy and morphology trait
TO:0000175 - bacterial blight disease resistance
TO:0000074 - blast disease
TO:0000615 - abscisic acid sensitivity
TO:0000021 - copper sensitivity
 PO:0025164 - root epidermal cell
Os10g0444700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g30790.1
LOC_Os10g30790.2
GER5 OsGLP1
GLP1
GER1
GLP110
OsGER1
OsGER5
OsGLP8-14
GLP8-14
OsCDP8.14
CDP8.14
 GERMIN-LIKE PROTEIN 5 Germin-like protein 8-14
Germin-like protein 5
Germin-like protein 1
Germin protein type 1
germin-like protein1
cupin domain protein 8.14
 8 Reproductive organ - panicle
Vegetative organ - Leaf
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Tolerance and resistance - Disease resistance
Seed - Physiological traits - Storage substances
 GO:0005829 - cytosol
GO:0010109 - regulation of photosynthesis
GO:0051553 - flavone biosynthetic process
GO:0010941 - regulation of cell death
GO:0051555 - flavonol biosynthetic process
GO:0010229 - inflorescence development
GO:0009812 - flavonoid metabolic process
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0010224 - response to UV-B
GO:0009409 - response to cold
 TO:0000227 - root length
TO:0001027 - net photosynthetic rate
TO:0000605 - hydrogen peroxide content
TO:0000601 - UV-B light sensitivity
TO:0000207 - plant height
TO:0000621 - inflorescence development trait
TO:0000303 - cold tolerance
TO:0000206 - leaf angle
TO:0000063 - mimic response
 PO:0001083 - inflorescence development stage
PO:0020104 - leaf sheath
Os08g0460000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g35760.1
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
AGPL3 OsAGPL3
APL3
OsAPL3
AGPlar
OsAGPL1
AGPL1
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 3 sativa ADP-glucose pyrophosphorylase large subunit 3
ADP-glucose Pyrophosphorylase large subunit 3
AGPase large subunit 3
AGPase large unit 1
AGPase L1
 5 Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Character as QTL - Yield and productivity
 GO:0009058 - biosynthetic process
GO:0009536 - plastid
GO:0009629 - response to gravity
GO:0009413 - response to flooding
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0016779 - nucleotidyltransferase activity
GO:0019252 - starch biosynthetic process
GO:0009959 - negative gravitropism
 TO:0000207 - plant height
TO:0000567 - tiller angle
TO:0000286 - submergence sensitivity
TO:0000396 - grain yield
TO:0000696 - starch content
TO:0000346 - tiller number
TO:0002693 - gravity response trait
 PO:0009066 - anther
PO:0025034 - leaf
PO:0004006 - mesophyll cell
PO:0005020 - vascular bundle
PO:0020104 - leaf sheath
PO:0000074 - parenchyma cell
PO:0009047 - stem
PO:0009010 - seed
PO:0009089 - endosperm
Os05g0580000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g50380.2
LOC_Os05g50380.1
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
AGO1B OsAGO1b
AGO1b
AGO1-2
 ARGONAUTE 1B Protein argonaute 1B
 4 Vegetative organ - Leaf
Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Pollination, fertilization, fertility
Vegetative organ - Culm
Other
 GO:0003676 - nucleic acid binding
GO:0005634 - nucleus
GO:0048366 - leaf development
GO:0031047 - gene silencing by RNA
GO:0005737 - cytoplasm
 TO:0000421 - pollen fertility
TO:0000655 - leaf development trait
TO:0000207 - plant height
TO:0000455 - seed set percent
TO:0000346 - tiller number
 PO:0025034 - leaf
PO:0001050 - leaf development stage
PO:0000002 - anther wall
Os04g0566500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g47870.2
LOC_Os04g47870.1
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
BC10 BC10
bc10
FC116
FC116/BC10
Osbc10
Osfc116
 BRITTLE CULM 10 brittle culm 10
fragile culm 116
 5 Vegetative organ - Culm
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0009808 - lignin metabolic process
GO:0009834 - secondary cell wall biogenesis
GO:0008375 - acetylglucosaminyltransferase activity
GO:0009531 - secondary cell wall
GO:0016020 - membrane
GO:0009809 - lignin biosynthetic process
GO:0045492 - xylan biosynthetic process
GO:0005886 - plasma membrane
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0031225 - anchored to membrane
 TO:0006006 - monosaccharide content
TO:0000300 - glucose content
TO:0000307 - hexose content
TO:0000051 - stem strength
TO:0000731 - lignin content
 Os05g0170000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g07790.1
BC1L1 OsBC1L1
OsPCS13
PCS13
 BRITTLE CULM-LIKE 1 (sativa BRITTLE CULM1-like 1)
Phytochelatin synthase 13
 3 Vegetative organ - Culm
 GO:0009531 - secondary cell wall
GO:0031225 - anchored to membrane
GO:0005886 - plasma membrane
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0016021 - integral to membrane
GO:0010215 - cellulose microfibril organization
GO:0009808 - lignin metabolic process
GO:0009834 - secondary cell wall biogenesis
 PO:0025034 - leaf
Os03g0301200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g18910.1
DCL3A OsDCL3a
 DICER-LIKE 3A Endoribonuclease Dicer homolog 3a
Dicer-like protein 3a
 1 Vegetative organ - Leaf
Biochemical character
Vegetative organ - Culm
Tolerance and resistance - Insect resistance
Reproductive organ - Inflorescence
Tolerance and resistance - Disease resistance
 GO:0005524 - ATP binding
GO:0005634 - nucleus
GO:0006396 - RNA processing
GO:0030145 - manganese ion binding
GO:0000287 - magnesium ion binding
GO:0031047 - gene silencing by RNA
GO:0003677 - DNA binding
GO:0004386 - helicase activity
GO:0004525 - ribonuclease III activity
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0003723 - RNA binding
GO:0002215 - defense response to nematode
GO:0009873 - ethylene mediated signaling pathway
GO:0009753 - response to jasmonic acid stimulus
GO:0050832 - defense response to fungus
GO:0009627 - systemic acquired resistance
GO:0009723 - response to ethylene stimulus
 TO:0000557 - secondary branch number
TO:0000124 - flag leaf angle
TO:0000074 - blast disease
TO:0000207 - plant height
TO:0000173 - ethylene sensitivity
TO:0000384 - nematode damage resistance
TO:0002667 - abscisic acid content
TO:0000172 - jasmonic acid sensitivity
 Os01g0909200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g68120.1
HB4 OSHB4
OsHox32
HOX32
OsHB4
Oshox32
PHB3
OsHDZ13
OsHDZIP13
HDZ13
HDZIP13
 HOMEODOMAIN CONTAINING PROTEIN 4 Homeobox-leucine zipper protein HOX32
Homeodomain transcription factor HOX32
HD-ZIP protein HOX32
rice homeobox gene 32
homeodomain-leucine zipper transcription factor 13
OsHDZIP transcription factor 13
 3 Other
Vegetative organ - Culm
Coloration - Chlorophyll
Vegetative organ - Leaf
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
 GO:0005634 - nucleus
GO:0005886 - plasma membrane
GO:0009416 - response to light stimulus
GO:0048366 - leaf development
GO:0009753 - response to jasmonic acid stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0046686 - response to cadmium ion
GO:0009733 - response to auxin stimulus
GO:0009414 - response to water deprivation
GO:0006350 - transcription
GO:0006355 - regulation of transcription, DNA-dependent
GO:0043565 - sequence-specific DNA binding
GO:0003700 - transcription factor activity
GO:0042546 - cell wall biogenesis
 TO:0000276 - drought tolerance
TO:0000370 - leaf width
TO:0000163 - auxin sensitivity
TO:0000207 - plant height
TO:0000615 - abscisic acid sensitivity
TO:0000655 - leaf development trait
TO:0000051 - stem strength
TO:0001017 - water use efficiency
TO:0000085 - leaf rolling
TO:0000172 - jasmonic acid sensitivity
TO:0001015 - photosynthetic rate
TO:0000206 - leaf angle
TO:0000495 - chlorophyll content
TO:0000075 - light sensitivity
 PO:0009049 - inflorescence
PO:0025034 - leaf
PO:0009005 - root
PO:0009089 - endosperm
PO:0001050 - leaf development stage
Os03g0640800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g43930.2
LOC_Os03g43930.1
PDR6 OsPDR6
OsABCG31
OsABCG31_1
 PLEIOTROPIC DRUG RESISTANCE 6 sativa pleiotropic drug resistance 6
Pleiotropic drug resistance protein 6
ABC transporter superfamily ABCG subgroup member 31
ATP-binding Cassette Transporter G31
 1 Vegetative organ - Culm
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0016020 - membrane
GO:0042335 - cuticle development
GO:0050832 - defense response to fungus
GO:0005524 - ATP binding
GO:0006810 - transport
GO:0016021 - integral to membrane
GO:0016887 - ATPase activity
GO:0010143 - cutin biosynthetic process
 TO:0000074 - blast disease
TO:0000207 - plant height
 Os01g0177900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g08260.1
LOC_Os01g08260.2
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
CKX5 OsCKX5
ckx5
 CYTOKININ OXIDASE/DEHYDROGENASE 5 Putative cytokinin oxidase 5
cytokinin oxidase 5
 1 Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
 GO:0042594 - response to starvation
GO:0032940 - secretion by cell
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009694 - jasmonic acid metabolic process
GO:0009753 - response to jasmonic acid stimulus
GO:0009725 - response to hormone stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0009823 - cytokinin catabolic process
GO:0009536 - plastid
GO:0016491 - oxidoreductase activity
GO:0019139 - cytokinin dehydrogenase activity
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0050660 - FAD binding
GO:0022900 - electron transport chain
 TO:0002660 - cytokinin content
TO:0000207 - plant height
TO:0000401 - plant growth hormone sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000266 - chalky endosperm
TO:0000011 - nitrogen sensitivity
TO:0000163 - auxin sensitivity
 Os01g0775400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g56810.2
LOC_Os01g56810.1
CKX9 OsCKX9
 CYTOKININ OXIDASE/DEHYDROGENASE 9 cytokinin oxidase 9
 5 Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Character as QTL - Yield and productivity
 GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0009735 - response to cytokinin stimulus
GO:0009733 - response to auxin stimulus
GO:0009725 - response to hormone stimulus
GO:0042594 - response to starvation
GO:0005829 - cytosol
GO:0009823 - cytokinin catabolic process
GO:0005634 - nucleus
GO:0019139 - cytokinin dehydrogenase activity
 TO:0000547 - primary branch number
TO:0000011 - nitrogen sensitivity
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000207 - plant height
TO:0000401 - plant growth hormone sensitivity
TO:0000582 - inflorescence number
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000447 - filled grain number
TO:0000346 - tiller number
 Os05g0374200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g31040.1
GT1 HOX12
Oshox12
OsHox12
OsGT1
 GRASSY TILLER 1 rice homeobox gene 12
Homeobox-leucine zipper protein HOX12
Homeodomain transcription factor HOX12
HD-ZIP protein HOX12
grassy tiller1
 3 Reproductive organ - panicle
Tolerance and resistance - Stress tolerance
Character as QTL - Germination
Other
Vegetative organ - Culm
 GO:0003700 - transcription factor activity
GO:0009845 - seed germination
GO:0005634 - nucleus
GO:0009413 - response to flooding
GO:0009409 - response to cold
GO:0009685 - gibberellin metabolic process
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0030912 - response to deep water
GO:0043565 - sequence-specific DNA binding
GO:0048658 - tapetal layer development
GO:0010336 - gibberellic acid homeostasis
 TO:0000329 - tillering ability
TO:0000346 - tiller number
TO:0002675 - gibberellic acid content
TO:0001002 - inflorescence exsertion
TO:0000303 - cold tolerance
TO:0000524 - submergence tolerance
 PO:0007045 - coleoptile emergence stage
PO:0009049 - inflorescence
PO:0009066 - anther
PO:0007057 - 0 seed germination stage
Os03g0198600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g10210.1
HOX24 Oshox24
OsHox24
OsSLI1
OsHDZ6
OsHDZIP6
HDZ6
HDZIP6
 HOMEOBOX GENE 24 rice homeobox gene 24
Homeobox-leucine zipper protein HOX24
Homeodomain transcription factor HOX24
HD-ZIP protein HOX24
stress largely induced 1
homeodomain-leucine zipper transcription factor 6
OsHDZIP transcription factor 6
 2 Tolerance and resistance - Stress tolerance
Other
Vegetative organ - Leaf
Vegetative organ - Culm
Reproductive organ - panicle
 GO:0006970 - response to osmotic stress
GO:0009651 - response to salt stress
GO:0043565 - sequence-specific DNA binding
GO:0005634 - nucleus
GO:0009408 - response to heat
GO:0009628 - response to abiotic stimulus
GO:0009751 - response to salicylic acid stimulus
GO:0009739 - response to gibberellin stimulus
GO:0006350 - transcription
GO:0006355 - regulation of transcription, DNA-dependent
GO:0003700 - transcription factor activity
GO:0010118 - stomatal movement
GO:0009269 - response to desiccation
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0006950 - response to stress
GO:0009733 - response to auxin stimulus
GO:0009409 - response to cold
 TO:0000516 - relative root length
TO:0000615 - abscisic acid sensitivity
TO:0000168 - abiotic stress trait
TO:0000507 - osmotic adjustment capacity
TO:0001016 - relative chlorophyll content
TO:0000163 - auxin sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000276 - drought tolerance
TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
TO:0000095 - osmotic response sensitivity
TO:0000259 - heat tolerance
TO:0000152 - panicle number
TO:0000346 - tiller number
 Os02g0649300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g43330.1
HOX28 Oshox28
OsHox28
OsHDZ18
OsHDZIP18
HDZ18
HDZIP18
 HOMEOBOX GENE 28 rice homeobox gene 28
Homeobox-leucine zipper protein HOX28
Homeodomain transcription factor HOX28
HD-ZIP protein HOX28
homeodomain-leucine zipper transcription factor 18
OsHDZIP transcription factor 18
 6 Other
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
 GO:0009651 - response to salt stress
GO:0043565 - sequence-specific DNA binding
GO:0010600 - regulation of auxin biosynthetic process
GO:0009741 - response to brassinosteroid stimulus
GO:0003700 - transcription factor activity
GO:0009959 - negative gravitropism
GO:0005634 - nucleus
GO:0030912 - response to deep water
GO:0010252 - auxin homeostasis
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0006001 - salt tolerance
TO:0002693 - gravity response trait
TO:0000524 - submergence tolerance
TO:0002677 - brassinosteroid sensitivity
TO:0000567 - tiller angle
TO:0002672 - auxin content
 PO:0025034 - leaf
PO:0009005 - root
PO:0009047 - stem
PO:0009049 - inflorescence
PO:0009030 - carpel
PO:0009009 - plant embryo
Os06g0140400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g04850.1
HAP2H OsHAP2H
NF-YA
CBF-B
NF-YA3
OsNF-YA3
NFYA3
 HAP2 SUBUNIT OF CCAAT-BOX BINDING COMPLEX NUCLEAR FACTOR-Y subunit A3
NUCLEAR FACTOR-Y subunit NF-YA3
NF-YA transcription factor 3
NF-YA subunit 3
NF-YA family 3
 3 Character as QTL - Plant growth activity
Tolerance and resistance - Disease resistance
Other
Vegetative organ - Leaf
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
 GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009753 - response to jasmonic acid stimulus
GO:0043565 - sequence-specific DNA binding
GO:0010728 - regulation of hydrogen peroxide biosynthetic process
GO:0009651 - response to salt stress
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0009740 - gibberellic acid mediated signaling
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0051607 - defense response to virus
GO:0090359 - negative regulation of abscisic acid biosynthetic process
GO:0006970 - response to osmotic stress
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0009788 - negative regulation of abscisic acid mediated signaling
GO:0009737 - response to abscisic acid stimulus
GO:0046345 - abscisic acid catabolic process
GO:0010119 - regulation of stomatal movement
GO:0051512 - positive regulation of unidimensional cell growth
GO:0006350 - transcription
GO:0047484 - regulation of response to osmotic stress
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005634 - nucleus
GO:0003700 - transcription factor activity
GO:0080006 - internode patterning
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0030104 - water homeostasis
 TO:0002662 - leaf rolling tolerance
TO:0000145 - internode length
TO:0000136 - relative water content
TO:0000019 - seedling height
TO:0000605 - hydrogen peroxide content
TO:0000148 - viral disease resistance
TO:0002667 - abscisic acid content
TO:0000207 - plant height
TO:0000615 - abscisic acid sensitivity
TO:0000357 - growth and development trait
TO:0006002 - proline content
TO:0000095 - osmotic response sensitivity
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000172 - jasmonic acid sensitivity
TO:0002675 - gibberellic acid content
TO:0000520 - stomatal closure rate
 Os03g0647600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g44540.1
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
DWL1 DWARFISM AND WITHERED LEAF TIP 1 3 Vegetative organ - Culm
 GO:0007275 - multicellular organismal development
 -
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
HSFA2D HSfA2d
OsHsfA2d
OsHsf-08
rHsf7
HSF08
OsHSF8
HSF8
HSF7
OsHSF7
OsHSFA2dI
OsHSFA2dII
OsHSFA2dIII
OsHsfA6b
HsfA6b
OsHsf2d
Hsf2d
HTG3
OsHTG3
 HEAT STRESS TRANSCRIPTION FACTOR A2D Heat stress transcription factor A2d
Heat stress transcription factor A-2d
Heat stress transcription factor 8
Heat stress transcription factor 7
heat-tolerance gene on chromosome 3
 3 Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
 GO:0003700 - transcription factor activity
GO:0009408 - response to heat
GO:0005739 - mitochondrion
GO:0009926 - auxin polar transport
GO:0009959 - negative gravitropism
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
GO:0009734 - auxin mediated signaling pathway
GO:0009629 - response to gravity
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005829 - cytosol
GO:0046686 - response to cadmium ion
GO:0005634 - nucleus
GO:0006986 - response to unfolded protein
GO:0048571 - long-day photoperiodism
GO:0006350 - transcription
GO:0006950 - response to stress
GO:0009735 - response to cytokinin stimulus
 TO:0000075 - light sensitivity
TO:0000259 - heat tolerance
TO:0000567 - tiller angle
TO:0002693 - gravity response trait
TO:0000207 - plant height
TO:0000167 - cytokinin sensitivity
 Os03g0161900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g06630.1
LOC_Os03g06630.2
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
SNK1 SK1
OsSK1
OsSNK1
SK1C9285
 SNORKEL 1 SNORKEL1
 12 Tolerance and resistance - Stress tolerance
Character as QTL
Vegetative organ - Culm
 GO:0001666 - response to hypoxia
GO:0009413 - response to flooding
GO:0030912 - response to deep water
GO:0080006 - internode patterning
GO:0003677 - DNA binding
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0006351 - transcription, DNA-dependent
 TO:0000103 - deepwater stress
TO:0000524 - submergence tolerance
TO:0000145 - internode length
 -
SNK2 SK2
OsSK2
OsSNK2
 SNORKEL 2 SNORKEL2
 12 Character as QTL
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
 GO:0001666 - response to hypoxia
GO:0030912 - response to deep water
GO:0080006 - internode patterning
GO:0009413 - response to flooding
GO:0003700 - transcription factor activity
GO:0003677 - DNA binding
GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
 TO:0000103 - deepwater stress
TO:0000145 - internode length
TO:0000524 - submergence tolerance
 -
LCS OsHAK1
HAK1
 LOW CS ACCUMULATION High-affinity Potassium(K+) Transporter 1
Potassium transporter 1
low Cs accumulation
 4 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Biochemical character
 GO:0051607 - defense response to virus
GO:0015079 - potassium ion transmembrane transporter activity
GO:0009414 - response to water deprivation
GO:0055075 - potassium ion homeostasis
GO:0016021 - integral to membrane
GO:0030955 - potassium ion binding
GO:0005886 - plasma membrane
GO:0006813 - potassium ion transport
GO:0009674 - potassium:sodium symporter activity
GO:0051365 - cellular response to potassium ion starvation
GO:0009651 - response to salt stress
 TO:0000276 - drought tolerance
TO:0006001 - salt tolerance
TO:0000213 - rice grassy stunt 1 and 2 virus resistance
TO:0000207 - plant height
 Os04g0401700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g32920.1
LOC_Os04g32920.2
LOC_Os04g32920.3
LOC_Os04g32920.4
LOC_Os04g32920.5
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
PROG1 OsPROG1
ZOS7-02
OsZOS7-02
 PROSTRATE GROWTH 1 zinc-finger nuclear transcription factor PROG1
zinc-finger protein TFIIIA class of Oryza sativa 7-02
ZPT of Oryza sativa 7-02
 7 Other
Character as QTL - Yield and productivity
Vegetative organ - Culm
 GO:0009536 - plastid
GO:0005634 - nucleus
GO:0048873 - homeostasis of number of cells within a tissue
GO:0016563 - transcription activator activity
 TO:0000547 - primary branch number
TO:0000207 - plant height
TO:0002759 - grain number
TO:0000567 - tiller angle
TO:0000440 - grain number per plant
TO:0000557 - secondary branch number
TO:0000152 - panicle number
TO:0000449 - grain yield per plant
 PO:0009081 - inflorescence branch
PO:0008019 - leaf lamina base
PO:0005001 - basal axillary shoot system
PO:0008017 - leaf sheath pulvinus
Os07g0153600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g05900.1
FC1 OsCAD7
fc1
CAD7
 FLEXIBLE CULM 1 flexible culm1
FLEXIBLE CULM1
Protein FLEXIBLE CULM 1
Cinnamyl alcohol dehydrogenase 7
 4 Vegetative organ - Culm
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0009626 - plant-type hypersensitive response
GO:0009809 - lignin biosynthetic process
GO:0044036 - cell wall macromolecule metabolic process
GO:0045551 - cinnamyl-alcohol dehydrogenase activity
GO:0048046 - apoplast
GO:0018456 - aryl-alcohol dehydrogenase activity
GO:0008270 - zinc ion binding
GO:0000166 - nucleotide binding
GO:0009617 - response to bacterium
GO:0055114 - oxidation reduction
GO:0009834 - secondary cell wall biogenesis
GO:0009808 - lignin metabolic process
 TO:0000011 - nitrogen sensitivity
TO:0000733 - lignin biosynthesis trait
TO:0000051 - stem strength
 PO:0009047 - stem
PO:0020104 - leaf sheath
Os04g0612700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g52280.1
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
LPS1 SDH2
SDHB
sdhB
RPS14
rps14
sdh2-1
SDH2-RPS14
OsLPS1
OsSDH2-1
 LATE PREMATURE SENESCENCE 1 SUCCINATE:UBIQUINONE OXIDOREDUCTASE
mitochondrial succinate dehydrogenase subunit B
ribosomal protein S14
succinate dehydrogenase (iron-sulphur protein subunit)
chimeric SDH2-RPS14
 8 Reproductive organ - Pollination, fertilization, fertility
Coloration - Chlorophyll
Coloration - Others
Character as QTL - Yield and productivity
Biochemical character
Reproductive organ - panicle
Vegetative organ - Culm
Vegetative organ - Leaf
Tolerance and resistance - Stress tolerance
 GO:0006099 - tricarboxylic acid cycle
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0007005 - mitochondrion organization
GO:0009658 - chloroplast organization
GO:0009055 - electron carrier activity
GO:0000104 - succinate dehydrogenase activity
GO:0016491 - oxidoreductase activity
GO:0010150 - leaf senescence
GO:0005739 - mitochondrion
GO:0010229 - inflorescence development
 TO:0000293 - chlorophyll-a content
TO:0001015 - photosynthetic rate
TO:0000316 - photosynthetic ability
TO:0000040 - panicle length
TO:0000522 - stomatal conductance
TO:0000447 - filled grain number
TO:0002715 - chloroplast development trait
TO:0000639 - seed fertility
TO:0000621 - inflorescence development trait
TO:0000249 - leaf senescence
TO:0000396 - grain yield
TO:0000207 - plant height
TO:0000137 - days to heading
TO:0000605 - hydrogen peroxide content
TO:0000455 - seed set percent
TO:0006032 - panicle size
TO:0000496 - carotenoid content
TO:0000295 - chlorophyll-b content
 PO:0001083 - inflorescence development stage
PO:0000025 - root tip
PO:0025034 - leaf
PO:0001054 - 4 leaf senescence stage
PO:0009066 - anther
PO:0009072 - plant ovary
Os08g0120000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g02640.1
LOC_Os08g02640.2
LOC_Os08g02640.3
LOC_Os08g02640.4
LOC_Os08g02640.5
RIM1 ONAC054
ONAC54
NAC54
ONAC054alpha
ONAC054beta
 RICE DWARF VIRUS MULTIPLICATION 1 NAC domain-containing protein 054
NAC domain-containing protein 54
 3 Tolerance and resistance - Disease resistance
Vegetative organ - Root
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
 GO:0003700 - transcription factor activity
GO:0009738 - abscisic acid mediated signaling
GO:0010150 - leaf senescence
GO:0009737 - response to abscisic acid stimulus
GO:0005634 - nucleus
GO:0009723 - response to ethylene stimulus
GO:0016021 - integral to membrane
 TO:0000207 - plant height
TO:0000249 - leaf senescence
TO:0000615 - abscisic acid sensitivity
TO:0002667 - abscisic acid content
TO:0000460 - light intensity sensitivity
TO:0000173 - ethylene sensitivity
TO:0000326 - leaf color
TO:0000495 - chlorophyll content
TO:0000316 - photosynthetic ability
TO:0000152 - panicle number
TO:0000172 - jasmonic acid sensitivity
TO:0000148 - viral disease resistance
TO:0000447 - filled grain number
TO:0000180 - spikelet fertility
TO:0000227 - root length
 PO:0001054 - 4 leaf senescence stage
Os03g0119966 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g02800.1
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
DOF7 OsDof7
Dof7
OsDof-7
OsDOF11
DOF11
OsDof9
Dof9
 DNA BINDING WITH ONE FINGER 7 DNA BINDING WITH ONE FINGER 11
 2 Biochemical character
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Vegetative organ - Root
 GO:0042742 - defense response to bacterium
GO:0010087 - phloem or xylem histogenesis
GO:0003677 - DNA binding
GO:0010067 - procambium histogenesis
GO:0003700 - transcription factor activity
GO:0009409 - response to cold
GO:0048364 - root development
GO:0005634 - nucleus
GO:0015770 - sucrose transport
GO:0045893 - positive regulation of transcription, DNA-dependent
 TO:0000346 - tiller number
TO:0006005 - fructose content
TO:0000303 - cold tolerance
TO:0006032 - panicle size
TO:0000207 - plant height
TO:0000175 - bacterial blight disease resistance
TO:0000328 - sucrose content
TO:0000300 - glucose content
TO:0000227 - root length
 PO:0005421 - parenchyma
PO:0000034 - vascular system
PO:0000071 - companion cell
PO:0005020 - vascular bundle
PO:0009005 - root
PO:0020141 - stem node
PO:0020110 - scutellum
Os02g0707200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g47810.1
SP3 OsDof15
Dof15
OsDof-15
DOF15
DLT3
OsDLT3
 SHORT PANICLE 3 Dof zinc factor 15
Dof transcription factor 15
DNA BINDING WITH ONE FINGER 15
Short Panicle 3
DWARF AND LESS TILLERS ON CHROMOSOME 3
 3 Vegetative organ - Root
Other
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Reproductive organ - Panicle, Mode of branching
Reproductive organ - Heading date
Character as QTL - Yield and productivity
Vegetative organ - Leaf
 GO:0048573 - photoperiodism, flowering
GO:0009873 - ethylene mediated signaling pathway
GO:0009651 - response to salt stress
GO:0008284 - positive regulation of cell proliferation
GO:0010229 - inflorescence development
GO:0006355 - regulation of transcription, DNA-dependent
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0009690 - cytokinin metabolic process
GO:0010081 - regulation of inflorescence meristem growth
GO:0048364 - root development
GO:0003677 - DNA binding
GO:0005634 - nucleus
GO:0010082 - regulation of root meristem growth
 TO:0000547 - primary branch number
TO:0000132 - basal internode diameter
TO:0000227 - root length
TO:0002758 - flag leaf lamina width
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000621 - inflorescence development trait
TO:0000040 - panicle length
TO:0000173 - ethylene sensitivity
TO:0000434 - root activity
TO:0000371 - yield trait
TO:0006001 - salt tolerance
TO:0000656 - root development trait
TO:0000396 - grain yield
TO:0000145 - internode length
TO:0000557 - secondary branch number
TO:0000734 - grain length
TO:0000207 - plant height
TO:0000592 - 1000-dehulled grain weight
TO:0002660 - cytokinin content
TO:0000456 - spikelet number
TO:0000050 - inflorescence branching
TO:0002692 - root meristem development
TO:0000397 - grain size
TO:0000455 - seed set percent
TO:0000346 - tiller number
TO:0000329 - tillering ability
TO:0006032 - panicle size
TO:0002616 - flowering time
TO:0000137 - days to heading
 PO:0004709 - axillary bud
PO:0009049 - inflorescence
Os03g0764900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g55610.1
GLW9 OsDof25
Dof25
OsDof-25
OsDof26
Dof26
OsGLW9
 GRAIN LENGTH AND WIDTH ON CHROMOSOME 9 DNA BINDING WITH ONE FINGER 25
Dof zinc factor 25
Dof transcription factor 25
DNA binding with one finger family transcription factor 25
 9 Other
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
Character as QTL - Grain quality
Character as QTL - Yield and productivity
 GO:0009733 - response to auxin stimulus
GO:0010928 - regulation of auxin mediated signaling pathway
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0003677 - DNA binding
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009734 - auxin mediated signaling pathway
GO:0005634 - nucleus
GO:0009740 - gibberellic acid mediated signaling
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000411 - seed length to width ratio
TO:0002672 - auxin content
TO:0000402 - grain width
TO:0000567 - tiller angle
TO:0000449 - grain yield per plant
TO:0002730 - grain shape
TO:0002675 - gibberellic acid content
TO:0000734 - grain length
TO:0000163 - auxin sensitivity
TO:0000456 - spikelet number
TO:0000447 - filled grain number
TO:0000162 - seed quality
TO:0000266 - chalky endosperm
 Os09g0475800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g29960.1
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/rice/oryzabase