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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
CENH3 OsCENH3
CenH3
 CENTROMERIC HISTONE 3C centromeric histone H3
centromere-specific histone H3
centromere-specific H3 histone
centromere-specific histone H3
 5 Character as QTL - Plant growth activity
Biochemical character
Reproductive organ - Pollination, fertilization, fertility
Reproductive organ - Heading date
 GO:0006334 - nucleosome assembly
GO:0005515 - protein binding
GO:0009567 - double fertilization forming a zygote and endosperm
GO:0051983 - regulation of chromosome segregation
GO:0000776 - kinetochore
GO:0046982 - protein heterodimerization activity
GO:0003677 - DNA binding
GO:0007276 - gamete generation
GO:0030527 - structural constituent of chromatin
GO:0009960 - endosperm development
GO:0048573 - photoperiodism, flowering
GO:0009793 - embryonic development ending in seed dormancy
GO:0000775 - chromosome, centromeric region
GO:0051382 - kinetochore assembly
GO:0000786 - nucleosome
GO:0005634 - nucleus
 TO:0000040 - panicle length
TO:0002616 - flowering time
TO:0000207 - plant height
TO:0000137 - days to heading
TO:0000620 - embryo development trait
TO:0002757 - flag leaf length
TO:0000455 - seed set percent
TO:0000421 - pollen fertility
 PO:0007631 - plant embryo stage
PO:0007633 - endosperm development stage
Os05g0489800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g41080.1
LOC_Os05g41080.2
MADS51 OsMADS51
OsMADS65
MADS65
qHd1
DLN36
OsDLN36
 MADS BOX GENE 51 MADS box gene51
DLN repressor 36
DLN motif protein 36
 1 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Seed - Morphological traits
Character as QTL - Plant growth activity
Other
Tolerance and resistance - Disease resistance
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009408 - response to heat
GO:0050832 - defense response to fungus
GO:0009409 - response to cold
GO:0043565 - sequence-specific DNA binding
 TO:0000396 - grain yield
TO:0000259 - heat tolerance
TO:0000432 - temperature response trait
TO:0000137 - days to heading
TO:0002616 - flowering time
TO:0000449 - grain yield per plant
TO:0000152 - panicle number
TO:0000455 - seed set percent
TO:0000329 - tillering ability
TO:0000357 - growth and development trait
TO:0000074 - blast disease
TO:0000590 - grain weight
TO:0000303 - cold tolerance
 Os01g0922800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g69850.1
CDPK19 OsCDPK19
OsCPK19
OsCDPK2
CPK2
CDPK2
 CALCIUM-DEPENDENT PROTEIN KINASE 19 calcium-dependent protein kinase
calcium-dependent protein kinase 2
 7 Tolerance and resistance - Disease resistance
Biochemical character
Reproductive organ - Heading date
 GO:0005886 - plasma membrane
GO:0010857 - calcium-dependent protein kinase activity
GO:0009733 - response to auxin stimulus
GO:0009739 - response to gibberellin stimulus
GO:0051607 - defense response to virus
GO:0004674 - protein serine/threonine kinase activity
GO:0005509 - calcium ion binding
GO:0005524 - ATP binding
 TO:0000163 - auxin sensitivity
TO:0000148 - viral disease resistance
TO:0000020 - black streak dwarf virus resistance
TO:0000166 - gibberellic acid sensitivity
 Os07g0515100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g33110.1
LOC_Os07g33110.2
LOC_Os07g33110.3
LOC_Os07g33110.4
LOC_Os07g33110.5
EHD2/RID1 Ehd2
RID1
OsID1
ID1
OsId1
OsID
Ehd2/RID1/OsId1
RID1/OsID1/Ehd2
 EARLY HEADING DATE 2 early heading date 2
Indeterminate 1
Indeterminate
Rice Indeterminate 1
 10 Reproductive organ - Heading date
 GO:0008270 - zinc ion binding
GO:0009648 - photoperiodism
GO:0048510 - regulation of timing of transition from vegetative to reproductive phase
GO:0048573 - photoperiodism, flowering
 TO:0000137 - days to heading
TO:0002616 - flowering time
 Os10g0419200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g28330.1
HD9 Hd9
qHd9
 HEADING DATE 9 heading date (QTL)-9
 3 Reproductive organ
Reproductive organ - Heading date
 GO:0009648 - photoperiodism
 -
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
HK5 OHK3
HK
OsHK5
Crl3
Ohk3
OsHK2
 HISTIDINE KINASE 5 histidine kinase 5
His kinase 5
 10 Reproductive organ - Pollination, fertilization, fertility
Reproductive organ - Heading date
Character as QTL - Plant growth activity
Biochemical character
 GO:0000156 - two-component response regulator activity
GO:0000155 - two-component sensor activity
GO:0009884 - cytokinin receptor activity
GO:0048831 - regulation of shoot development
GO:0005524 - ATP binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0016020 - membrane
GO:0018106 - peptidyl-histidine phosphorylation
GO:0048573 - photoperiodism, flowering
GO:0009735 - response to cytokinin stimulus
GO:0048364 - root development
GO:0004673 - protein histidine kinase activity
GO:0009909 - regulation of flower development
GO:0009736 - cytokinin mediated signaling
 TO:0000656 - root development trait
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000370 - leaf width
TO:0000654 - shoot development trait
TO:0000137 - days to heading
TO:0000357 - growth and development trait
TO:0000167 - cytokinin sensitivity
TO:0000622 - flower development trait
TO:0002616 - flowering time
TO:0000152 - panicle number
TO:0000485 - sterility related trait
 Os10g0362300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g21810.1
LOC_Os10g21810.2
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
RR1 rr1
OsRR1
Rra9
OsRRA9
 A-TYPE RESPONSE REGULATOR 1 A-TYPE response regulator 1
Type A response regulator 1
A-type RR 9
 4 Reproductive organ - Heading date
 GO:2000028 - regulation of photoperiodism, flowering
GO:0045449 - regulation of transcription
GO:0009733 - response to auxin stimulus
GO:0000156 - two-component response regulator activity
GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0009735 - response to cytokinin stimulus
 TO:0000163 - auxin sensitivity
TO:0000137 - days to heading
TO:0000167 - cytokinin sensitivity
 Os04g0442300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g36070.1
RAP1A OsMADS15
FDRMADS3
RMADS215
MADS15
DEP
 RICE APETALA 1A MADS-box transcription factor 15
Protein APETALA1-like A
degenerative palea
MADS box gene15
 7 Reproductive organ - panicle
Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Heading date
Other
Tolerance and resistance - Stress tolerance
Reproductive organ
Vegetative organ - Leaf
 GO:0031667 - response to nutrient levels
GO:0010229 - inflorescence development
GO:0042594 - response to starvation
GO:0006355 - regulation of transcription, DNA-dependent
GO:0003700 - transcription factor activity
GO:0005515 - protein binding
GO:0005634 - nucleus
GO:0016036 - cellular response to phosphate starvation
GO:0043565 - sequence-specific DNA binding
GO:0048573 - photoperiodism, flowering
GO:0010228 - vegetative to reproductive phase transition
GO:0003006 - reproductive developmental process
GO:0006350 - transcription
 TO:0000206 - leaf angle
TO:0000102 - phosphorus sensitivity
TO:0000137 - days to heading
TO:0002616 - flowering time
TO:0000621 - inflorescence development trait
 PO:0001083 - inflorescence development stage
PO:0020094 - plant egg cell
Os07g0108900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g01820.6
LOC_Os07g01820.5
LOC_Os07g01820.4
LOC_Os07g01820.1
LOC_Os07g01820.2
LOC_Os07g01820.3
HAP3D OsHAP3D
OsEnS-83
OsNF-YB9
NF-YB9
NFYB9
OsLEC1A
LEC1A
 HAP3D SUBUNIT OF CCAAT-BOX BINDING COMPLEX HAP3 subunit D
LEC1-type 3 subunit protein-D
endosperm-specific gene 83
NUCLEAR FACTOR-Y subunit B9
NUCLEAR FACTOR-Y subunit NF-YB9
HAP3 SUBUNIT D
NF-YB subunit 9
NF-YB family 9
 6 Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Other
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0042127 - regulation of cell proliferation
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009790 - embryonic development
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0005737 - cytoplasm
GO:0009845 - seed germination
 TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000266 - chalky endosperm
TO:0000391 - seed size
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0020033 - glume length
TO:0000487 - endosperm color
TO:0000575 - endosperm related trait
TO:0000064 - embryo related trait
TO:0000485 - sterility related trait
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0000276 - drought tolerance
TO:0000211 - gel consistency
TO:0000162 - seed quality
TO:0000222 - head rice
TO:0000207 - plant height
TO:0000382 - 1000-seed weight
TO:0000346 - tiller number
TO:0000639 - seed fertility
TO:0000421 - pollen fertility
 PO:0001170 - seed development stage
PO:0009009 - plant embryo
PO:0009089 - endosperm
PO:0020094 - plant egg cell
PO:0000003 - whole plant
PO:0009010 - seed
Os06g0285200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g17480.1
LEC1 OsHAP3E
HAP3E
OsLEC1/OsHAP3E
OsLEC1
LEC1
OsNF-YB7
NF-YB7
NFYB7
L1L
OsLEC1B
LEC1B
 LEAFY COTYLEDON 1 HAP3 subunit E
LEC1-type 3 subunit protein-E
leafy cotyledon 1
NUCLEAR FACTOR-Y subunit B7
NUCLEAR FACTOR-Y subunit NF-YB7
LEC1-LIKE
LEAFY COTYLEDON1-LIKE
HAP3 SUBUNIT E
NF-YB subunit 7
NF-YB family 7
LEAFY COTYLEDON1
 2 Coloration - Chlorophyll
Character as QTL - Germination
Reproductive organ - Heading date
Seed - Morphological traits - Embryo
Tolerance and resistance - Stress tolerance
Other
Seed - Physiological traits - Dormancy
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0009790 - embryonic development
GO:0010109 - regulation of photosynthesis
GO:0048700 - acquisition of desiccation tolerance
GO:0010099 - regulation of photomorphogenesis
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0010187 - negative regulation of seed germination
GO:0009269 - response to desiccation
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010431 - seed maturation
GO:0048316 - seed development
GO:0015995 - chlorophyll biosynthetic process
GO:0009734 - auxin mediated signaling pathway
GO:0043565 - sequence-specific DNA binding
GO:0009740 - gibberellic acid mediated signaling
GO:0009733 - response to auxin stimulus
GO:0008284 - positive regulation of cell proliferation
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0009738 - abscisic acid mediated signaling
GO:0015979 - photosynthesis
GO:0009845 - seed germination
 TO:0000430 - germination rate
TO:0000428 - callus induction
TO:0000397 - grain size
TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000163 - auxin sensitivity
TO:0000620 - embryo development trait
TO:0000391 - seed size
TO:0002661 - seed maturation
TO:0000276 - drought tolerance
TO:0000485 - sterility related trait
TO:0000064 - embryo related trait
TO:0000495 - chlorophyll content
TO:0000207 - plant height
TO:0000488 - seed composition based quality trait
 PO:0001170 - seed development stage
PO:0007057 - 0 seed germination stage
PO:0007631 - plant embryo stage
PO:0009010 - seed
PO:0020110 - scutellum
PO:0005421 - parenchyma
PO:0009009 - plant embryo
PO:0005052 - plant callus
PO:0007632 - seed maturation stage
Os02g0725700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g49370.1
LOC_Os02g49370.2
HAP3F OsHAP3F
NF-YB
CBF-A
NF-YB10
OsNF-YB10
NFYB10
 HAP3F SUBUNIT OF CCAAT-BOX BINDING COMPLEX NUCLEAR FACTOR-Y subunit B10
NUCLEAR FACTOR-Y subunit NF-YB10
NF-YB subunit 10
NF-YB family 10
 7 Reproductive organ - Heading date
Other
 GO:0043565 - sequence-specific DNA binding
GO:0006350 - transcription
GO:0005634 - nucleus
GO:2000028 - regulation of photoperiodism, flowering
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0002616 - flowering time
TO:0000137 - days to heading
 Os07g0606600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g41580.1
HAP3I OsHAP3I
NF-YB
CBF-A
NF-YB8
OsNF-YB8
NFYB8
 HAP3I SUBUNIT OF CCAAT-BOX BINDING COMPLEX NUCLEAR FACTOR-Y subunit B8
NUCLEAR FACTOR-Y subunit NF-YB8
NF-YB subunit 8
NF-YB family 8
 3 Other
Reproductive organ - Heading date
 GO:0005634 - nucleus
GO:0006350 - transcription
GO:0006355 - regulation of transcription, DNA-dependent
GO:2000028 - regulation of photoperiodism, flowering
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
 TO:0002616 - flowering time
 Os03g0413000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g29970.1
HAP5A OsHAP5A
NF-YC
CBF-C
OsNF-YC1
Os-NF-YC1
NF-YC1
NFYC1
OsNF-YC4-2
NF-YC4-2
 HAP5A SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C1 subunit
Nuclear factor Y C subunit 1
NUCLEAR FACTOR-Y subunit C1
NUCLEAR FACTOR-Y subunit NF-YC1
NF-YC subunit 1
NF-YC family 1
 2 Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
Other
 GO:0008284 - positive regulation of cell proliferation
GO:0005634 - nucleus
GO:0050688 - regulation of defense response to virus
GO:0009414 - response to water deprivation
GO:0009737 - response to abscisic acid stimulus
GO:0009651 - response to salt stress
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
GO:0006350 - transcription
GO:0051607 - defense response to virus
GO:0080050 - regulation of seed development
GO:0030307 - positive regulation of cell growth
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000919 - grain weight
TO:0000653 - seed development trait
TO:0000615 - abscisic acid sensitivity
TO:0006001 - salt tolerance
TO:0000137 - days to heading
TO:0000590 - grain weight
TO:0000276 - drought tolerance
TO:0000397 - grain size
TO:0000148 - viral disease resistance
TO:0000391 - seed size
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000382 - 1000-seed weight
TO:0000399 - grain thickness
TO:0000975 - grain width
TO:0001034 - relative plant height
TO:0000402 - grain width
 PO:0009049 - inflorescence
PO:0001170 - seed development stage
Os02g0170500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07450.1
LOC_Os02g07450.2
HAP5B OsHAP5B
NF-YC
CBF-C
OsNF-YC4
Os-NF-YC4
NF-YC4
NFYC4
OsNF-YC4-3
NF-YC4-3
 HAP5B SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C4 subunit
Nuclear factor Y C subunit 4
NUCLEAR FACTOR-Y subunit C4
NUCLEAR FACTOR-Y subunit NF-YC4
NF-YC subunit 4
NF-YC family 4
 6 Tolerance and resistance - Stress tolerance
Other
Reproductive organ - Heading date
 GO:0009414 - response to water deprivation
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0009651 - response to salt stress
GO:0009737 - response to abscisic acid stimulus
GO:0043565 - sequence-specific DNA binding
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0003700 - transcription factor activity
GO:0005737 - cytoplasm
GO:0016602 - CCAAT-binding factor complex
GO:0048573 - photoperiodism, flowering
 TO:0000276 - drought tolerance
TO:0002616 - flowering time
TO:0000615 - abscisic acid sensitivity
TO:0000137 - days to heading
TO:0006001 - salt tolerance
 Os06g0667100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g45640.1
HAP5C OsHAP5C
NF-YC
CBF-C
OsNF-YC2
Os-NF-YC2
NF-YC2
NFYC2
OsNF-YC4-1
NF-YC4-1
 HAP5C SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C2 subunit
Nuclear factor Y C subunit 2
NUCLEAR FACTOR-Y subunit C2
NUCLEAR FACTOR-Y subunit NF-YC2
NF-YC subunit 2
NF-YC family 2
 3 Other
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Seed - Physiological traits - Storage substances
Reproductive organ - Heading date
 GO:0006355 - regulation of transcription, DNA-dependent
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
GO:0005634 - nucleus
GO:0051607 - defense response to virus
GO:0009737 - response to abscisic acid stimulus
GO:0006350 - transcription
GO:0050688 - regulation of defense response to virus
GO:0009414 - response to water deprivation
 TO:0000291 - carbohydrate content
TO:0000598 - protein content
TO:0000696 - starch content
TO:0000615 - abscisic acid sensitivity
TO:0001034 - relative plant height
TO:0000148 - viral disease resistance
TO:0002616 - flowering time
TO:0000276 - drought tolerance
 Os03g0251350 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g14669.1
LOC_Os03g14669.2
HAP5D OsHAP5D
NF-YC
CBF-C
OsNF-YC6
Os-NF-YC6
NF-YC6
NFYC6
 HAP5D SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C6 subunit
Nuclear factor Y C subunit 6
NUCLEAR FACTOR-Y subunit C6
NUCLEAR FACTOR-Y subunit NF-YC6
NF-YC subunit 6
NF-YC family 6
 8 Tolerance and resistance - Stress tolerance
Other
Reproductive organ - Heading date
 GO:0048578 - positive regulation of long-day photoperiodism, flowering
GO:0043565 - sequence-specific DNA binding
GO:0005634 - nucleus
GO:0006350 - transcription
GO:0009651 - response to salt stress
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
GO:0003700 - transcription factor activity
GO:0005737 - cytoplasm
GO:0016602 - CCAAT-binding factor complex
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000276 - drought tolerance
TO:0000615 - abscisic acid sensitivity
TO:0002616 - flowering time
TO:0006001 - salt tolerance
 Os08g0496500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g38780.1
DRAP2 OsDrAp2
DrAp2
OsHAPL1
HAPL1
DLN150
OsDLN150
OsNF-YC15
NF-YC15
 DR1 ASSOCIATED PROTEIN 2 Dr1-associated protein2
eukaryotic general repressor DrAp2
Heme Activator Protein like 1
DLN repressor 150
DLN motif protein 150
Nuclear factor Y C subunit 15
 5 Other
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
 GO:0005515 - protein binding
GO:0005634 - nucleus
GO:0016564 - transcription repressor activity
GO:0043565 - sequence-specific DNA binding
GO:0009648 - photoperiodism
GO:0048573 - photoperiodism, flowering
GO:2000028 - regulation of photoperiodism, flowering
GO:0048579 - negative regulation of long-day photoperiodism, flowering
 TO:0000207 - plant height
TO:0000346 - tiller number
TO:0000040 - panicle length
TO:0000547 - primary branch number
TO:0000557 - secondary branch number
TO:0000447 - filled grain number
TO:0000137 - days to heading
TO:0000382 - 1000-seed weight
TO:0002616 - flowering time
 PO:0025034 - leaf
Os05g0494100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g41450.1
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
EHD4 OsC3H20
C3H20
Ehd4
DLN73
DLN73a
DLN73b
OsDLN73
OsDLN73a
OsDLN73b
 EARLY HEADING DATE 4 Zinc finger CCCH domain-containing protein 20
Early heading date 4
DLN repressor 73
DLN motif protein 73
CCCH Zinc Finger Family Gene 20
 3 Reproductive organ - Heading date
Other
Tolerance and resistance - Stress tolerance
 GO:0010378 - temperature compensation of the circadian clock
GO:0005634 - nucleus
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:2000028 - regulation of photoperiodism, flowering
GO:0009266 - response to temperature stimulus
GO:0003677 - DNA binding
GO:0008270 - zinc ion binding
GO:0007623 - circadian rhythm
 TO:0000432 - temperature response trait
TO:0002616 - flowering time
 Os03g0112700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g02160.3
LOC_Os03g02160.2
LOC_Os03g02160.1
PLDvarphi OsPLDvarphi
spPLD
OsspPLD
 PHOSPHOLIPASE D varphi 6 Reproductive organ - Heading date
Biochemical character
 GO:0048577 - negative regulation of short-day photoperiodism, flowering
GO:0005615 - extracellular space
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0034638 - phosphatidylcholine catabolic process
GO:0004630 - phospholipase D activity
GO:0048573 - photoperiodism, flowering
 TO:0002616 - flowering time
TO:0000137 - days to heading
 PO:0009005 - root
PO:0009049 - inflorescence
Os06g0649900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g44060.1
LOC_Os06g44060.2
HD16 Hd16
EL1
CK1
Hd16/CKI
Hd16/EL1
 HEADING DATE 16 EARLY FLOWERING 1
Early flowering1
Casein Kinase I
 3 Reproductive organ - Heading date
Biochemical character
 GO:0048573 - photoperiodism, flowering
GO:0009648 - photoperiodism
GO:2000028 - regulation of photoperiodism, flowering
 TO:0002616 - flowering time
TO:0000137 - days to heading
 Os03g0793500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g57940.1
LOC_Os03g57940.2
LOC_Os03g57940.3
LOC_Os03g57940.4
HD3B Hd17
EF7
Ef7
OsELF3-1
ELF3-1
OsELF3
ELF3
ELF3_chr.6
OsELF3.1
ELF3.1
OsELF3a
ELF3a
 HEADING DATE 3B HEADING DATE 17
EARLINESS 7
EARLY FLOWERING 3-1
EARLY FLOWERING3.1
EARLY FLOWERING 3.1
ELF3 homolog 1
Heading date from Qingluzhan 11
EARLY FLOWERING3
 6 Tolerance and resistance - Disease resistance
Reproductive organ - Heading date
Vegetative organ - Leaf
Character as QTL - Yield and productivity
 GO:0009648 - photoperiodism
GO:0048576 - positive regulation of short-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0050832 - defense response to fungus
GO:0048573 - photoperiodism, flowering
GO:0031348 - negative regulation of defense response
GO:0007623 - circadian rhythm
GO:0048578 - positive regulation of long-day photoperiodism, flowering
GO:0009908 - flower development
 TO:0001034 - relative plant height
TO:0000229 - photoperiod sensitivity
TO:0000011 - nitrogen sensitivity
TO:0000153 - relative yield
TO:0000074 - blast disease
TO:0001032 - relative panicle number
TO:0000249 - leaf senescence
TO:0000396 - grain yield
TO:0000207 - plant height
TO:0002616 - flowering time
TO:0000137 - days to heading
TO:0000590 - grain weight
 PO:0025034 - leaf
PO:0009005 - root
PO:0001054 - 4 leaf senescence stage
PO:0009049 - inflorescence
PO:0009047 - stem
Os06g0142600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g05060.1
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
PRR73 OsPRR73
Os-PRR73
Prr3
OsPRR3
OsRRA20
OsCCT11
CCT11
 PSEUDO-RESPONSE REGULATOR 73 A-type RR 20
pseudo-response regulator 3
CCT domain-containing gene 11
CCT (CO, CO-LIKE and TOC1) domain protein 11
CCT domain protein 11
 3 Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
 GO:0009651 - response to salt stress
GO:0006351 - transcription, DNA-dependent
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005634 - nucleus
GO:0009414 - response to water deprivation
GO:0006970 - response to osmotic stress
GO:0000156 - two-component response regulator activity
GO:0048511 - rhythmic process
GO:0048573 - photoperiodism, flowering
GO:0009611 - response to wounding
GO:0006979 - response to oxidative stress
GO:0010446 - response to alkalinity
GO:0007623 - circadian rhythm
 TO:0002657 - oxidative stress
TO:0000608 - sodium content
TO:0000276 - drought tolerance
TO:0002616 - flowering time
TO:0000481 - alkali sensitivity
TO:0000095 - osmotic response sensitivity
TO:0000137 - days to heading
TO:0000605 - hydrogen peroxide content
TO:0006001 - salt tolerance
 PO:0006070 - mesophyll
PO:0009006 - shoot system
PO:0009005 - root
Os03g0284100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g17570.6
LOC_Os03g17570.5
LOC_Os03g17570.4
LOC_Os03g17570.3
LOC_Os03g17570.2
LOC_Os03g17570.1
PRR59 OsPRR59
Os-PRR59
Prr5
OsPRR5
OsCCT38
CCT38
 PSEUDO-RESPONSE REGULATOR 59 pseudo-response regulator 5
CCT domain-containing gene 38
CCT (CO, CO-LIKE and TOC1) domain protein 38
CCT domain protein 38
 11 Vegetative organ - Culm
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
 GO:0048576 - positive regulation of short-day photoperiodism, flowering
GO:0000156 - two-component response regulator activity
GO:0007623 - circadian rhythm
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000207 - plant height
TO:0002616 - flowering time
TO:0000137 - days to heading
TO:0000456 - spikelet number
 Os11g0157600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g05930.1
LOC_Os11g05930.2
LOC_Os11g05930.3
LOC_Os11g05930.4
LOC_Os11g05930.5
FKF1 OsFbox609
Fbox609
Os_F0370
F0370
OsFKF1
OsFBO10
FBO10
 FLAVIN-BINDING, KELCH REPEAT, F BOX 1 F-box protein 609
"FLAVIN-BINDING
KELCH REPEAT
F-BOX 1"
F-box-type E3 ubiquitin ligase O10
 11 Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
 GO:0048578 - positive regulation of long-day photoperiodism, flowering
GO:0032434 - regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0048576 - positive regulation of short-day photoperiodism, flowering
GO:0009416 - response to light stimulus
GO:0007623 - circadian rhythm
GO:0010228 - vegetative to reproductive phase transition
GO:0019005 - SCF ubiquitin ligase complex
GO:0009414 - response to water deprivation
GO:0048573 - photoperiodism, flowering
GO:0009266 - response to temperature stimulus
 TO:0000137 - days to heading
TO:0000075 - light sensitivity
TO:0000276 - drought tolerance
TO:0002616 - flowering time
TO:0000432 - temperature response trait
 Os11g0547000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g34460.1
LOC_Os11g34460.2
LOC_Os11g34460.3
EMF2A OsEMF2a
OsEMF2
EMF2
ZOS4-02
OsZOS4-02
OsPcG3
PcG3
 EMBRYONIC FLOWER 2A EMBRYONIC FLOWER 2
Embryonic Flower2a
zinc-finger protein TFIIIA class of Oryza sativa 4-02
ZPT of Oryza sativa 4-02
Polycomb group protein 3
 4 Seed - Morphological traits
Seed - Morphological traits - Embryo
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
 GO:0009960 - endosperm development
GO:0009790 - embryonic development
GO:0031490 - chromatin DNA binding
GO:0009651 - response to salt stress
GO:0010431 - seed maturation
GO:0007275 - multicellular organismal development
GO:0010581 - regulation of starch biosynthetic process
GO:0007349 - cellularization
GO:0009691 - cytokinin biosynthetic process
GO:0006349 - genetic imprinting
GO:0009910 - negative regulation of flower development
GO:0048316 - seed development
GO:0008270 - zinc ion binding
GO:0010342 - cellularization of endosperm
GO:0006325 - chromatin organization
GO:0010600 - regulation of auxin biosynthetic process
GO:0051726 - regulation of cell cycle
GO:0005634 - nucleus
GO:0030154 - cell differentiation
GO:0046872 - metal ion binding
GO:0005622 - intracellular
 TO:0000622 - flower development trait
TO:0006020 - shoot apical meristem development
TO:0006001 - salt tolerance
TO:0000653 - seed development trait
TO:0002660 - cytokinin content
TO:0002661 - seed maturation
TO:0000620 - embryo development trait
TO:0002653 - endosperm storage protein content
TO:0000300 - glucose content
TO:0000137 - days to heading
TO:0006005 - fructose content
TO:0000328 - sucrose content
TO:0002672 - auxin content
TO:0000696 - starch content
TO:0000487 - endosperm color
TO:0000345 - seed viability
 PO:0007631 - plant embryo stage
PO:0025034 - leaf
PO:0007633 - endosperm development stage
PO:0025281 - pollen
PO:0009006 - shoot system
PO:0009005 - root
PO:0009049 - inflorescence
PO:0009089 - endosperm
PO:0001170 - seed development stage
Os04g0162100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g08034.6
LOC_Os04g08034.5
LOC_Os04g08034.1
LOC_Os04g08034.2
LOC_Os04g08034.3
LOC_Os04g08034.4
EMF2B OsEMF2b
EMF2b
GW9
OsGW9
GW9/OsEMF2b
OsPcG4
PcG4
 EMBRYONIC FLOWER 2B EMBRYONIC FLOWER 2b
grain weight 9
Polycomb group protein 4
 9 Seed - Morphological traits - Grain shape
Character as QTL - Germination
Reproductive organ - Heading date
Seed - Morphological traits - Embryo
Vegetative organ - Culm
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
 GO:0001558 - regulation of cell growth
GO:0042127 - regulation of cell proliferation
GO:0046872 - metal ion binding
GO:0005634 - nucleus
GO:0048573 - photoperiodism, flowering
GO:0010187 - negative regulation of seed germination
GO:0005622 - intracellular
GO:0031519 - PcG protein complex
GO:0005677 - chromatin silencing complex
GO:0048497 - maintenance of floral organ identity
GO:0031490 - chromatin DNA binding
GO:0070734 - histone H3-K27 methylation
GO:0048586 - regulation of long-day photoperiodism, flowering
GO:0008270 - zinc ion binding
GO:0009908 - flower development
GO:0030154 - cell differentiation
GO:0031507 - heterochromatin formation
GO:0010336 - gibberellic acid homeostasis
GO:0009740 - gibberellic acid mediated signaling
GO:0009651 - response to salt stress
 TO:0000137 - days to heading
TO:0006001 - salt tolerance
TO:0000411 - seed length to width ratio
TO:0000145 - internode length
TO:0006019 - floral organ identity
TO:0000447 - filled grain number
TO:0000382 - 1000-seed weight
TO:0000339 - stem thickness
TO:0000430 - germination rate
TO:0002675 - gibberellic acid content
TO:0000734 - grain length
TO:0000657 - spikelet anatomy and morphology trait
TO:0000346 - tiller number
TO:0000590 - grain weight
TO:0000397 - grain size
TO:0000207 - plant height
TO:0002616 - flowering time
TO:0000557 - secondary branch number
 PO:0009005 - root
PO:0009006 - shoot system
PO:0009047 - stem
PO:0025034 - leaf
PO:0009049 - inflorescence
PO:0020104 - leaf sheath
PO:0025281 - pollen
PO:0007633 - endosperm development stage
PO:0020056 - tegmen
Os09g0306800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g13630.1
CLF OsSET24
SET24
OsSDG711
SDG711
EZ1
OsEZ1
OsCLF
OsPcG1
PcG1
 CURLY LEAF SET protein 24
polycomb protein EZ1
SET DOMAIN GROUP 711
Polycomb group protein 1
 6 Reproductive organ - panicle
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Plant growth activity
Seed - Morphological traits - Endosperm
Seed - Morphological traits
Seed - Physiological traits - Storage substances
Vegetative organ - Leaf
Seed
Other
 GO:0009960 - endosperm development
GO:0009823 - cytokinin catabolic process
GO:0048316 - seed development
GO:0001558 - regulation of cell growth
GO:0003677 - DNA binding
GO:0040014 - regulation of multicellular organism growth
GO:0048586 - regulation of long-day photoperiodism, flowering
GO:0009651 - response to salt stress
GO:0006306 - DNA methylation
GO:0010048 - vernalization response
GO:0009908 - flower development
GO:0042127 - regulation of cell proliferation
GO:0031047 - gene silencing by RNA
GO:0045857 - negative regulation of molecular function, epigenetic
GO:0051567 - histone H3-K9 methylation
GO:0040029 - regulation of gene expression, epigenetic
GO:0009965 - leaf morphogenesis
GO:0005634 - nucleus
GO:0031519 - PcG protein complex
GO:0003700 - transcription factor activity
GO:0009690 - cytokinin metabolic process
GO:0009294 - DNA mediated transformation
GO:0034968 - histone lysine methylation
GO:0003727 - single-stranded RNA binding
GO:0006349 - genetic imprinting
GO:0048574 - long-day photoperiodism, flowering
GO:0046976 - histone methyltransferase activity (H3-K27 specific)
GO:0009691 - cytokinin biosynthetic process
GO:0010228 - vegetative to reproductive phase transition
GO:0016571 - histone methylation
GO:0005982 - starch metabolic process
GO:0010229 - inflorescence development
 TO:0002637 - leaf size
TO:0000539 - large vascular bundle number
TO:0000357 - growth and development trait
TO:0000558 - small vascular bundle number
TO:0002758 - flag leaf lamina width
TO:0000132 - basal internode diameter
TO:0000145 - internode length
TO:0000590 - grain weight
TO:0000152 - panicle number
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000397 - grain size
TO:0000339 - stem thickness
TO:0000207 - plant height
TO:0006001 - salt tolerance
TO:0000621 - inflorescence development trait
TO:0002616 - flowering time
TO:0006032 - panicle size
TO:0000653 - seed development trait
TO:0000696 - starch content
TO:0000391 - seed size
TO:0000231 - endospermless
 PO:0007633 - endosperm development stage
PO:0001170 - seed development stage
PO:0009089 - endosperm
PO:0000230 - inflorescence meristem
PO:0020056 - tegmen
PO:0001083 - inflorescence development stage
Os06g0275500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g16390.1
SET1 OsiEZ1
OsSET1
iEZ1
OsEZ1/OsiEZ1
OsEZ1
EZ1
ez1
OsSET15
SDG718
DLN84
OsDLN84
OsSDG718
OsPcG2
PcG2
 SET-DOMAIN-CONTAINING PROTEIN 1 indica Enhancer of Zeste 1
SET protein 15
DLN repressor 84
DLN motif protein 84
Polycomb group protein 2
ENHANCER OF ZESTE 1
 3 Seed
Tolerance and resistance - Stress tolerance
Other
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
 GO:0003727 - single-stranded RNA binding
GO:0048587 - regulation of short-day photoperiodism, flowering
GO:0003677 - DNA binding
GO:0009960 - endosperm development
GO:0048575 - short-day photoperiodism, flowering
GO:0031519 - PcG protein complex
GO:0009790 - embryonic development
GO:0009651 - response to salt stress
GO:0006349 - genetic imprinting
 TO:0000428 - callus induction
TO:0002616 - flowering time
TO:0006001 - salt tolerance
 PO:0020056 - tegmen
PO:0009089 - endosperm
Os03g0307800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g19480.1
EF6 ef6
 EARLINESS 6 7 Reproductive organ - Heading date
 GO:0009648 - photoperiodism
 TO:0000137 - days to heading
 -
RSR1 AP2/EREBP#090
AP2/EREBP90
OsTOE1
TOE1
qHD5
AP2-1
AP2/EREBP/RSR1
OsRSR1
DLN130
DLN130a
DLN130b
OsDLN130
OsDLN130a
OsDLN130b
 RICE STRACH REGULATOR 1 AP2/EREBP family transcription factor
APETALA2/ethylene-responsive element binding protein 90
Rice Starch Regulator1
APETALA2-1
DLN repressor 130
DLN motif protein 130
 5 Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
Reproductive organ - Heading date
Reproductive organ - panicle
Seed - Morphological traits
 GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
GO:0003677 - DNA binding
GO:0009887 - organ morphogenesis
GO:0010228 - vegetative to reproductive phase transition
GO:0010581 - regulation of starch biosynthetic process
GO:0048437 - floral organ development
GO:0003700 - transcription factor activity
GO:0010077 - maintenance of inflorescence meristem identity
GO:0009408 - response to heat
GO:0048573 - photoperiodism, flowering
 TO:0006032 - panicle size
TO:0000137 - days to heading
TO:0000382 - 1000-seed weight
TO:0006030 - spikelet meristem identity
TO:0000259 - heat tolerance
TO:0000397 - grain size
 Os05g0121600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g03040.3
LOC_Os05g03040.2
LOC_Os05g03040.1
PPS OsWD40-55
OsCOP1
COP1
YEL
OsYEL
OsPPS
COP1-1
OsCOP1-1
OsRING347
RING347
 PETER PAN SYNDROME COP1 ortholog
CONSTITUTIVE PHOTOMORPHOGENIC 1
yellowish-pericarp embryo lethal
RING-type E3 ubiquitin ligase 347
 2 Seed - Morphological traits - Grain shape
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Embryo
Coloration - Others
Heterochrony
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
 GO:0010218 - response to far red light
GO:0046283 - anthocyanin metabolic process
GO:0005634 - nucleus
GO:0010119 - regulation of stomatal movement
GO:0008270 - zinc ion binding
GO:0016874 - ligase activity
GO:0009416 - response to light stimulus
GO:0009628 - response to abiotic stimulus
GO:0010228 - vegetative to reproductive phase transition
GO:0046685 - response to arsenic
GO:0009640 - photomorphogenesis
GO:0009641 - shade avoidance
GO:0048573 - photoperiodism, flowering
GO:0009637 - response to blue light
GO:0010224 - response to UV-B
GO:0006281 - DNA repair
GO:0009793 - embryonic development ending in seed dormancy
GO:0009266 - response to temperature stimulus
GO:0009962 - regulation of flavonoid biosynthetic process
 TO:0000229 - photoperiod sensitivity
TO:0000064 - embryo related trait
TO:0000601 - UV-B light sensitivity
TO:0000326 - leaf color
TO:0000675 - ferulic acid content
TO:0006006 - monosaccharide content
TO:0000397 - grain size
TO:0006007 - polysaccharide content
TO:0000137 - days to heading
TO:0000707 - pericarp color
TO:0000051 - stem strength
TO:0000430 - germination rate
TO:0000159 - blue light sensitivity
TO:0000168 - abiotic stress trait
TO:0000590 - grain weight
TO:0000075 - light sensitivity
TO:0000432 - temperature response trait
TO:0000396 - grain yield
TO:0002616 - flowering time
TO:0000130 - far red light sensitivity
TO:0000290 - flavonoid content
 Os02g0771100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g53140.1
WRKY104 OsWRKY104
CRPG32
OsCRPG32
 WRKY GENE 104 collar region-preferential gene 32
 11 Tolerance and resistance - Disease resistance
Tolerance and resistance - Insect resistance
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0051607 - defense response to virus
GO:0009753 - response to jasmonic acid stimulus
GO:0048573 - photoperiodism, flowering
GO:0042742 - defense response to bacterium
GO:0050832 - defense response to fungus
GO:0010224 - response to UV-B
GO:0002213 - defense response to insect
GO:0006952 - defense response
 TO:0000137 - days to heading
TO:0000205 - white-backed planthopper resistance
TO:0000175 - bacterial blight disease resistance
TO:0000731 - lignin content
TO:0000074 - blast disease
TO:0000172 - jasmonic acid sensitivity
TO:0000601 - UV-B light sensitivity
TO:0000148 - viral disease resistance
TO:0000145 - internode length
TO:0002616 - flowering time
 PO:0006012 - leaf collar
Os11g0117400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g02520.1
ACEF1 Ac ef1
Acef1
 ACCELERATION OF HEADING EF 1 Acceleration of heading (ef1)
Acceleration of heading (fl21)
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
 TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
E2 HEADING DATE 2 Heading date2
Heading date 2
Heading date-2
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
EF2 ef2 (=lf-1)
ef2(t) (lf1)
lf1
ef2
 EARLINESS 2 late heading2
late heading 2
late heading-2
 9 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
EF3 ef3(t)
ef3
 EARLINESS 3 late heading3
late heading 3
late heading-3
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
EF4 ef4
ef4(t)
 EARLINESS 4 late heading4
late heading 4
late heading-4
 3 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
FON2 fon2
OsFON2
FON4
OsFON4
FON2/FON4
TG1
 FLORAL ORGAN NUMBER 2 floral organ number2
floral organ number 2
floral organ number-2
floral organ number4
floral organ number 4
twin-grain1
twin-grain 1
 11 Reproductive organ - Spikelet, flower, glume, awn
Character as QTL - Yield and productivity
Reproductive organ - Heading date
 GO:0007275 - multicellular organismal development
GO:0009887 - organ morphogenesis
GO:0009888 - tissue development
GO:0030154 - cell differentiation
GO:0005576 - extracellular region
GO:0019827 - stem cell maintenance
 TO:0000499 - flower anatomy and morphology trait
TO:0002759 - grain number
TO:0000445 - seed number
TO:0006038 - floral organ number
 PO:0009046 - flower
Os11g0595400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g38270.1
image Id ( 6704 )
ISE1 iSe1
i-Se-1
 RECESSIVE INHIBITOR FOR PHOTOSENSITIVITY (SE1) recessive inhibitor for photosensitivity (Se1)
 Reproductive organ - Heading date
 GO:0009648 - photoperiodism
GO:0003700 - transcription factor activity
 TO:0000137 - days to heading
TO:0000229 - photoperiod sensitivity
TO:0000469 - days to maturity
 PO:0009049 - inflorescence
PO:0009010 - seed
PO:0009013 - portion of meristem tissue
PO:0009082 - spikelet floret
-
SE4 Se4(t)
 PHOTOSENSITIVITY 4 Photosensitivity4
Photosensitivity 4
Photoperiod-sensitivity-4
 Reproductive organ - Heading date
 GO:0009648 - photoperiodism
GO:0003700 - transcription factor activity
 TO:0000469 - days to maturity
TO:0000229 - photoperiod sensitivity
TO:0000137 - days to heading
 PO:0009082 - spikelet floret
PO:0009010 - seed
PO:0009013 - portion of meristem tissue
PO:0009049 - inflorescence
-
SE6 se6(t)
 PHOTOSENSITIVITY 6 photosensitivity6 (W1623)
photosensitivity6
photosensitivity 6
photosensitivity-6
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000229 - photoperiod sensitivity
TO:0000137 - days to heading
 PO:0009011 - plant structure
PO:0009049 - inflorescence
PO:0000003 - whole plant
-
SE7 se7(t)
 PHOTOSENSITIVITY 7 photosensitivity7 (W593)
photosensitivity 7
photoperiod-sensitivity-7(W593)
photoperiod-sensitivity-7
photosensitivity7
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000229 - photoperiod sensitivity
TO:0000137 - days to heading
 PO:0009049 - inflorescence
PO:0000003 - whole plant
PO:0009011 - plant structure
-
SPL11 spl11
spl11*
OsPUB11
PUB11
OsPUB11/SPL11
PUB11/SPL11
 SPOTTED LEAF 11 spotted leaf11
spotted leaf-11
Protein spotted leaf 11
Cell death-related protein SPL11
plant U-box-containing protein 11
U-box protein 11
U-box-type E3 ubiquitin ligase 11
 12 Tolerance and resistance - Disease resistance
Tolerance and resistance - Lesion mimic
Reproductive organ - Heading date
 GO:0043066 - negative regulation of apoptosis
GO:0009614 - disease resistance
GO:0045824 - negative regulation of innate immune response
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:2000028 - regulation of photoperiodism, flowering
GO:0042742 - defense response to bacterium
GO:0050832 - defense response to fungus
GO:0000151 - ubiquitin ligase complex
GO:0005488 - binding
GO:0016567 - protein ubiquitination
GO:0019941 - modification-dependent protein catabolic process
GO:0043067 - regulation of programmed cell death
GO:0031347 - regulation of defense response
GO:0004842 - ubiquitin-protein ligase activity
 TO:0000069 - variegated leaf
TO:0000112 - disease resistance
TO:0000175 - bacterial blight disease resistance
TO:0000063 - mimic response
TO:0000074 - blast disease
 PO:0009025 - vascular leaf
Os12g0570000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g38210.1
image Id ( 6711 )
SUSE1 SuSe1(t)*
Su Se1(t)*
 SUPPRESSOR FOR PHOTOSENSITIVITY SE 1 Suppressor for photosensitivity (Se1)
Suppressor for photoperiod-sensitivity (Se1)
 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000137 - days to heading
TO:0000229 - photoperiod sensitivity
 PO:0000003 - whole plant
PO:0009049 - inflorescence
PO:0009011 - plant structure
-
WEF1 wEfl
 WEAKENING EARLY HEADING OF EF 1 weakening early heading of Ef1
weakening effect for Fl21.2
 10 Reproductive organ - Heading date
 GO:0003700 - transcription factor activity
GO:0009648 - photoperiodism
 TO:0000229 - photoperiod sensitivity
TO:0000137 - days to heading
 PO:0009049 - inflorescence
-
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/rice/oryzabase