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CGSNL
Gene
Symbol 		Gene symbol synonym(s) CGSNL Gene Name Gene name synonym(s) Chr. No. Trait Class Gene Ontology Trait Ontology Plant Ontology RAP ID MSU ID Mutant
Image
CIPK01 OsCIPK01
CIPK1
OsCIPK1
OsSnRK3.3
SnRK3.3
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 1 CBL-interacting protein kinase 1
Sucrose nonfermenting-1-related protein kinase 3.3
 1 Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Biochemical character
Character as QTL - Yield and productivity
 GO:0009409 - response to cold
GO:0004674 - protein serine/threonine kinase activity
GO:0005524 - ATP binding
GO:0004713 - protein tyrosine kinase activity
GO:0030307 - positive regulation of cell growth
GO:0009740 - gibberellic acid mediated signaling
GO:0009413 - response to flooding
GO:0009651 - response to salt stress
GO:0030145 - manganese ion binding
GO:0006468 - protein amino acid phosphorylation
GO:0007165 - signal transduction
GO:0009414 - response to water deprivation
 TO:0000303 - cold tolerance
TO:0000382 - 1000-seed weight
TO:0000432 - temperature response trait
TO:0020033 - glume length
TO:0020034 - glume width
TO:0000734 - grain length
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000396 - grain yield
TO:0000391 - seed size
TO:0000397 - grain size
TO:0000590 - grain weight
TO:0000114 - flooding related trait
 PO:0025034 - leaf
Os01g0292200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g18800.3
LOC_Os01g18800.4
LOC_Os01g18800.1
LOC_Os01g18800.2
LOC_Os01g18800.5
FLO27 OsbZIP58
bZIP58
OsEnS-92
OsSMF1
SMF1
OsRISBZ1
RISBZ1/bZIP58
RISBZ1
OsFLO27
 FLOURY ENDOSPERM 27 bZIP transcription factor 58
rice seed b-Zipper 1
endosperm-specific gene 92
seed maturation factor 1
rice seed basic leucine zipper 1
RICE SEED bZIP1
 7 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Grain shape
Seed - Morphological traits - Endosperm
Other
 GO:0034976 - response to endoplasmic reticulum stress
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010581 - regulation of starch biosynthetic process
GO:0009960 - endosperm development
GO:0012501 - programmed cell death
GO:0010431 - seed maturation
GO:0043565 - sequence-specific DNA binding
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0030968 - endoplasmic reticulum unfolded protein response
 TO:0002653 - endosperm storage protein content
TO:0002661 - seed maturation
TO:0000104 - floury endosperm
TO:0000432 - temperature response trait
TO:0000259 - heat tolerance
TO:0002673 - amino acid content
TO:0000590 - grain weight
TO:0000399 - grain thickness
TO:0000402 - grain width
TO:0000734 - grain length
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0002656 - starch grain shape
TO:0000100 - shrunken endosperm
TO:0000487 - endosperm color
TO:0000490 - protein composition related trait
 PO:0007057 - 0 seed germination stage
PO:0007632 - seed maturation stage
PO:0009089 - endosperm
PO:0005360 - aleurone layer
PO:0007633 - endosperm development stage
Os07g0182000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g08420.1
SBE4 RBE4
OsSBE4
BEIIa
QEIIb
BEIIA
OsBEIIa
 STARCH BRANCHING ENZYME 4 Q-enzyme IIb
starch branching enzyme IIb
Starch branching enzyme IIa
 4 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
 GO:0005982 - starch metabolic process
GO:0019252 - starch biosynthetic process
GO:0003844 - 1,4-alpha-glucan branching enzyme activity
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0005976 - polysaccharide metabolic process
GO:0009501 - amyloplast
GO:0009568 - amyloplast starch grain
 TO:0000099 - sugary endosperm
TO:0000097 - amylopectin content
TO:0000162 - seed quality
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0000489 - carbohydrate composition related trait
 PO:0025034 - leaf
Os04g0409200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g33460.1
GHD7 Ghd2
Ghd7
OsGhd7
OsCCT26
OsCMF8
OsI
Ghd7/Hd4
Hd4
EH7-1/Hd4
Ghd7-0a
EH7-1
EH7/Ghd7
EH7
OsEH7
GLW7.1
OsGLW7.1
 HEADING DATE 7 heading date 7
"Grain number
plant height
and heading date7"
"GRAIN NUMBER
PLANT HEIGHT AND HEADING DATE 7"
CCT domain-containing gene 26
CCT (CO, CO-LIKE and TOC1) domain protein 26
CCT domain protein 26
CCT MOTIF FAMILY (CMF) gene 8
Early heading 7
"Grain Length
Width and Weight 7.1"
Grain height date 7
 7 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Heterochrony
Seed - Physiological traits
Vegetative organ - Culm
Seed - Physiological traits - Storage substances
Seed - Physiological traits - Taste
 GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009648 - photoperiodism
GO:0005985 - sucrose metabolic process
GO:0042128 - nitrate assimilation
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0045848 - positive regulation of nitrogen utilization
GO:0006521 - regulation of cellular amino acid metabolic process
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0008643 - carbohydrate transport
GO:0048573 - photoperiodism, flowering
GO:0051781 - positive regulation of cell division
GO:0009416 - response to light stimulus
GO:0009740 - gibberellic acid mediated signaling
GO:0010229 - inflorescence development
GO:0007623 - circadian rhythm
GO:0030307 - positive regulation of cell growth
GO:0006109 - regulation of carbohydrate metabolic process
GO:0015770 - sucrose transport
GO:0006808 - regulation of nitrogen utilization
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0010109 - regulation of photosynthesis
GO:0009744 - response to sucrose stimulus
GO:0009745 - sucrose mediated signaling
 TO:0000621 - inflorescence development trait
TO:0000397 - grain size
TO:0000382 - 1000-seed weight
TO:0000734 - grain length
TO:0002653 - endosperm storage protein content
TO:0000590 - grain weight
TO:0002675 - gibberellic acid content
TO:0000266 - chalky endosperm
TO:0000469 - days to maturity
TO:0000456 - spikelet number
TO:0000229 - photoperiod sensitivity
TO:0000207 - plant height
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000050 - inflorescence branching
TO:0002759 - grain number
TO:0000011 - nitrogen sensitivity
TO:0000196 - amylose content
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0000152 - panicle number
TO:0000696 - starch content
TO:0000107 - endosperm storage protein-1 content
TO:0000109 - endosperm storage protein-2 content
TO:0000137 - days to heading
TO:0000019 - seedling height
TO:0000211 - gel consistency
TO:0002616 - flowering time
TO:0000710 - globulin protein content
TO:0000449 - grain yield per plant
TO:0000352 - plant dry weight
TO:0002680 - albumin content
TO:0000357 - growth and development trait
 PO:0001083 - inflorescence development stage
Os07g0261200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g15770.1
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
ABI5 OsABI5
OsbZIP10
OsABF1
OREB1
OsABI5-1
OsABI5-2
OsOREB1
OREB1
 ABA INSENSITIVE 5 ABA Insensitive 5
bZIP-type transcription factor ABI5
bZIP transcription factors OsABI5
bZIP transcription factor 10
Abscisic acid insensitive 5
 1 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
Reproductive organ - Pollination, fertilization, fertility - Male sterility
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Character as QTL - Germination
Character as QTL - Grain quality
Character as QTL - Yield and productivity
 GO:0009725 - response to hormone stimulus
GO:0010029 - regulation of seed germination
GO:0010162 - seed dormancy
GO:0045449 - regulation of transcription
GO:0009787 - regulation of abscisic acid mediated signaling
GO:0010581 - regulation of starch biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0045454 - cell redox homeostasis
GO:0005982 - starch metabolic process
GO:0006995 - cellular response to nitrogen starvation
GO:0005985 - sucrose metabolic process
GO:0009753 - response to jasmonic acid stimulus
GO:0010187 - negative regulation of seed germination
GO:0042744 - hydrogen peroxide catabolic process
GO:0009409 - response to cold
GO:0046345 - abscisic acid catabolic process
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009651 - response to salt stress
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0031667 - response to nutrient levels
GO:0010152 - pollen maturation
GO:0003700 - transcription factor activity
GO:0009845 - seed germination
GO:0042594 - response to starvation
GO:0009739 - response to gibberellin stimulus
GO:0009733 - response to auxin stimulus
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0019740 - nitrogen utilization
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0030187 - melatonin biosynthetic process
 TO:0000615 - abscisic acid sensitivity
TO:0000303 - cold tolerance
TO:0000276 - drought tolerance
TO:0000250 - vigor related trait
TO:0000401 - plant growth hormone sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000430 - germination rate
TO:0000696 - starch content
TO:0000196 - amylose content
TO:0000097 - amylopectin content
TO:0000382 - 1000-seed weight
TO:0002658 - starch grain synthesis
TO:0002656 - starch grain shape
TO:0000266 - chalky endosperm
TO:0000399 - grain thickness
TO:0000590 - grain weight
TO:0000134 - alkali digestion
TO:0002667 - abscisic acid content
TO:0000011 - nitrogen sensitivity
TO:0000396 - grain yield
TO:0000172 - jasmonic acid sensitivity
TO:0000053 - pollen sterility
TO:0000253 - seed dormancy
TO:0002672 - auxin content
TO:0000604 - fat and essential oil content
TO:0002653 - endosperm storage protein content
TO:0000300 - glucose content
TO:0000455 - seed set percent
TO:0000040 - panicle length
TO:0000462 - gelatinization temperature
TO:0000211 - gel consistency
TO:0000487 - endosperm color
TO:0000162 - seed quality
TO:0000166 - gibberellic acid sensitivity
TO:0000163 - auxin sensitivity
TO:0000919 - grain weight
TO:0000397 - grain size
TO:0000483 - germinability at low temperature
TO:0000420 - fertility related trait
TO:0000429 - salt sensitivity
 PO:0009049 - inflorescence
PO:0007057 - 0 seed germination stage
PO:0020091 - obsolete microgametophyte
PO:0025500 - whole plant fruit development stage
PO:0009010 - seed
Os01g0859300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g64000.1
LOC_Os01g64000.2
LOC_Os01g64000.3
AGO2 OsAGO2
 ARGONAUTE 2 sativa Argonaute 2
Protein argonaute 2
ARGONAUTE2
 4 Tolerance and resistance - Stress tolerance
Other
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Coloration - Chlorophyll
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
 GO:0009409 - response to cold
GO:0009658 - chloroplast organization
GO:0003676 - nucleic acid binding
GO:0043067 - regulation of programmed cell death
GO:0051607 - defense response to virus
GO:0031047 - gene silencing by RNA
GO:0046466 - membrane lipid catabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0009690 - cytokinin metabolic process
GO:0048316 - seed development
GO:0009651 - response to salt stress
GO:0050687 - negative regulation of defense response to virus
GO:0006306 - DNA methylation
GO:0010150 - leaf senescence
 TO:0000734 - grain length
TO:0000455 - seed set percent
TO:0000615 - abscisic acid sensitivity
TO:0002660 - cytokinin content
TO:0000249 - leaf senescence
TO:0006001 - salt tolerance
TO:0002715 - chloroplast development trait
TO:0000495 - chlorophyll content
TO:0000020 - black streak dwarf virus resistance
TO:0000326 - leaf color
TO:0001015 - photosynthetic rate
TO:0000269 - 100-seed weight
TO:0000605 - hydrogen peroxide content
TO:0000449 - grain yield per plant
TO:0000396 - grain yield
TO:0000316 - photosynthetic ability
TO:0000303 - cold tolerance
 Os04g0615700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g52540.1
CKX4 OsCKX4
ckx4
OsSCRM
OsSCRM2
SCRM
SCRM2
 CYTOKININ OXIDASE/DEHYDROGENASE 4 Putative cytokinin dehydrogenase 4
cytokinin oxidase 4
 1 Character as QTL - Grain quality
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Biochemical character
 GO:0009725 - response to hormone stimulus
GO:0019139 - cytokinin dehydrogenase activity
GO:0048364 - root development
GO:0009736 - cytokinin mediated signaling
GO:0042594 - response to starvation
GO:0009735 - response to cytokinin stimulus
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0032940 - secretion by cell
GO:0009733 - response to auxin stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009734 - auxin mediated signaling pathway
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0022900 - electron transport chain
GO:0016491 - oxidoreductase activity
GO:0051607 - defense response to virus
GO:0009823 - cytokinin catabolic process
 TO:0000227 - root length
TO:0000346 - tiller number
TO:0000456 - spikelet number
TO:0000401 - plant growth hormone sensitivity
TO:0006032 - panicle size
TO:0000734 - grain length
TO:0000402 - grain width
TO:0002660 - cytokinin content
TO:0000656 - root development trait
TO:0000011 - nitrogen sensitivity
TO:0000207 - plant height
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000148 - viral disease resistance
TO:0000019 - seedling height
TO:0000020 - black streak dwarf virus resistance
TO:0000382 - 1000-seed weight
TO:0000172 - jasmonic acid sensitivity
TO:0002685 - crown root number
TO:0000449 - grain yield per plant
TO:0000430 - germination rate
TO:0000455 - seed set percent
 PO:0009105 - inflorescence branch meristem
PO:0009005 - root
PO:0007520 - root development stage
PO:0025034 - leaf
Os01g0940000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g71310.1
CKX7 OsCKX7
 CYTOKININ OXIDASE/DEHYDROGENASE 7 cytokinin oxidase 7
 2 Biochemical character
Reproductive organ - panicle
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
 GO:0019139 - cytokinin dehydrogenase activity
GO:0050660 - FAD binding
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0005615 - extracellular space
GO:0050832 - defense response to fungus
GO:0009823 - cytokinin catabolic process
 TO:0000734 - grain length
TO:0000255 - sheath blight disease resistance
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000402 - grain width
TO:0000266 - chalky endosperm
TO:0000455 - seed set percent
 PO:0020104 - leaf sheath
Os02g0220100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g12780.1
CKX8 OsCKX8
 CYTOKININ OXIDASE/DEHYDROGENASE 8 cytokinin oxidase 8
 4 Reproductive organ - Panicle, Mode of branching
Seed - Morphological traits - Grain shape
Biochemical character
 GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0050660 - FAD binding
GO:0009690 - cytokinin metabolic process
GO:0019139 - cytokinin dehydrogenase activity
GO:0009735 - response to cytokinin stimulus
 TO:0000167 - cytokinin sensitivity
TO:0000557 - secondary branch number
TO:0000382 - 1000-seed weight
TO:0002660 - cytokinin content
TO:0002759 - grain number
TO:0000734 - grain length
 Os04g0523500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g44230.1
HOX29 Oshox29
OsHox29
OSHB5
HB5
 HOMEOBOX GENE 29 rice homeobox gene 29
Homeobox-leucine zipper protein HOX29
Homeodomain transcription factor HOX29
HD-ZIP protein HOX29
HOMEODOMAIN CONTAINING PROTEIN 5
 1 Other
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000397 - grain size
 Os01g0200300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g10320.1
HAP2I OsHAP2I
NF-YA
CBF-B
NF-YA8
OsNF-YA8
OsEnS-136
NFYA8
 HAP2 SUBUNIT OF CCAAT-BOX BINDING COMPLEX NUCLEAR FACTOR-Y subunit A8
NUCLEAR FACTOR-Y subunit NF-YA8
NF-YA transcription factor 8
endosperm-specific gene 136
NF-YA subunit 8
NF-YA family 8
 10 Character as QTL - Yield and productivity
Other
Seed - Morphological traits - Endosperm
Seed - Morphological traits - Grain shape
Character as QTL - Grain quality
Tolerance and resistance - Disease resistance
 GO:0010167 - response to nitrate
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009753 - response to jasmonic acid stimulus
GO:0051607 - defense response to virus
GO:0043565 - sequence-specific DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005634 - nucleus
GO:0005737 - cytoplasm
GO:0006350 - transcription
 TO:0000148 - viral disease resistance
TO:0000598 - protein content
TO:0000011 - nitrogen sensitivity
TO:0000172 - jasmonic acid sensitivity
TO:0000266 - chalky endosperm
TO:0000696 - starch content
 PO:0009089 - endosperm
Os10g0397900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g25850.1
HAP3D OsHAP3D
OsEnS-83
OsNF-YB9
NF-YB9
NFYB9
OsLEC1A
LEC1A
 HAP3D SUBUNIT OF CCAAT-BOX BINDING COMPLEX HAP3 subunit D
LEC1-type 3 subunit protein-D
endosperm-specific gene 83
NUCLEAR FACTOR-Y subunit B9
NUCLEAR FACTOR-Y subunit NF-YB9
HAP3 SUBUNIT D
NF-YB subunit 9
NF-YB family 9
 6 Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Other
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0042127 - regulation of cell proliferation
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009790 - embryonic development
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0005737 - cytoplasm
GO:0009845 - seed germination
 TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000266 - chalky endosperm
TO:0000391 - seed size
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0020033 - glume length
TO:0000487 - endosperm color
TO:0000575 - endosperm related trait
TO:0000064 - embryo related trait
TO:0000485 - sterility related trait
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0000276 - drought tolerance
TO:0000211 - gel consistency
TO:0000162 - seed quality
TO:0000222 - head rice
TO:0000207 - plant height
TO:0000382 - 1000-seed weight
TO:0000346 - tiller number
TO:0000639 - seed fertility
TO:0000421 - pollen fertility
 PO:0001170 - seed development stage
PO:0009009 - plant embryo
PO:0009089 - endosperm
PO:0020094 - plant egg cell
PO:0000003 - whole plant
PO:0009010 - seed
Os06g0285200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g17480.1
HAP3K OsHAP3K/OsNF-YB1
OsHAP3K
OsNF-YB1
NF-YB1
nf-yb1
OsLEC1
OsNF-YB-1
NFYB1
OsEnS-41
 HAP3K SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear transcription factor Y subunit B-1
CCAAT-binding transcription factor subunit NF-YB1
leafy cotyledon 1
endosperm-specific gene 41
Nuclear Factor YB1
NUCLEAR FACTOR-Y subunit B1
NUCLEAR FACTOR-Y subunit NF-YB1
NF-YB subunit 1
NF-YB family 1
 2 Seed - Morphological traits - Grain shape
Seed - Morphological traits - Endosperm
Seed - Physiological traits - Dormancy
Seed - Physiological traits - Storage substances
Seed - Morphological traits
Other
Character as QTL - Germination
Character as QTL - Grain quality
Tolerance and resistance - Stress tolerance
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0048623 - seed germination on parent plant
GO:0010162 - seed dormancy
GO:0009737 - response to abscisic acid stimulus
GO:0010600 - regulation of auxin biosynthetic process
GO:0043565 - sequence-specific DNA binding
GO:0008283 - cell proliferation
GO:0009960 - endosperm development
GO:0009738 - abscisic acid mediated signaling
GO:0010431 - seed maturation
GO:0045449 - regulation of transcription
GO:0005829 - cytosol
GO:0009651 - response to salt stress
GO:0005737 - cytoplasm
 TO:0000734 - grain length
TO:0000184 - seed anatomy and morphology trait
TO:0000408 - hot paste viscosity
TO:0000409 - peak viscosity
TO:0000653 - seed development trait
TO:0000162 - seed quality
TO:0000266 - chalky endosperm
TO:0000397 - grain size
TO:0000196 - amylose content
TO:0000379 - cool paste viscosity
TO:0000391 - seed size
TO:0000619 - vivipary
TO:0000399 - grain thickness
TO:0002661 - seed maturation
TO:0002672 - auxin content
TO:0000396 - grain yield
TO:0000696 - starch content
TO:0000604 - fat and essential oil content
TO:0000462 - gelatinization temperature
TO:0000211 - gel consistency
TO:0000382 - 1000-seed weight
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000253 - seed dormancy
 PO:0007633 - endosperm development stage
PO:0009089 - endosperm
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
PO:0006220 - central endosperm
PO:0005360 - aleurone layer
Os02g0725900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g49410.1
HAP5A OsHAP5A
NF-YC
CBF-C
OsNF-YC1
Os-NF-YC1
NF-YC1
NFYC1
OsNF-YC4-2
NF-YC4-2
 HAP5A SUBUNIT OF CCAAT-BOX BINDING COMPLEX Nuclear factor Y C1 subunit
Nuclear factor Y C subunit 1
NUCLEAR FACTOR-Y subunit C1
NUCLEAR FACTOR-Y subunit NF-YC1
NF-YC subunit 1
NF-YC family 1
 2 Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Reproductive organ - Heading date
Other
 GO:0008284 - positive regulation of cell proliferation
GO:0005634 - nucleus
GO:0050688 - regulation of defense response to virus
GO:0009414 - response to water deprivation
GO:0009737 - response to abscisic acid stimulus
GO:0009651 - response to salt stress
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005737 - cytoplasm
GO:0043565 - sequence-specific DNA binding
GO:0006350 - transcription
GO:0051607 - defense response to virus
GO:0080050 - regulation of seed development
GO:0030307 - positive regulation of cell growth
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000919 - grain weight
TO:0000653 - seed development trait
TO:0000615 - abscisic acid sensitivity
TO:0006001 - salt tolerance
TO:0000137 - days to heading
TO:0000590 - grain weight
TO:0000276 - drought tolerance
TO:0000397 - grain size
TO:0000148 - viral disease resistance
TO:0000391 - seed size
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000382 - 1000-seed weight
TO:0000399 - grain thickness
TO:0000975 - grain width
TO:0001034 - relative plant height
TO:0000402 - grain width
 PO:0009049 - inflorescence
PO:0001170 - seed development stage
Os02g0170500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07450.1
LOC_Os02g07450.2
DEP1 OsDEP1
EP
qPE9-1
DN1
DEP1/DN1/qPE9-1
qNGR9
qDEP1
RGG4/DEP1/DN1/qPE9-1/OsGGC3
RGG4
OsDN1
OsGGC3
GGC3
 DENSE AND ERECT PANICLE 1 dense and erect panicle 1
erect-pose panicle
DENSE PANICLE 1
DENSE AND ERECT PANICLE1
DENSE AND ERECT PANICLES 1
G gamma subunit DEP1
Heterotrimeric G Protein gamma4 Subunit
 9 Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Vegetative organ - Root
Reproductive organ - Panicle, Mode of branching
Vegetative organ - Culm
Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
 GO:0035330 - regulation of hippo signaling cascade
GO:0010729 - positive regulation of hydrogen peroxide biosynthetic process
GO:0010618 - aerenchyma formation
GO:0010229 - inflorescence development
GO:0051171 - regulation of nitrogen compound metabolic process
GO:0043068 - positive regulation of programmed cell death
GO:0005882 - intermediate filament
GO:0005886 - plasma membrane
GO:0009414 - response to water deprivation
GO:0009409 - response to cold
GO:0009651 - response to salt stress
GO:0048573 - photoperiodism, flowering
GO:0005634 - nucleus
GO:0007186 - G-protein coupled receptor protein signaling pathway
 TO:0000207 - plant height
TO:0000152 - panicle number
TO:0000397 - grain size
TO:0000456 - spikelet number
TO:0000734 - grain length
TO:0000276 - drought tolerance
TO:0000303 - cold tolerance
TO:0000050 - inflorescence branching
TO:0002731 - grain length to width ratio
TO:0006001 - salt tolerance
TO:0000455 - seed set percent
TO:0002759 - grain number
TO:0000396 - grain yield
TO:0000382 - 1000-seed weight
TO:0000605 - hydrogen peroxide content
TO:0000137 - days to heading
TO:0000043 - root anatomy and morphology trait
TO:0000621 - inflorescence development trait
TO:0000625 - spikelet density
TO:0000040 - panicle length
 Os09g0441900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g26999.1
LOC_Os09g26999.3
LOC_Os09g26999.2
DLT dlt
OsGRAS32
OsDLT
OsDLT1
DTL1
OsGRAS-32
OsGRAS32
GRAS-32
GRAS32
SMOS2/DLT
SMOS2
OsSMOS2
OsGS6
GS6
DLT/GS6/SMOS2
 DWARF AND LOW-TILLERING GRAS protein 32
SMALL ORGAN SIZE 2
 6 Vegetative organ - Root
Character as QTL - Plant growth activity
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Vegetative organ - Leaf
Reproductive organ - Heading date
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
Seed - Morphological traits
 GO:0010422 - regulation of brassinosteroid biosynthetic process
GO:0080006 - internode patterning
GO:0009742 - brassinosteroid mediated signaling
GO:0009741 - response to brassinosteroid stimulus
GO:0009734 - auxin mediated signaling pathway
GO:0010229 - inflorescence development
GO:0007275 - multicellular organismal development
GO:0051302 - regulation of cell division
GO:0008283 - cell proliferation
GO:0000226 - microtubule cytoskeleton organization
GO:0016131 - brassinosteroid metabolic process
GO:0005634 - nucleus
GO:0009755 - hormone-mediated signaling
GO:0010928 - regulation of auxin mediated signaling pathway
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006351 - transcription, DNA-dependent
 TO:0002616 - flowering time
TO:0000326 - leaf color
TO:0002637 - leaf size
TO:0000040 - panicle length
TO:0002688 - leaf lamina joint bending
TO:0000346 - tiller number
TO:0000011 - nitrogen sensitivity
TO:0002677 - brassinosteroid sensitivity
TO:0000152 - panicle number
TO:0000227 - root length
TO:0000145 - internode length
TO:0000621 - inflorescence development trait
TO:0000357 - growth and development trait
TO:0002676 - brassinosteroid content
TO:0001035 - stem width
TO:0000206 - leaf angle
TO:0000397 - grain size
TO:0002684 - plant cell size
TO:0000329 - tillering ability
TO:0002601 - stamen size
TO:0002602 - pistil size
TO:0000019 - seedling height
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000576 - stem length
 PO:0001083 - inflorescence development stage
Os06g0127800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g03710.1
C3H33 OsC3H33
OsTZF5
TZF5
OsCCCH-Zn-5
CCCH-Zn-5
OsC3H36
C3H36
 ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 33 Zinc finger CCCH domain-containing protein 33
Tandem zinc finger protein 5
CCCH Zinc Finger Family Gene 36
 5 Seed - Morphological traits - Grain shape
Other
Tolerance and resistance - Stress tolerance
 GO:0030912 - response to deep water
GO:0009651 - response to salt stress
GO:0003677 - DNA binding
GO:0008270 - zinc ion binding
GO:0005737 - cytoplasm
GO:0009753 - response to jasmonic acid stimulus
GO:0009409 - response to cold
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
 TO:0000172 - jasmonic acid sensitivity
TO:0000276 - drought tolerance
TO:0000524 - submergence tolerance
TO:0000382 - 1000-seed weight
TO:0000402 - grain width
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000357 - growth and development trait
TO:0000615 - abscisic acid sensitivity
TO:0001016 - relative chlorophyll content
TO:0000136 - relative water content
TO:0000396 - grain yield
 PO:0008037 - seedling
PO:0025034 - leaf
PO:0009046 - flower
PO:0009010 - seed
PO:0009047 - stem
PO:0009005 - root
PO:0009049 - inflorescence
Os05g0128200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g03760.1
LIC OsC3H46
C3H46
OsLIC
OsFLA6
FLA6
OsC3H52
C3H52
 LEAF AND TILLER ANGLE INCREASED CONTROLLER Zinc finger CCCH domain-containing protein 46
LEAF and TILLER ANGLE INCREASED CONTROLLER
Flag leaf angle 6
CCCH Zinc Finger Family Gene 52
 6 Other
Reproductive organ - panicle
Character as QTL - Yield and productivity
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
 GO:0009742 - brassinosteroid mediated signaling
GO:0003677 - DNA binding
GO:0008270 - zinc ion binding
GO:0005634 - nucleus
GO:0009741 - response to brassinosteroid stimulus
GO:0005737 - cytoplasm
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005739 - mitochondrion
 TO:0000547 - primary branch number
TO:0000445 - seed number
TO:0002688 - leaf lamina joint bending
TO:0000207 - plant height
TO:0000124 - flag leaf angle
TO:0000449 - grain yield per plant
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000206 - leaf angle
TO:0002677 - brassinosteroid sensitivity
TO:0000040 - panicle length
TO:0000396 - grain yield
TO:0000397 - grain size
TO:0000402 - grain width
TO:0000567 - tiller angle
 Os06g0704300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g49080.1
KNAT7 HOS66
HB365
OsKNAT7
 KNOTTED ARABIDOPSIS THALIANA 7 HOMEOBOX ORYZA SATIVA 66
Homeobox protein knotted-1-like 3
Homeobox protein HOS66
KNOTTED ARABIDOPSIS THALIANA7
KNOX ARABIDOPSIS THALIANA7
 3 Tolerance and resistance - Stress tolerance
Other
Reproductive organ - Inflorescence
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
 GO:0030244 - cellulose biosynthetic process
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009834 - secondary cell wall biogenesis
GO:0052386 - cell wall thickening
GO:0003700 - transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0080006 - internode patterning
GO:0010229 - inflorescence development
GO:0009664 - plant-type cell wall organization
GO:0001558 - regulation of cell growth
GO:0009809 - lignin biosynthetic process
GO:0030308 - negative regulation of cell growth
GO:0005634 - nucleus
 TO:0000068 - lodging incidence
TO:0000051 - stem strength
TO:0000621 - inflorescence development trait
TO:0000731 - lignin content
TO:0000397 - grain size
 PO:0001083 - inflorescence development stage
Os03g0123500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g03164.3
LOC_Os03g03164.2
LOC_Os03g03164.1
GAMYBL2 OsGAMYBL2
Os2R_MYB40
2R_MYB40
MYB2-45
OsMYB2-45
 GAMYB-LIKE 2 R2R3-MYB Transcription Factor 40
R2R3-MYB transcription factor 2-45
 3 Other
Seed - Morphological traits - Grain shape
Tolerance and resistance - Insect resistance
Character as QTL - Yield and productivity
Character as QTL - Plant growth activity
 GO:0009742 - brassinosteroid mediated signaling
GO:0005634 - nucleus
GO:0002213 - defense response to insect
GO:0010476 - gibberellin-mediated signaling
GO:0009908 - flower development
 TO:0000357 - growth and development trait
TO:0000424 - brown planthopper resistance
TO:0000397 - grain size
 Os03g0578900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g38210.1
NADP-ME2 OscytME1
OsNADP-ME2-3
NADP-ME2-3
 NADP-MALIC ENZYME 2 cytosolic NADP malic enzyme 1
 1 Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Grain shape
Biochemical character
Vegetative organ - Culm
Reproductive organ - panicle
Tolerance and resistance - Disease resistance
 GO:0009740 - gibberellic acid mediated signaling
GO:0042866 - pyruvate biosynthetic process
GO:0006108 - malate metabolic process
GO:0009739 - response to gibberellin stimulus
GO:0055114 - oxidation reduction
GO:0046872 - metal ion binding
GO:0051287 - NAD or NADH binding
GO:0009507 - chloroplast
GO:0009626 - plant-type hypersensitive response
GO:0004473 - malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity
GO:0005829 - cytosol
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0050832 - defense response to fungus
 TO:0000166 - gibberellic acid sensitivity
TO:0000447 - filled grain number
TO:0000145 - internode length
TO:0000382 - 1000-seed weight
TO:0000734 - grain length
TO:0000397 - grain size
TO:0000152 - panicle number
TO:0000040 - panicle length
TO:0000207 - plant height
TO:0000455 - seed set percent
TO:0002675 - gibberellic acid content
TO:0000074 - blast disease
 Os01g0723400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g52500.1
LOC_Os01g52500.2
LOC_Os01g52500.3
LOC_Os01g52500.4
LOC_Os01g52500.5
EP2 ep2
EP2/DEP2/SRS1
SRS1/DEP2
DEP2
SRS1
OsSRS1
CL7(t)
OsRELA
RELA
SUG1
OsSUG1
 ERECT PANICLE 2 erect panical 2
Erect panicle2
erect panicle2-1
erect panicle2-2
dense and erect panicle 2
small and round seed 1
cleistogamy 7
cleistogamy gene on chromosome 7
regulator of leaf angle
suppressor of GS2AA 1
 7 Tolerance and resistance - Disease resistance
Character as QTL - Plant growth activity
Seed - Morphological traits - Grain shape
Vegetative organ - Leaf
Character as QTL - Yield and productivity
Reproductive organ - Panicle, Mode of branching
 GO:0050777 - negative regulation of immune response
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0032491 - detection of molecule of fungal origin
GO:0002679 - respiratory burst during defense response
GO:0002221 - pattern recognition receptor signaling pathway
GO:0050832 - defense response to fungus
GO:0009742 - brassinosteroid mediated signaling
GO:0005737 - cytoplasm
GO:0009741 - response to brassinosteroid stimulus
GO:0010200 - response to chitin
GO:0001558 - regulation of cell growth
GO:0009739 - response to gibberellin stimulus
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009740 - gibberellic acid mediated signaling
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0010422 - regulation of brassinosteroid biosynthetic process
 TO:0000050 - inflorescence branching
TO:0000074 - blast disease
TO:0002637 - leaf size
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000590 - grain weight
TO:0000397 - grain size
TO:0002677 - brassinosteroid sensitivity
TO:0000472 - vascular bundle number
TO:0002759 - grain number
TO:0000342 - panicle axis angle
TO:0000734 - grain length
TO:0000339 - stem thickness
TO:0000040 - panicle length
TO:0000207 - plant height
TO:0000557 - secondary branch number
TO:0000180 - spikelet fertility
TO:0000402 - grain width
TO:0000382 - 1000-seed weight
TO:0000051 - stem strength
TO:0002688 - leaf lamina joint bending
TO:0000166 - gibberellic acid sensitivity
TO:0000206 - leaf angle
TO:0002730 - grain shape
TO:0000399 - grain thickness
 PO:0009082 - spikelet floret
PO:0025034 - leaf
PO:0009037 - lemma
PO:0009049 - inflorescence
PO:0009038 - palea
PO:0001083 - inflorescence development stage
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0009005 - root
PO:0005020 - vascular bundle
Os07g0616000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g42410.1
BU1 ILI4
OsILI4
OsBU1
BU1/ILI4
OsbHLH172
bHLH172
 BRASSINOSTEROID UPREGULATED 1 BRASSINOSTEROID UPREGULATED1
Increased Leaf Inclination4
BR upregulated 1
basic helix-loop-helix protein 172
 6 Seed - Morphological traits - Grain shape
Seed - Morphological traits
Character as QTL - Plant growth activity
Reproductive organ - Pollination, fertilization, fertility
Vegetative organ - Culm
Vegetative organ - Leaf
Other
Character as QTL - Yield and productivity
 GO:0006355 - regulation of transcription, DNA-dependent
GO:0005737 - cytoplasm
GO:0009741 - response to brassinosteroid stimulus
GO:0009742 - brassinosteroid mediated signaling
GO:0046983 - protein dimerization activity
GO:0040008 - regulation of growth
GO:0006351 - transcription, DNA-dependent
GO:0005634 - nucleus
GO:0009723 - response to ethylene stimulus
GO:0009753 - response to jasmonic acid stimulus
 TO:0000326 - leaf color
TO:0000492 - leaf shape
TO:0000590 - grain weight
TO:0000402 - grain width
TO:0002677 - brassinosteroid sensitivity
TO:0000206 - leaf angle
TO:0000734 - grain length
TO:0000397 - grain size
TO:0000145 - internode length
TO:0000207 - plant height
TO:0000361 - stem anatomy and morphology trait
TO:0000485 - sterility related trait
TO:0000357 - growth and development trait
TO:0002688 - leaf lamina joint bending
TO:0000172 - jasmonic acid sensitivity
TO:0000173 - ethylene sensitivity
 PO:0005052 - plant callus
Os06g0226500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g12210.1
SP3 OsDof15
Dof15
OsDof-15
DOF15
DLT3
OsDLT3
 SHORT PANICLE 3 Dof zinc factor 15
Dof transcription factor 15
DNA BINDING WITH ONE FINGER 15
Short Panicle 3
DWARF AND LESS TILLERS ON CHROMOSOME 3
 3 Vegetative organ - Root
Other
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Reproductive organ - Panicle, Mode of branching
Reproductive organ - Heading date
Character as QTL - Yield and productivity
Vegetative organ - Leaf
 GO:0048573 - photoperiodism, flowering
GO:0009873 - ethylene mediated signaling pathway
GO:0009651 - response to salt stress
GO:0008284 - positive regulation of cell proliferation
GO:0010229 - inflorescence development
GO:0006355 - regulation of transcription, DNA-dependent
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0009690 - cytokinin metabolic process
GO:0010081 - regulation of inflorescence meristem growth
GO:0048364 - root development
GO:0003677 - DNA binding
GO:0005634 - nucleus
GO:0010082 - regulation of root meristem growth
 TO:0000547 - primary branch number
TO:0000132 - basal internode diameter
TO:0000227 - root length
TO:0002758 - flag leaf lamina width
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000621 - inflorescence development trait
TO:0000040 - panicle length
TO:0000173 - ethylene sensitivity
TO:0000434 - root activity
TO:0000371 - yield trait
TO:0006001 - salt tolerance
TO:0000656 - root development trait
TO:0000396 - grain yield
TO:0000145 - internode length
TO:0000557 - secondary branch number
TO:0000734 - grain length
TO:0000207 - plant height
TO:0000592 - 1000-dehulled grain weight
TO:0002660 - cytokinin content
TO:0000456 - spikelet number
TO:0000050 - inflorescence branching
TO:0002692 - root meristem development
TO:0000397 - grain size
TO:0000455 - seed set percent
TO:0000346 - tiller number
TO:0000329 - tillering ability
TO:0006032 - panicle size
TO:0002616 - flowering time
TO:0000137 - days to heading
 PO:0004709 - axillary bud
PO:0009049 - inflorescence
Os03g0764900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g55610.1
GLW9 OsDof25
Dof25
OsDof-25
OsDof26
Dof26
OsGLW9
 GRAIN LENGTH AND WIDTH ON CHROMOSOME 9 DNA BINDING WITH ONE FINGER 25
Dof zinc factor 25
Dof transcription factor 25
DNA binding with one finger family transcription factor 25
 9 Other
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
Character as QTL - Grain quality
Character as QTL - Yield and productivity
 GO:0009733 - response to auxin stimulus
GO:0010928 - regulation of auxin mediated signaling pathway
GO:0009937 - regulation of gibberellic acid mediated signaling
GO:0003677 - DNA binding
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0009734 - auxin mediated signaling pathway
GO:0005634 - nucleus
GO:0009740 - gibberellic acid mediated signaling
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000411 - seed length to width ratio
TO:0002672 - auxin content
TO:0000402 - grain width
TO:0000567 - tiller angle
TO:0000449 - grain yield per plant
TO:0002730 - grain shape
TO:0002675 - gibberellic acid content
TO:0000734 - grain length
TO:0000163 - auxin sensitivity
TO:0000456 - spikelet number
TO:0000447 - filled grain number
TO:0000162 - seed quality
TO:0000266 - chalky endosperm
 Os09g0475800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g29960.1
SMG1 OsMKK4
MKK4
OsMKK4/SMG1
OsMAPKK4
MAPKK4
OsMEK4
MEK4
OsSMG1
SMG1/OsMEK6
OsMEK6
MEK6
OsSTS
STS
 SMALL GRAIN 1 MAPK kinase 4
mitogen-activated protein kinase kinase 4
small grain1
LARGE11
large grain 11
salt-tolerant and small grains
 2 Tolerance and resistance - Insect resistance
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Disease resistance
Reproductive organ - Panicle, Mode of branching
Biochemical character
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Seed - Morphological traits
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
 GO:0016020 - membrane
GO:0009690 - cytokinin metabolic process
GO:0009611 - response to wounding
GO:0005737 - cytoplasm
GO:0009751 - response to salicylic acid stimulus
GO:0009651 - response to salt stress
GO:0006970 - response to osmotic stress
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0048364 - root development
GO:0009414 - response to water deprivation
GO:0005634 - nucleus
GO:0008283 - cell proliferation
GO:0009741 - response to brassinosteroid stimulus
GO:0042742 - defense response to bacterium
GO:0009737 - response to abscisic acid stimulus
GO:0000165 - MAPKKK cascade
GO:0010200 - response to chitin
GO:0010229 - inflorescence development
GO:0002213 - defense response to insect
GO:0009739 - response to gibberellin stimulus
GO:0080027 - response to herbivore
GO:0050832 - defense response to fungus
GO:0009738 - abscisic acid mediated signaling
GO:0009743 - response to carbohydrate stimulus
GO:0042127 - regulation of cell proliferation
GO:0009742 - brassinosteroid mediated signaling
GO:0009409 - response to cold
GO:0045595 - regulation of cell differentiation
 TO:0000040 - panicle length
TO:0000656 - root development trait
TO:0000163 - auxin sensitivity
TO:0001034 - relative plant height
TO:0006001 - salt tolerance
TO:0000166 - gibberellic acid sensitivity
TO:0000276 - drought tolerance
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000206 - leaf angle
TO:0000454 - stem borer resistance
TO:0000621 - inflorescence development trait
TO:0000303 - cold tolerance
TO:0000439 - fungal disease resistance
TO:0000074 - blast disease
TO:0000175 - bacterial blight disease resistance
TO:0002660 - cytokinin content
TO:0000516 - relative root length
TO:0000167 - cytokinin sensitivity
TO:0000382 - 1000-seed weight
TO:0000615 - abscisic acid sensitivity
TO:0002677 - brassinosteroid sensitivity
TO:0000557 - secondary branch number
TO:0002669 - diterpenoid phytoalexin content
TO:0000547 - primary branch number
TO:0000455 - seed set percent
TO:0000342 - panicle axis angle
TO:0000590 - grain weight
TO:0000447 - filled grain number
TO:0000734 - grain length
TO:0000456 - spikelet number
TO:0002759 - grain number
TO:0000396 - grain yield
TO:0000397 - grain size
TO:0000160 - UV light sensitivity
TO:0000095 - osmotic response sensitivity
 PO:0007520 - root development stage
PO:0020104 - leaf sheath
PO:0025034 - leaf
PO:0001083 - inflorescence development stage
Os02g0787300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g54600.1
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
G1L1 OsG1L1
 G1 LIKE PROTEIN 1 OsG1-like 1
 2 Seed - Morphological traits - Grain shape
Reproductive organ - Panicle, Mode of branching
Other
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility
Reproductive organ - Inflorescence
 GO:0009414 - response to water deprivation
GO:0003677 - DNA binding
GO:0009299 - mRNA transcription
GO:0007275 - multicellular organismal development
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005634 - nucleus
GO:0010229 - inflorescence development
GO:0010228 - vegetative to reproductive phase transition
GO:0009416 - response to light stimulus
GO:0009737 - response to abscisic acid stimulus
 TO:0000621 - inflorescence development trait
TO:0000050 - inflorescence branching
TO:0000734 - grain length
TO:0000641 - primary branch length
TO:0000276 - drought tolerance
TO:0000397 - grain size
TO:0006030 - spikelet meristem identity
TO:0000040 - panicle length
TO:0000547 - primary branch number
TO:0000456 - spikelet number
TO:0000615 - abscisic acid sensitivity
TO:0000392 - sterility or fertility trait
 PO:0009049 - inflorescence
PO:0006327 - spikelet meristem
PO:0009105 - inflorescence branch meristem
PO:0001083 - inflorescence development stage
PO:0001170 - seed development stage
PO:0000230 - inflorescence meristem
PO:0020104 - leaf sheath
Os02g0166800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07030.3
LOC_Os02g07030.2
LOC_Os02g07030.1
G1L2 OsG1L2
 G1 LIKE PROTEIN 2 OsG1-like 2
 6 Reproductive organ - Inflorescence
Reproductive organ - Pollination, fertilization, fertility
Other
Reproductive organ - Panicle, Mode of branching
Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
 GO:0010228 - vegetative to reproductive phase transition
GO:0009414 - response to water deprivation
GO:0005634 - nucleus
GO:0010229 - inflorescence development
GO:0009416 - response to light stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0003677 - DNA binding
GO:0009299 - mRNA transcription
GO:0007275 - multicellular organismal development
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000040 - panicle length
TO:0000456 - spikelet number
TO:0000615 - abscisic acid sensitivity
TO:0000397 - grain size
TO:0000392 - sterility or fertility trait
TO:0000276 - drought tolerance
TO:0000641 - primary branch length
TO:0000621 - inflorescence development trait
TO:0000557 - secondary branch number
TO:0006030 - spikelet meristem identity
TO:0000050 - inflorescence branching
TO:0000547 - primary branch number
 PO:0009105 - inflorescence branch meristem
PO:0001083 - inflorescence development stage
PO:0020104 - leaf sheath
PO:0005052 - plant callus
PO:0009047 - stem
PO:0000230 - inflorescence meristem
PO:0006327 - spikelet meristem
PO:0009005 - root
PO:0009049 - inflorescence
PO:0020148 - shoot apical meristem
Os06g0672400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g46030.1
BLS1 OsBLS1
OsG1L6
G1L6
TH1
OsTH1
TH1/BSG1/BLS1/AFD1
BSG1
OsBSG1
AFD1
OsAFD1
BH1
OsBH1
 BEAK LIKE SPIKELET 1 G1 LIKE PROTEIN 6
TRIANGULAR HULL1
TRIANGULAR HULL 1
BEAK LIKE SPIKELET1
abnormal ower and dwarf1
beak-shaped grain1
BEAK-SHAPED GRAIN 1
ABNORMAL FLOWER AND DWARF 1
 2 Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
Other
 GO:0003677 - DNA binding
GO:0009416 - response to light stimulus
GO:0051302 - regulation of cell division
GO:0009414 - response to water deprivation
GO:0009908 - flower development
GO:0010229 - inflorescence development
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0007275 - multicellular organismal development
GO:0001558 - regulation of cell growth
GO:0008361 - regulation of cell size
GO:0048437 - floral organ development
GO:0009299 - mRNA transcription
 TO:0000145 - internode length
TO:0000207 - plant height
TO:0000421 - pollen fertility
TO:0000396 - grain yield
TO:0000040 - panicle length
TO:0000180 - spikelet fertility
TO:0000621 - inflorescence development trait
TO:0000276 - drought tolerance
TO:0002762 - width of grain with hull
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0006011 - lodicule shape
TO:0000564 - spikelet width
TO:0000657 - spikelet anatomy and morphology trait
TO:0000614 - lemma shape
TO:0002730 - grain shape
TO:0000397 - grain size
TO:0000590 - grain weight
 PO:0001170 - seed development stage
PO:0009049 - inflorescence
PO:0025585 - floral organ formation stage
PO:0001083 - inflorescence development stage
PO:0020104 - leaf sheath
PO:0001048 - palea development stage
PO:0009037 - lemma
PO:0001047 - lemma development stage
PO:0009038 - palea
PO:0020032 - plumule
Os02g0811000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g56610.1
GW2 OsGW2
OsRING429
RING429
GNL44
OsGNL44
 GRAIN WEIGHT 2 GRAIN WIDTH AND WEIGHT2
Grain width 2
RING-type E3 ubiquitin ligase 429
GRAIN NUMBER AND LARGE GRAIN SIZE 44
 2 Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
Seed - Physiological traits - Taste
Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
 GO:0005737 - cytoplasm
GO:0030308 - negative regulation of cell growth
GO:0005634 - nucleus
GO:0005829 - cytosol
GO:0006109 - regulation of carbohydrate metabolic process
GO:0048480 - stigma development
GO:0016567 - protein ubiquitination
GO:0010498 - proteasomal protein catabolic process
GO:0051302 - regulation of cell division
GO:0080050 - regulation of seed development
GO:0016874 - ligase activity
GO:0008270 - zinc ion binding
 TO:0000382 - 1000-seed weight
TO:0000402 - grain width
TO:0002658 - starch grain synthesis
TO:0002653 - endosperm storage protein content
TO:0000409 - peak viscosity
TO:0000590 - grain weight
TO:0000374 - breakdown viscosity
TO:0000196 - amylose content
TO:0000097 - amylopectin content
TO:0000044 - stigma exsertion
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000396 - grain yield
TO:0000547 - primary branch number
TO:0000397 - grain size
TO:0000040 - panicle length
TO:0000211 - gel consistency
TO:0000734 - grain length
TO:0000391 - seed size
TO:0000487 - endosperm color
TO:0000266 - chalky endosperm
 PO:0001170 - seed development stage
PO:0005360 - aleurone layer
PO:0009005 - root
PO:0009049 - inflorescence
PO:0025034 - leaf
PO:0009066 - anther
Os02g0244100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g14720.2
LOC_Os02g14720.1
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
EP3 EP3/LP
LP
OsLP
OsFbox076
OsFbox76
Os_F0106
OsEP3
OsFBK5
FBK5
 ERECT PANICLE 3 LARGER PANICLE
F-box protein 76
F-box-type E3 ubiquitin ligase K5
 2 Reproductive organ - Panicle, Mode of branching
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
Vegetative organ - Leaf
Vegetative organ - Culm
Reproductive organ - Spikelet, flower, glume, awn
 GO:0010118 - stomatal movement
GO:0005634 - nucleus
GO:0010052 - guard cell differentiation
GO:0009760 - C4 photosynthesis
GO:0005737 - cytoplasm
GO:0009908 - flower development
GO:0010229 - inflorescence development
GO:0048437 - floral organ development
GO:0048513 - organ development
GO:0048316 - seed development
 TO:0000625 - spikelet density
TO:0006013 - carpel number
TO:0000357 - growth and development trait
TO:0000622 - flower development trait
TO:0000421 - pollen fertility
TO:0000371 - yield trait
TO:0000621 - inflorescence development trait
TO:0000653 - seed development trait
TO:0002600 - flower organ size
TO:0006038 - floral organ number
TO:0000397 - grain size
TO:0000590 - grain weight
TO:0000207 - plant height
TO:0000135 - leaf length
TO:0000370 - leaf width
TO:0006022 - floral organ development trait
TO:0000040 - panicle length
TO:0000447 - filled grain number
TO:0000734 - grain length
TO:0000269 - 100-seed weight
TO:0000391 - seed size
TO:0006029 - glume number
TO:0002759 - grain number
TO:0000396 - grain yield
TO:0000225 - stamen number
TO:0000050 - inflorescence branching
TO:0002768 - spikelet length
TO:0000564 - spikelet width
TO:0000531 - anther length
 PO:0025034 - leaf
PO:0004010 - meristematic cell
PO:0006023 - bundle sheath
PO:0009046 - flower
PO:0001170 - seed development stage
PO:0009010 - seed
PO:0009066 - anther
PO:0025281 - pollen
PO:0025585 - floral organ formation stage
PO:0001083 - inflorescence development stage
PO:0007615 - flower development stage
PO:0020127 - primary root
PO:0009013 - portion of meristem tissue
PO:0025178 - stem epidermis
PO:0009072 - plant ovary
PO:0020123 - root cap
PO:0009047 - stem
PO:0006036 - root epidermis
PO:0009005 - root
Os02g0260200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g15950.1
FZP fzp*
fzp
OsBD1
BD1
OsERF#078
OsERF078
OsERF78
ERF78
AP2/EREBP#133
AP2/EREBP133
BFL1
SGDP7
OsSGDP7
 FRIZZY PANICLE frizzy panicle
BRANCHED SILKLESS 1 homolog
ethylene response factor 78
APETALA2/ethylene-responsive element binding protein 133
BRANCHED FLORETLESS 1
FRIZZLE PANICLE
Small Grain and Dense Panicle 7
 7 Reproductive organ - panicle
Character as QTL - Yield and productivity
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Grain shape
Reproductive organ - Inflorescence
 GO:0008284 - positive regulation of cell proliferation
GO:0030307 - positive regulation of cell growth
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0010600 - regulation of auxin biosynthetic process
GO:0043067 - regulation of programmed cell death
GO:0048449 - floral organ formation
GO:0009690 - cytokinin metabolic process
GO:0010074 - maintenance of meristem identity
GO:0010582 - floral meristem determinacy
GO:0045449 - regulation of transcription
GO:0048497 - maintenance of floral organ identity
GO:0010093 - specification of floral organ identity
GO:0010229 - inflorescence development
GO:0003700 - transcription factor activity
GO:0003677 - DNA binding
GO:0005634 - nucleus
GO:0006351 - transcription, DNA-dependent
GO:0007275 - multicellular organismal development
GO:0010073 - meristem maintenance
 TO:0000152 - panicle number
TO:0000499 - flower anatomy and morphology trait
TO:0002660 - cytokinin content
TO:0000557 - secondary branch number
TO:0000734 - grain length
TO:0000262 - panicle shape
TO:0000621 - inflorescence development trait
TO:0000396 - grain yield
TO:0000050 - inflorescence branching
TO:0002759 - grain number
TO:0000592 - 1000-dehulled grain weight
TO:0000089 - panicle type
TO:0000456 - spikelet number
TO:0000397 - grain size
TO:0000240 - sterile lemma length
TO:0000449 - grain yield per plant
TO:0000382 - 1000-seed weight
TO:0000657 - spikelet anatomy and morphology trait
TO:0000605 - hydrogen peroxide content
TO:0000040 - panicle length
TO:0000447 - filled grain number
TO:0000650 - lemma length
TO:0000472 - vascular bundle number
TO:0002672 - auxin content
 PO:0001047 - lemma development stage
PO:0009049 - inflorescence
PO:0009013 - portion of meristem tissue
PO:0009037 - lemma
PO:0009046 - flower
PO:0001083 - inflorescence development stage
PO:0007602 - floral organ primordium development stage
PO:0009038 - palea
PO:0009040 - sterile lemma
PO:0009051 - spikelet
Os07g0669500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g47330.1
KR1 Kr1*
Kr1
 SHORT GRAIN Short grain
 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
TO:0000391 - seed size
 PO:0009010 - seed
-
KR2 Kr2*
Kr2
 LONG GRAIN Long grain
 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
TO:0000391 - seed size
 PO:0009010 - seed
-
LKG Lk g
 LONG KERNEL GIMBOUZU 'Gimbozu mutant' long grain
 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
 -
LKI2 lki2
 LONG KERNEL IRAT13 2 IRAT 13' long grain2
IRAT 13' long grain 2
'IRAT 13' long grain-2
 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
 PO:0009010 - seed
-
LK1 lk1(t)
lkna
lk1
 NAGAYAMA 77402A LONG GRAIN 1 Nagayama 77402a long grain1
'Nagayama 77402a (N179)' long grain
long kernel-1
 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
 PO:0009010 - seed
-
PLA1 pla1
OsPLA1
plt1
CYP78A11
 PLASTOCHRON 1 plastochron1
plastochron 1
plastochron-1
Cytochrome P450 78A11
Protein PLASTOCHRON1
 10 Coloration - Anthocyanin
Seed - Morphological traits - Grain shape
Heterochrony
Reproductive organ - panicle
Vegetative organ - Leaf
Reproductive organ - Panicle, Mode of branching
Vegetative organ - Culm
 GO:0010228 - vegetative to reproductive phase transition
GO:0010432 - bract development
GO:0051781 - positive regulation of cell division
GO:0055114 - oxidation reduction
GO:0004497 - monooxygenase activity
GO:0007275 - multicellular organismal development
GO:0009055 - electron carrier activity
GO:0010229 - inflorescence development
GO:0020037 - heme binding
GO:0048366 - leaf development
GO:0009740 - gibberellic acid mediated signaling
GO:0009739 - response to gibberellin stimulus
 TO:0000369 - vegetative growth time
TO:0000207 - plant height
TO:0000621 - inflorescence development trait
TO:0000346 - tiller number
TO:0000391 - seed size
TO:0002638 - shoot meristem development
TO:0000659 - phyllochron
TO:0000166 - gibberellic acid sensitivity
TO:0000050 - inflorescence branching
TO:0000730 - mitotic cell cycle trait
 PO:0020122 - inflorescence axis
PO:0001083 - inflorescence development stage
PO:0020148 - shoot apical meristem
Os10g0403000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g26340.1
image Id ( 6707 )
S s Kr*
skr
 SUPPRESSOR FOR GRAIN SIZE suppressor for grain size (Kr1, Kr2)
 Seed - Morphological traits - Grain shape
 TO:0000391 - seed size
 PO:0009010 - seed
-
D2 d2
dwf2
CYP90D2
D2/CYP90D2
OsD2
SMG11
OsSMG11
D2/SMG11
OsD2a
OsD2b
 DWARF EBISU ebisu dwarf
dwarf-2
cytochrome P450 CYP90D2
Ebisu dwarf/Dwarf2
Dwarf2
SMALL GRAIN 11
cytochrome P450 D2
 1 Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Tolerance and resistance - Disease resistance
Seed - Morphological traits - Grain shape
Character as QTL - Germination
Vegetative organ - Leaf
Vegetative organ - Culm
 GO:0051607 - defense response to virus
GO:0004497 - monooxygenase activity
GO:0009055 - electron carrier activity
GO:0005506 - iron ion binding
GO:0009742 - brassinosteroid mediated signaling
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016132 - brassinosteroid biosynthetic process
GO:0050832 - defense response to fungus
GO:0010029 - regulation of seed germination
GO:0006970 - response to osmotic stress
GO:0009409 - response to cold
GO:0010224 - response to UV-B
GO:0009651 - response to salt stress
GO:0009741 - response to brassinosteroid stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0020037 - heme binding
GO:0016021 - integral to membrane
GO:0009961 - response to 1-aminocyclopropane-1-carboxylic acid
GO:0007275 - multicellular organismal development
 TO:0000207 - plant height
TO:0000255 - sheath blight disease resistance
TO:0000346 - tiller number
TO:0000329 - tillering ability
TO:0002677 - brassinosteroid sensitivity
TO:0000132 - basal internode diameter
TO:0000391 - seed size
TO:0000303 - cold tolerance
TO:0000206 - leaf angle
TO:0000095 - osmotic response sensitivity
TO:0006001 - salt tolerance
TO:0000430 - germination rate
TO:0000020 - black streak dwarf virus resistance
TO:0000601 - UV-B light sensitivity
TO:0000382 - 1000-seed weight
TO:0000396 - grain yield
TO:0002759 - grain number
TO:0000397 - grain size
TO:0000567 - tiller angle
TO:0006032 - panicle size
TO:0000262 - panicle shape
TO:0000172 - jasmonic acid sensitivity
TO:0000135 - leaf length
TO:0000299 - leaf lamina color
TO:0000040 - panicle length
 PO:0007057 - 0 seed germination stage
Os01g0197100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g10040.2
LOC_Os01g10040.1
LGT lgt
 LONG TWISTED GRAIN long twisted grain
 1 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000484 - seed shape
TO:0000146 - seed length
 PO:0009010 - seed
-
TRI tri
 TRIANGULAR HULL triangular hull
 2 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000484 - seed shape
TO:0000079 - lemma and palea anatomy and morphology trait
 PO:0009010 - seed
PO:0009082 - spikelet floret
PO:0009037 - lemma
PO:0009038 - palea
- image Id ( 6732 )
LKF Lk f
Lkf
 LONG KERNEL FUSAYOSHI 'Fusayoshi' long grain
 3 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000181 - seed weight
TO:0000146 - seed length
 PO:0009010 - seed
-
MI Mii
Mi1
 MINUTE GRAIN Minute grain
Minute grain-1
 3 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000181 - seed weight
TO:0000146 - seed length
TO:0000089 - panicle type
 PO:0009010 - seed
PO:0009049 - inflorescence
-
RK1 rk1
 ROUND KERNEL 1 round kernel1
round kernel-1
 4 Seed - Morphological traits - Grain shape
 TO:0000287 - brown rice shape
TO:0000391 - seed size
TO:0000149 - seed width
 PO:0009010 - seed
- image Id ( 6750 )
LKI1 lk i1
lki1
lk-i-1
 LONG KERNEL IRAT13 1 IRAT 13' long grain1
IRAT 13' long grain 1
'IRAT 13' long grain-1
 4 Seed - Morphological traits - Grain shape
 GO:0007275 - multicellular organismal development
 TO:0000146 - seed length
 PO:0009010 - seed
-
D11 d11(d8)
dwf10
d8
D11/CYP724B1
d11
CYP724B1
GNS4
OsD11
PMM1
OsPMM1
PMM1/D11
NBG4
OsCPB1
CPB1
CPB1/D11
 DWARF SHINKANEAIKOKU OR NOHRIN 28 shinkaneaikoku or nohrin 28 dwarf
DWARF SHINKANEAIKOKU OR NOHRIN 28
OsDWARF11
dwarf-11
Cytochrome P450 724B1
Dwarf protein 11
cytochrome P450 CYP724B1
DWARF11
grain number and size on chromosome 4
Panicle Morphology Mutant 1
Notched Belly Grain 4
CLUSTERED PRIMARY BRANCH 1
 4 Tolerance and resistance - Disease resistance
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
Vegetative organ - Leaf
Reproductive organ - Heading date
Seed - Physiological traits - Taste
Tolerance and resistance - Stress tolerance
Seed - Morphological traits
Reproductive organ - Inflorescence
Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Panicle, Mode of branching
 GO:0009055 - electron carrier activity
GO:0004497 - monooxygenase activity
GO:0016021 - integral to membrane
GO:0008199 - ferric iron binding
GO:0007275 - multicellular organismal development
GO:0006879 - cellular iron ion homeostasis
GO:0016020 - membrane
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0016132 - brassinosteroid biosynthetic process
GO:0009742 - brassinosteroid mediated signaling
GO:0009414 - response to water deprivation
GO:0051607 - defense response to virus
GO:0006826 - iron ion transport
GO:0055114 - oxidation reduction
GO:0009741 - response to brassinosteroid stimulus
GO:0022900 - electron transport chain
GO:0009826 - unidimensional cell growth
GO:0009647 - skotomorphogenesis
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 - heme binding
GO:0009753 - response to jasmonic acid stimulus
GO:0051512 - positive regulation of unidimensional cell growth
GO:0010029 - regulation of seed germination
GO:0048573 - photoperiodism, flowering
 TO:0000020 - black streak dwarf virus resistance
TO:0006032 - panicle size
TO:0000276 - drought tolerance
TO:0000641 - primary branch length
TO:0002730 - grain shape
TO:0002759 - grain number
TO:0000567 - tiller angle
TO:0000592 - 1000-dehulled grain weight
TO:0000484 - seed shape
TO:0002677 - brassinosteroid sensitivity
TO:0000455 - seed set percent
TO:0000456 - spikelet number
TO:0000137 - days to heading
TO:0000557 - secondary branch number
TO:0000172 - jasmonic acid sensitivity
TO:0000139 - grains per panicle
TO:0000396 - grain yield
TO:0000040 - panicle length
TO:0000145 - internode length
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000206 - leaf angle
TO:0000329 - tillering ability
TO:0000346 - tiller number
TO:0002676 - brassinosteroid content
TO:0000371 - yield trait
TO:0000501 - spikelet weight
TO:0002616 - flowering time
TO:0000050 - inflorescence branching
TO:0002688 - leaf lamina joint bending
TO:0000402 - grain width
TO:0000397 - grain size
TO:0000052 - primary branching of inflorescence
TO:0000180 - spikelet fertility
TO:0000576 - stem length
TO:0000657 - spikelet anatomy and morphology trait
TO:0000547 - primary branch number
 PO:0006321 - primary inflorescence branch
PO:0020122 - inflorescence axis
PO:0009049 - inflorescence
PO:0009047 - stem
PO:0009010 - seed
PO:0020142 - stem internode
Os04g0469800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g39430.1
LOC_Os04g39430.2
image Id ( 6753 )
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