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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
NYC1 nyc1
OsNYC1
 NON-YELLOW COLORING 1 Chlorophyl b degrading enzyme
Chlase
Non-Yellow Coloring 1
non-yellow coloring1
Probable chlorophyll(ide) b reductase NYC1
chloroplastic
Protein NON-YELLOW COLORING 1
short-chain dehydrogenase/reductase NYC1
 1 Coloration - Chlorophyll
Vegetative organ - Leaf
Biochemical character
 GO:0005488 - binding
GO:0009535 - chloroplast thylakoid membrane
GO:0010304 - PSII associated light-harvesting complex II catabolic process
GO:0010150 - leaf senescence
GO:0016021 - integral to membrane
GO:0034256 - chlorophyll(ide) b reductase activity
GO:0055114 - oxidation reduction
GO:0015996 - chlorophyll catabolic process
GO:0009536 - plastid
GO:0016491 - oxidoreductase activity
GO:0042170 - plastid membrane
 TO:0002712 - stay green trait
TO:0000249 - leaf senescence
TO:0000599 - enzyme activity
TO:0000495 - chlorophyll content
 PO:0009037 - lemma
PO:0001054 - 4 leaf senescence stage
PO:0020104 - leaf sheath
PO:0020122 - inflorescence axis
PO:0009025 - vascular leaf
PO:0009038 - palea
Os01g0227100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g12710.2
LOC_Os01g12710.1
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
CIPK02 OsCIPK02
CIPK2
OsCIPK2
OsSnRK3.26
SnRK3.26
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 2 CBL-interacting protein kinase 2
Sucrose nonfermenting-1-related protein kinase 3.26
 7 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Vegetative organ - Root
 GO:0015770 - sucrose transport
GO:0034219 - carbohydrate transmembrane transport
GO:0009409 - response to cold
GO:0009737 - response to abscisic acid stimulus
GO:0005524 - ATP binding
GO:0042128 - nitrate assimilation
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0031667 - response to nutrient levels
GO:0004674 - protein serine/threonine kinase activity
GO:0006995 - cellular response to nitrogen starvation
GO:0042594 - response to starvation
GO:0019740 - nitrogen utilization
GO:0006468 - protein amino acid phosphorylation
GO:0007165 - signal transduction
GO:0009651 - response to salt stress
GO:0044136 - development of symbiont on or near host rhizosphere
GO:0030145 - manganese ion binding
 TO:0000371 - yield trait
TO:0001027 - net photosynthetic rate
TO:0000495 - chlorophyll content
TO:0000644 - relative root dry weight
TO:0000636 - relative shoot dry weight
TO:0000455 - seed set percent
TO:0000152 - panicle number
TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000291 - carbohydrate content
TO:0000011 - nitrogen sensitivity
TO:0000382 - 1000-seed weight
TO:0000449 - grain yield per plant
TO:0000128 - harvest index
 PO:0009005 - root
Os07g0678600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g48100.1
CIPK09 OsCIPK09
CIPK9
OsCIPK9
OsSnRK3.10
SnRK3.10
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 9 CBL-interacting protein kinase 9
Sucrose nonfermenting-1-related protein kinase 3.10
 3 Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0009409 - response to cold
GO:0007165 - signal transduction
GO:0009414 - response to water deprivation
GO:0009651 - response to salt stress
GO:0006468 - protein amino acid phosphorylation
GO:0005524 - ATP binding
GO:0060359 - response to ammonium ion
GO:0004674 - protein serine/threonine kinase activity
GO:0030145 - manganese ion binding
 TO:0000276 - drought tolerance
TO:0000303 - cold tolerance
TO:0000227 - root length
TO:0006001 - salt tolerance
 PO:0009005 - root
Os03g0126800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g03510.2
LOC_Os03g03510.1
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
DMI3 OsDMI3
OsCCaMK1
OsCCaMK
OsCCAMK
CCAMK
 DOESN'T MAKE INFECTIONS 3 DOESN'T MAKE INFECTIONS3
calcium and calmodulin-dependent protein kinase 1
Ca2+/calmodulin (CaM)-dependent protein kinase
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE
 5 Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Character as QTL - Germination
 GO:0009610 - response to symbiotic fungus
GO:0005737 - cytoplasm
GO:0005634 - nucleus
GO:0009734 - auxin mediated signaling pathway
GO:0009651 - response to salt stress
GO:0048364 - root development
GO:0019722 - calcium-mediated signaling
GO:0010726 - positive regulation of hydrogen peroxide metabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0005524 - ATP binding
GO:0005509 - calcium ion binding
GO:0006979 - response to oxidative stress
GO:0009789 - positive regulation of abscisic acid mediated signaling
GO:0010030 - positive regulation of seed germination
GO:0050832 - defense response to fungus
GO:0047484 - regulation of response to osmotic stress
GO:0006970 - response to osmotic stress
GO:0018107 - peptidyl-threonine phosphorylation
GO:0060267 - positive regulation of respiratory burst
GO:0030104 - water homeostasis
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0042542 - response to hydrogen peroxide
GO:0010729 - positive regulation of hydrogen peroxide biosynthetic process
GO:0004683 - calmodulin-dependent protein kinase activity
GO:0043408 - regulation of MAPKKK cascade
GO:0009738 - abscisic acid mediated signaling
GO:0009845 - seed germination
GO:0009414 - response to water deprivation
GO:0016021 - integral to membrane
 TO:0000615 - abscisic acid sensitivity
TO:0000656 - root development trait
TO:0002657 - oxidative stress
TO:0000136 - relative water content
TO:0000074 - blast disease
TO:0000605 - hydrogen peroxide content
TO:0000095 - osmotic response sensitivity
TO:0006001 - salt tolerance
TO:0000516 - relative root length
TO:0000276 - drought tolerance
TO:0002672 - auxin content
 PO:0007520 - root development stage
PO:0007057 - 0 seed germination stage
Os05g0489900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g41090.1
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
-
YUCCA1 OsYUCCA1
OsYUC1
YUC1
 YUCCA-LIKE GENE 1 (YUCCA-like gene)
 1 Tolerance and resistance - Disease resistance
Vegetative organ - Root
Character as QTL - Yield and productivity
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0010229 - inflorescence development
GO:0048364 - root development
GO:0009609 - response to symbiotic bacterium
GO:0051607 - defense response to virus
GO:0034059 - response to anoxia
GO:0009737 - response to abscisic acid stimulus
GO:0004499 - flavin-containing monooxygenase activity
GO:0009851 - auxin biosynthetic process
GO:0046686 - response to cadmium ion
GO:0046685 - response to arsenic
GO:0048830 - adventitious root development
GO:0009408 - response to heat
GO:0009414 - response to water deprivation
 TO:0000396 - grain yield
TO:0000031 - silicon sensitivity
TO:0000227 - root length
TO:0000020 - black streak dwarf virus resistance
TO:0000084 - root number
TO:0000656 - root development trait
TO:0000428 - callus induction
TO:0000615 - abscisic acid sensitivity
TO:0000447 - filled grain number
TO:0000259 - heat tolerance
TO:0000276 - drought tolerance
TO:0002672 - auxin content
TO:0000578 - root fresh weight
TO:0000621 - inflorescence development trait
TO:0001013 - lateral root number
TO:0000557 - secondary branch number
TO:0001006 - adventitious root number
TO:0000449 - grain yield per plant
 PO:0020103 - flag leaf
PO:0009105 - inflorescence branch meristem
Os01g0645400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g45760.1
LOC_Os01g45760.2
RBOHB rbohB
OsrbohB
Os rbohB
OsRbohB
OsNox1
Nox1
Os-RbohB
RbohB
OsRboh1
Rboh1
 RESPIRATORY BURST OXIDASE HOMOLOG B Respiratory Burst Oxidase Homolog B
Respiratory Burst Oxidase Homologue B
NADPH oxidase 1
 1 Biochemical character
Vegetative organ - Root
Reproductive organ - Pollination, fertilization, fertility
Character as QTL - Germination
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
 GO:0009687 - abscisic acid metabolic process
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0009751 - response to salicylic acid stimulus
GO:0004601 - peroxidase activity
GO:0005509 - calcium ion binding
GO:0009408 - response to heat
GO:0009734 - auxin mediated signaling pathway
GO:0009845 - seed germination
GO:0006952 - defense response
GO:0009626 - plant-type hypersensitive response
GO:0030104 - water homeostasis
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0002238 - response to molecule of fungal origin
GO:0009753 - response to jasmonic acid stimulus
GO:0005886 - plasma membrane
GO:0010266 - response to vitamin B1
GO:0050832 - defense response to fungus
GO:0009737 - response to abscisic acid stimulus
GO:0043621 - protein self-association
GO:0009733 - response to auxin stimulus
GO:0050665 - hydrogen peroxide biosynthetic process
GO:0006970 - response to osmotic stress
GO:0009413 - response to flooding
GO:0048364 - root development
GO:0006979 - response to oxidative stress
GO:0016174 - NAD(P)H oxidase activity
GO:0002679 - respiratory burst during defense response
GO:0009738 - abscisic acid mediated signaling
GO:0016021 - integral to membrane
GO:0009566 - fertilization
GO:0010118 - stomatal movement
GO:0043020 - NADPH oxidase complex
GO:0042742 - defense response to bacterium
 TO:0000112 - disease resistance
TO:0000605 - hydrogen peroxide content
TO:0000175 - bacterial blight disease resistance
TO:0000656 - root development trait
TO:0002657 - oxidative stress
TO:0006002 - proline content
TO:0000276 - drought tolerance
TO:0000163 - auxin sensitivity
TO:0000074 - blast disease
TO:0000439 - fungal disease resistance
TO:0000136 - relative water content
TO:0000172 - jasmonic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000524 - submergence tolerance
TO:0006001 - salt tolerance
TO:0002667 - abscisic acid content
TO:0000095 - osmotic response sensitivity
TO:0000129 - false smut disease resistance
TO:0000520 - stomatal closure rate
TO:0000430 - germination rate
TO:0000382 - 1000-seed weight
 PO:0025034 - leaf
Os01g0360200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g25820.2
LOC_Os01g25820.1
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
YGL1 OsYGL1
CHLG
Ygl1
CS
OsCHLG
 YELLOW-GREEN LEAF 1 chlorina
Chl synthetase
Chlorophyll synthase
yellow green leaf 1
 5 Tolerance and resistance - Disease resistance
Coloration - Chlorophyll
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
 GO:0051707 - response to other organism
GO:0006098 - pentose-phosphate shunt
GO:0006364 - rRNA processing
GO:0009073 - aromatic amino acid family biosynthetic process
GO:0009965 - leaf morphogenesis
GO:0010027 - thylakoid membrane organization
GO:0009534 - chloroplast thylakoid
GO:0015994 - chlorophyll metabolic process
GO:0042793 - transcription from plastid promoter
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0016021 - integral to membrane
GO:0016117 - carotenoid biosynthetic process
GO:0019344 - cysteine biosynthetic process
GO:0019288 - isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway
GO:0030154 - cell differentiation
GO:0046408 - chlorophyll synthetase activity
GO:0051607 - defense response to virus
GO:0046686 - response to cadmium ion
GO:0009902 - chloroplast relocation
GO:0015995 - chlorophyll biosynthetic process
GO:0031969 - chloroplast membrane
GO:0009416 - response to light stimulus
 TO:0000075 - light sensitivity
TO:0000148 - viral disease resistance
TO:0000020 - black streak dwarf virus resistance
 Os05g0349700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g28200.2
LOC_Os05g28200.1
CDPK5 OsCDPK5
OsCPK5
CPK5
 CALCIUM-DEPENDENT PROTEIN KINASE 5 calcium-dependent protein kinase
 2 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Biochemical character
Vegetative organ - Root
 GO:0009733 - response to auxin stimulus
GO:0009651 - response to salt stress
GO:0050832 - defense response to fungus
GO:0004674 - protein serine/threonine kinase activity
GO:0002679 - respiratory burst during defense response
GO:0005634 - nucleus
GO:0006468 - protein amino acid phosphorylation
GO:0043068 - positive regulation of programmed cell death
GO:0009739 - response to gibberellin stimulus
GO:0032874 - positive regulation of stress-activated MAPK cascade
GO:0016020 - membrane
GO:0005509 - calcium ion binding
GO:0005524 - ATP binding
GO:0002221 - pattern recognition receptor signaling pathway
GO:0010618 - aerenchyma formation
GO:0009414 - response to water deprivation
GO:0009735 - response to cytokinin stimulus
 TO:0006001 - salt tolerance
TO:0000074 - blast disease
TO:0000605 - hydrogen peroxide content
TO:0000276 - drought tolerance
TO:0000167 - cytokinin sensitivity
TO:0000163 - auxin sensitivity
TO:0000166 - gibberellic acid sensitivity
 PO:0000258 - root cortex
Os02g0685900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g46090.1
ESL4 CDPK12
OsCDPK12
OsCPK12
CPK12
OsESL4
 EARLY SENESCENCE LEAF 4 calcium-dependent protein kinase
Calcium-dependent protein kinase 12
Early senescence leaf 4
 4 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Tolerance and resistance
Character as QTL - Plant growth activity
Vegetative organ - Leaf
 GO:0005634 - nucleus
GO:0016020 - membrane
GO:0009414 - response to water deprivation
GO:0005509 - calcium ion binding
GO:0005524 - ATP binding
GO:0004674 - protein serine/threonine kinase activity
GO:0031000 - response to caffeine
GO:0005737 - cytoplasm
GO:0005886 - plasma membrane
GO:0009627 - systemic acquired resistance
GO:0009697 - salicylic acid biosynthetic process
GO:0006979 - response to oxidative stress
GO:0018105 - peptidyl-serine phosphorylation
GO:0010310 - regulation of hydrogen peroxide metabolic process
GO:0006807 - nitrogen compound metabolic process
GO:0010150 - leaf senescence
 TO:0000371 - yield trait
TO:0000495 - chlorophyll content
TO:0000440 - grain number per plant
TO:0000276 - drought tolerance
TO:0000271 - inflorescence length
TO:0000605 - hydrogen peroxide content
TO:0002657 - oxidative stress
TO:0000455 - seed set percent
TO:0000249 - leaf senescence
 PO:0007633 - endosperm development stage
PO:0020104 - leaf sheath
PO:0009047 - stem
PO:0025034 - leaf
Os04g0560600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g47300.1
CAB2R Oscab2R
CAB-2
OsLhcp
Lhcb1
Lhcb1a
OsLhcb1
OsLhcb1a
 CHLOROPHYLL A/B BINDING PROTEIN 2R "Chlorophyll a-b binding protein 2
chloroplastic"
LHCII type I CAB-2
light harvesting chlorophyll a/b binding protein 2
 1 Vegetative organ - Leaf
 GO:0009522 - photosystem I
GO:0009658 - chloroplast organization
GO:0009523 - photosystem II
GO:0009765 - photosynthesis, light harvesting
GO:0009536 - plastid
GO:0016021 - integral to membrane
GO:0015979 - photosynthesis
GO:0016168 - chlorophyll binding
GO:0009535 - chloroplast thylakoid membrane
GO:0018298 - protein-chromophore linkage
GO:0000287 - magnesium ion binding
GO:0009507 - chloroplast
 TO:0002715 - chloroplast development trait
 Os01g0600900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g41710.1
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
COW1 OsCOW1
oscow1
OsYUC8
YUC8
NAL7
OsNAL7
OsYUCCA8
YUCCA8
FMO
OsFMO(t)
REIN7
YUC8/REIN7
 CONSTITUTIVELY WILTED 1 CONSTITUTIVELY WILTED1
Constitutively wilted 1
NARROW LEAF7
NARROW LEAF 7
YUCCA-LIKE GENE 8
flavin monooxygenase
rice ethylene-insensitive 7
 3 Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
Vegetative organ - Root
Tolerance and resistance - Disease resistance
 GO:0009851 - auxin biosynthetic process
GO:0009873 - ethylene mediated signaling pathway
GO:0022603 - regulation of anatomical structure morphogenesis
GO:0000139 - Golgi membrane
GO:0004499 - flavin-containing monooxygenase activity
GO:0005654 - nucleoplasm
GO:0009409 - response to cold
GO:0048366 - leaf development
GO:0047434 - indolepyruvate decarboxylase activity
GO:0009612 - response to mechanical stimulus
GO:0030104 - water homeostasis
GO:0009734 - auxin mediated signaling pathway
GO:0050661 - NADP or NADPH binding
GO:0050660 - FAD binding
GO:0048825 - cotyledon development
GO:0010229 - inflorescence development
GO:0009911 - positive regulation of flower development
GO:0007275 - multicellular organismal development
GO:0005829 - cytosol
GO:0048364 - root development
GO:0051607 - defense response to virus
 TO:0000655 - leaf development trait
TO:0000227 - root length
TO:0000656 - root development trait
TO:0002672 - auxin content
TO:0000303 - cold tolerance
TO:0000492 - leaf shape
TO:0000471 - root penetration index
TO:0002665 - root hair length
TO:0000148 - viral disease resistance
 PO:0000025 - root tip
PO:0020141 - stem node
PO:0009047 - stem
PO:0025034 - leaf
PO:0007520 - root development stage
Os03g0162000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g06654.2
LOC_Os03g06654.1
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
CKT1 OHK5
HK
OsHK6
HK6
Crl1a
Ohk5
OsHK1
OsCKT1
ABL1
OsABL1
 CYTOKININ TOLERANT 1 histidine kinase 6
His kinase 6
cytokinin tolerant 1
adaxial-abaxial bipolar leaf1
ADAXIAL-ABAXIAL BIPOLAR LEAF 1
 2 Vegetative organ - Leaf
Biochemical character
Reproductive organ - Heading date
Reproductive organ - Pollination, fertilization, fertility
Character as QTL - Plant growth activity
Vegetative organ - Root
 GO:0010109 - regulation of photosynthesis
GO:0048573 - photoperiodism, flowering
GO:0000155 - two-component sensor activity
GO:0048364 - root development
GO:0004673 - protein histidine kinase activity
GO:0051302 - regulation of cell division
GO:0005783 - endoplasmic reticulum
GO:0005982 - starch metabolic process
GO:0005985 - sucrose metabolic process
GO:0009735 - response to cytokinin stimulus
GO:0009736 - cytokinin mediated signaling
GO:0009884 - cytokinin receptor activity
GO:0015995 - chlorophyll biosynthetic process
GO:0018106 - peptidyl-histidine phosphorylation
GO:0043455 - regulation of secondary metabolic process
GO:0048831 - regulation of shoot development
GO:0000156 - two-component response regulator activity
GO:0048366 - leaf development
GO:0009909 - regulation of flower development
GO:0005524 - ATP binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0016020 - membrane
 TO:0000152 - panicle number
TO:0000655 - leaf development trait
TO:0001015 - photosynthetic rate
TO:0000522 - stomatal conductance
TO:0000055 - leaf lamina pubescence
TO:0000135 - leaf length
TO:0002758 - flag leaf lamina width
TO:0000399 - grain thickness
TO:0002759 - grain number
TO:0000040 - panicle length
TO:0000316 - photosynthetic ability
TO:0000656 - root development trait
TO:0000167 - cytokinin sensitivity
TO:0002637 - leaf size
TO:0000485 - sterility related trait
TO:0002616 - flowering time
TO:0000137 - days to heading
TO:0006020 - shoot apical meristem development
TO:0000654 - shoot development trait
TO:0000622 - flower development trait
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000370 - leaf width
TO:0000357 - growth and development trait
 PO:0000027 - lateral root tip
PO:0005029 - root primordium
PO:0007520 - root development stage
PO:0000025 - root tip
PO:0020121 - lateral root
Os02g0738400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g50480.1
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
RR21 OsRR21
Rrb1
Orr1
OsRR19
RR19
OsRRB1
ORR1
OsRRB4
RRB4
 B-TYPE RESPONSE REGULATOR 1 B-type response regulator 1
B-type RR 1
ORYZA SATIVA RESPONSE REGULATOR 1
 3 Reproductive organ - Inflorescence
Tolerance and resistance - Stress tolerance
Reproductive organ - panicle
Heterochrony
Vegetative organ - Root
 GO:0010229 - inflorescence development
GO:0009737 - response to abscisic acid stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009735 - response to cytokinin stimulus
GO:0045449 - regulation of transcription
GO:0009414 - response to water deprivation
GO:0009723 - response to ethylene stimulus
GO:0009736 - cytokinin mediated signaling
GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0000156 - two-component response regulator activity
GO:0009409 - response to cold
GO:0005634 - nucleus
 TO:0000173 - ethylene sensitivity
TO:0000040 - panicle length
TO:0006031 - inflorescence size
TO:0000276 - drought tolerance
TO:0000621 - inflorescence development trait
TO:0000167 - cytokinin sensitivity
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000557 - secondary branch number
TO:0000172 - jasmonic acid sensitivity
TO:0000547 - primary branch number
 PO:0001083 - inflorescence development stage
PO:0009010 - seed
PO:0025034 - leaf
PO:0009006 - shoot system
PO:0009089 - endosperm
PO:0008037 - seedling
Os03g0224200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g12350.1
LOC_Os03g12350.2
LOC_Os03g12350.4
RR2 rr2
Osrr2
OsRR2
Rra10
OsRRA10
 A-TYPE RESPONSE REGULATOR 2 A-TYPE response regulator 2
Type A response regulator 2
A-type RR 10
 2 Tolerance and resistance - Stress tolerance
Vegetative organ - Root
 GO:0009414 - response to water deprivation
GO:0009269 - response to desiccation
GO:0000156 - two-component response regulator activity
GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0048364 - root development
GO:0009736 - cytokinin mediated signaling
GO:0009735 - response to cytokinin stimulus
GO:0045449 - regulation of transcription
GO:0045454 - cell redox homeostasis
GO:0009733 - response to auxin stimulus
GO:0009408 - response to heat
GO:0070482 - response to oxygen levels
GO:0006970 - response to osmotic stress
 TO:0000507 - osmotic adjustment capacity
TO:0000095 - osmotic response sensitivity
TO:0000015 - oxygen sensitivity
TO:0000276 - drought tolerance
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000656 - root development trait
TO:0000259 - heat tolerance
 PO:0007504 - crown root primordium formation stage
Os02g0557800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g35180.1
AM1 OsAM1
prx53
OsPRX53
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 1 class III peroxidase 53
 4 Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Root
Tolerance and resistance - Disease resistance
 GO:0009610 - response to symbiotic fungus
GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os04g0134800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g04750.1
AM2 OsAM2
OsPI8-1a
PI8-1a
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 2 proteinase inhibitor 8-1a
 8 Tolerance and resistance - Stress tolerance
Vegetative organ - Root
 GO:0009845 - seed germination
GO:0009610 - response to symbiotic fungus
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0048658 - tapetal layer development
GO:0012501 - programmed cell death
GO:0009611 - response to wounding
 TO:0000357 - growth and development trait
 PO:0001004 - anther development stage
PO:0020148 - shoot apical meristem
PO:0020002 - anther wall endothecium
PO:0009047 - stem
PO:0007057 - 0 seed germination stage
Os08g0441200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g34249.1
AM3 OsAM3
OsLysMe2
LysMe2
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 3 LysM extracellular 2
lysin motif extracellular 2
lysin motif extracellular protein 2
 1 Vegetative organ - Root
 GO:0008061 - chitin binding
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0009610 - response to symbiotic fungus
GO:0044111 - development during symbiotic interaction
GO:0048046 - apoplast
GO:0052031 - modulation by symbiont of host defense response
GO:0050777 - negative regulation of immune response
GO:0010200 - response to chitin
 PO:0000258 - root cortex
Os01g0783000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g57400.1
AM10 AM10
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 10 5 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os05g0289700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g22300.1
AM11 AM11
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 11 6 Vegetative organ - Root
 GO:0009610 - response to symbiotic fungus
GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os06g0305400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g20120.1
LOC_Os06g20110.1
AM14 OsAM14
OsARK1
ARK1
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 14 ARBUSCULAR RECEPTOR-LIKE KINASE 1
 11 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0075328 - formation by symbiont of arbuscule for nutrient acquisition from host
GO:0009610 - response to symbiotic fungus
 Os11g0448200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g26140.1
AM15 OsAM15
OsLysMe1
LysMe1
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 15 lysin motif extracellular protein 1
 1 Vegetative organ - Root
 GO:0052031 - modulation by symbiont of host defense response
GO:0008061 - chitin binding
GO:0009610 - response to symbiotic fungus
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0044111 - development during symbiotic interaction
GO:0010200 - response to chitin
GO:0048046 - apoplast
GO:0050777 - negative regulation of immune response
 PO:0000258 - root cortex
Os01g0782901 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g57390.1
GRAS16 AM18
OsAM1
OsGRAS-16
OsGRAS16
GRAS-16
PsiOsGRAS4
PsiGRAS4
 GRAS PROTEIN 16 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 18
GRAS protein 16
 3 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0009651 - response to salt stress
GO:0042742 - defense response to bacterium
GO:0009737 - response to abscisic acid stimulus
GO:0050832 - defense response to fungus
 TO:0000175 - bacterial blight disease resistance
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000255 - sheath blight disease resistance
 - LOC_Os03g40080
AM20 AM20
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 20 4 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os04g0280600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g21160.1
AM24 AM24
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 24 2 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os02g0124300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g03190.1
AM25 AM25
OsNIP1;4
NIP1-4
OsNIP1.4
NIP1.4
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 25 Aquaporin NIP1-4
NOD26-like intrinsic protein 1-4
 6 Biochemical character
Vegetative organ - Root
 GO:0016021 - integral to membrane
GO:0005215 - transporter activity
GO:0016020 - membrane
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0055085 - transmembrane transport
 Os06g0552700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g35930.1
AM26 AM26
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 26 12 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os12g0487250 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 )
AM29 AM29
OsRING405
RING405
OsC3HC4_066
C3HC4_066
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 29 RING-type E3 ubiquitin ligase 405
C3HC4-type RING zinc finger protein 066
 6 Biochemical character
Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0016740 - transferase activity
GO:0008270 - zinc ion binding
 Os06g0535900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g34470.1
AM31 AM31
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 31 2 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os02g0124000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g03150.1
AM34 AM34
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 34 10 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os10g0332000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g18510.1
AM39 AM39
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 39 4 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os04g0207600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g13090.1
AM42 AM42
 ARBUSCULAR MYCORRHIZAL SPECIFIC MARKER 42 3 Vegetative organ - Root
 GO:0044403 - symbiosis, encompassing mutualism through parasitism
 Os03g0582300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g38600.1
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
PT11 OsPT11
PHT1-11
OsPht1;11
ORYsa;PHT1;11
 PHOSPHATE TRANSPORTER 11 Inorganic phosphate transporter 1-11
PHOSPHATE TRANSPORTER1;11
 1 Biochemical character
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
 GO:0007623 - circadian rhythm
GO:0006810 - transport
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0009737 - response to abscisic acid stimulus
GO:0009733 - response to auxin stimulus
GO:0009739 - response to gibberellin stimulus
GO:0005215 - transporter activity
GO:0006817 - phosphate transport
GO:0015293 - symporter activity
GO:0016021 - integral to membrane
GO:0009610 - response to symbiotic fungus
GO:0055085 - transmembrane transport
GO:0075328 - formation by symbiont of arbuscule for nutrient acquisition from host
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0009735 - response to cytokinin stimulus
GO:0009642 - response to light intensity
 TO:0000163 - auxin sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000102 - phosphorus sensitivity
TO:0000460 - light intensity sensitivity
TO:0000167 - cytokinin sensitivity
 PO:0020031 - radicle
PO:0000025 - root tip
PO:0009010 - seed
PO:0025034 - leaf
PO:0009029 - stamen
PO:0009005 - root
PO:0009049 - inflorescence
PO:0009089 - endosperm
PO:0007057 - 0 seed germination stage
PO:0020104 - leaf sheath
Os01g0657100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g46860.1
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
RL10 rl10
 ROLLED LEAF 10 9 Vegetative organ - Leaf
 GO:0030154 - cell differentiation
 -
RL7 rl7
 ROLLED LEAF 7 5 Vegetative organ - Leaf
 GO:0030154 - cell differentiation
 -
RL8 rl8
 ROLLED LEAF 8 5 Vegetative organ - Leaf
 GO:0030154 - cell differentiation
 -
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
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/rice/oryzabase