Alk / Starch Synthase II
Grain cooking texture
4 Mutations:
Coding
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Umemoto T; Yano M; Satoh H ; et al. (2002)
Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and [...]
2 Additional References
GP00000078
SSII-3
Q0DDE3
Physiology
4 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Alk / Starch Synthase II
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Bradbury LM; Fitzgerald TL; Henry RJ ; et al. (2005)
The gene for fragrance in rice.
1 Additional References
GP00000134
BADH2
Q84LK3
Physiology
8bp deletion resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Shi Weiwei; Yang Yi; Chen Saihua ; et al. (2008
)
Discovery of a new fragrance allele and the development of functional markers for the breeding of fr[...]
1 Additional References
GP00001772
BADH2
Q84LK3
Physiology
7-bp deletion in exon 2 resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001773
BADH2
Q84LK3
Physiology
2-bp deletion in exon 1 resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001774
BADH2
Q84LK3
Physiology
insertion of 1 bp (T) in exon 10 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001775
BADH2
Q84LK3
Physiology
G>T substitution in exon 10 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001776
BADH2
Q84LK3
Physiology
G>T substitution in exon 14 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001777
BADH2
Q84LK3
Physiology
C>T substitution in exon 13 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001778
BADH2
Q84LK3
Physiology
1-bp deletion in exon 10 - causes a frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001779
BADH2
Q84LK3
Physiology
1-bp insertion (G) in exon 14 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001780
BADH2
Q84LK3
Physiology
3-bp insertion (TAT) in exon 13 - causes a frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
Bh4
Coloration (seed hull)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhu BF; Si L; Wang Z ; et al. (2011)
Genetic control of a transition from black to straw-white seed hull in rice domestication.
1 Additional References
GP00000143
Bh4
A0A0H3ZGK8
Morphology
22-bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Bh4
Oryza sativa
rice - (species)
Published - Accepted by Curator
Chalk5
Grain chalkiness
Amylose content
Grain yield
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Li Y; Fan C; Xing Y ; et al. (2014)
Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice.
GP00001309
Chalk5
A2Y0L3
Morphology
Physiology
Physiology
Two candidate SNPs at positions -721 and - 485 in promoter region
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Chalk5
Oryza sativa
rice - (species)
Published - Accepted by Curator
DEEPER ROOTING 1
Drought tolerance
Root growth
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Uga Y; Sugimoto K; Ogawa S ; et al. (2013)
Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought condition[...]
GP00000215
Dro1
Q69P88
Physiology
Morphology
1bp deletion within exon 4 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEEPER ROOTING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
DEP1
Grain yield
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Huang X; Qian Q; Liu Z ; et al. (2009)
Natural variation at the DEP1 locus enhances grain yield in rice.
GP00000218
P0046G12.12-1
Q67UU9
Morphology
replacement of a 637bp stretch of the middle of exon5 by a 12-bp sequence creating a premature stop codon and consequently a loss of 230 residues from the C-terminus N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEP1
Oryza sativa
rice - (species)
Published - Accepted by Curator
DTH2
Flowering time
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Wu W; Zheng XM; Lu G ; et al. (2013)
Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cult[...]
GP00000239
DTH2
O82118
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DTH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
EARLY FLOWERING 3/Hd17
Flowering time
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Matsubara K; Ogiso-Tanaka E; Hori K ; et al. (2012)
Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flow[...]
GP00000247
ELF3
O82804
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
EARLY FLOWERING 3/Hd17
Oryza sativa
rice - (species)
Published - Accepted by Curator
Early flowering1 (EL1)
Flowering time (heading date)
Coding,
SNP
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Kwon CT; Yoo SC; Koo BH ; et al. (2014)
Natural variation in Early flowering1 contributes to early flowering in japonica rice under long day[...]
GP00001636
HD16
Q852L0
Physiology
G476C p.Gly159Ala in the serine/threonine kinase domain leading to non-functional protein
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Early flowering1 (EL1)
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
Early flowering1 (EL1)
Flowering time (heading date)
Coding,
SNP
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Kwon CT; Yoo SC; Koo BH ; et al. (2014)
Natural variation in Early flowering1 contributes to early flowering in japonica rice under long day[...]
GP00001637
HD16
Q852L0
Physiology
G991A p.Ala331Thr in the serine/threonine kinase domain leading to non-functional protein
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Early flowering1 (EL1)
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
Ehd1 (Response regulator)
Flowering time
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Doi K; Izawa T; Fuse T ; et al. (2004)
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-[...]
GP00000263
EHD1
Q9H4M9
Physiology
G218R in highly conserved region in GARP domain
Oryza glaberrima
African rice - (species)
Oryza sativa
rice - (species)
Ehd1 (Response regulator)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Ghd7
Flowering time
Inflorescence morphology
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Xue W; Xing Y; Weng X ; et al. (2008)
Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.
GP00000393
GHD7
E5RQA1
Physiology
Morphology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Ghd7
Oryza sativa
rice - (species)
Published - Accepted by Curator
GL3.1
Grain size
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Qi P; Lin YS; Song XJ ; et al. (2012)
The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;[...]
GP00000397
GL3
Q9FN69
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL3.1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GL7
Grain size
Grain quality
Gene Amplification,
Indel
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001541
LNG1
Q9LF24
Morphology
Physiology
tandem duplication of a 17.1 kb segment containing GL7. Both copies encode exactly the same polypeptide and exhibit similar transcript levels leading to upregulation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL7
Oryza sativa
rice - (species)
Published - Accepted by Curator
GRAIN INCOMPLETE FILLING 1
Grain weight
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang E; Wang J; Zhu X ; et al. (2008)
Control of rice grain-filling and yield by a gene with a potential signature of domestication.
GP00000413
CIN2
Q0JDC5
Morphology
unknown
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
GRAIN INCOMPLETE FILLING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GS3
Grain size
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Fan C; Xing Y; Mao H ; et al. (2006)
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, en[...]
1 Additional References
GP00000417
GS3
C6L686
Morphology
C55*;TGC>TGA causing a 178-aa truncation in the C-terminus of the predicted protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS3
Oryza sativa
rice - (species)
Published - Accepted by Curator
GS5
Grain size
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Li Y; Fan C; Xing Y ; et al. (2011)
Natural variation in GS5 plays an important role in regulating grain size and yield in rice.
GP00000418
GS5
B8AYD6
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS5
Oryza sativa
rice - (species)
Published - Accepted by Curator
GW2
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Song XJ; Huang W; Shi M ; et al. (2007)
A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.
GP00000424
GW2
A4GWX9
Morphology
1bp deletion resulting in a premature stop codon in exon 4; the premature stop codon led to truncation of 310 amino acid residues N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
GW2
Oryza sativa
rice - (species)
Published - Accepted by Curator
GW7
Grain shape
Grain quality
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Li S; Liu Q ; et al. (2015)
The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and [...]
GP00001540
TON1A
Q9FQ25
Morphology
Physiology
18 SNPs and 9 indels observed in the promoter region and exon 1 and in particular an 11-bp deletion and 18-bp insertion near GTAC motifs which are normally binded by OsSPL16 repressor (reduced binding increasing transcription)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GW7
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Doi K; Izawa T; Fuse T ; et al. (2004)
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-[...]
GP00000439
HD1
Q9FDX8
Physiology
Retro-element-like inserted in exon 2 N
Oryza glaberrima
African rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Yano M; Katayose Y; Ashikari M ; et al. (2000)
Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Ara[...]
1 Additional References
GP00000441
HD1
Q9FDX8
Physiology
2bp deletion in the putative exon 2 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001722
HD1
Q9FDX8
Physiology
1bp deletion at position 606 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001723
HD1
Q9FDX8
Physiology
1bp deletion at position 321 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001724
HD1
Q9FDX8
Physiology
4bp deletion at position 1089 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001725
HD1
Q9FDX8
Physiology
C to T – stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd6a
Flowering time
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Takahashi Y; Shomura A; Sasaki T ; et al. (2001)
Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit [...]
GP00000442
HD6
Q9AR27
Physiology
K91*; AAG>TAG N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Hd6a
Oryza sativa
rice - (species)
Published - Accepted by Curator
HEADING DATE 1
Flowering time (latitudinal adaptation)
Cis-regulatory,
Insertion
N
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Candidate Gene
Goretti D; Martignago D; Landini M ; et al. (2017)
Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Ric[...]
GP00001674
HD1
Q9FDX8
Physiology
Hd1(EH) allele with a 4.4 kb mobile element inserted at position -166pb that suppressed gene transcription N
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
HEADING DATE 1
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
heavy metal atpase3 (HMA3)
Metal tolerance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ueno D; Yamaji N; Kono I ; et al. (2010)
Gene limiting cadmium accumulation in rice.
GP00000445
HMA3
P0CW78
Physiology
H80R
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
heavy metal atpase3 (HMA3)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Nramp aluminum transporter1
Metal tolerance
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Famoso AN; Zhao K; Clark RT ; et al. (2011)
Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide ass[...]
GP00000740
NRAT1
Q6ZG85
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Nramp aluminum transporter1
Oryza sativa
rice - (species)
Published - Accepted by Curator
NRT1.1B
Nitrogen use (metabolism)
Coding,
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Hu B; Wang W; Ou S ; et al. (2015)
Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.
GP00001375
NPF6.3
Q05085
Physiology
c.980C>T p.Met327Thr
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
NRT1.1B
Oryza sativa
rice - (species)
Published - Accepted by Curator
Os07g0603400
Grain size
Grain quality
2 Mutations:
Coding
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001542
Os07g0603400
A3BLY4
Morphology
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Os07g0603400
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000805
C
Q76B79
Morphology
10bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000806
C
Q76B79
Morphology
2bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000807
CKX2
Q4ADV8
Morphology
11bp deletion causing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000808
CKX2
Q4ADV8
Morphology
Not identified
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsGA20ox1
Seedling vigor
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Abe A; Takagi H; Fujibe T ; et al. (2012)
OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice.
GP00000810
GA20OX1
P93771
Physiology
unknown ; no coding variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsGA20ox1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsLG1
Seed shattering (panicle shape)
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ishii T; Numaguchi K; Miura K ; et al. (2013)
OsLG1 regulates a closed panicle trait in domesticated rice.
GP00000811
SPL8
Q7XPY1
Morphology
unknown but fine-mapped 9.3kb region
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
OsLG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsPPKL1/qGL3
Grain size
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhang X; Wang J; Huang J ; et al. (2012)
Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield[...]
GP00000812
qLTG-3-1
B3IWI0
Morphology
Asp364Glu
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsPPKL1/qGL3
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL13
Grain size
Cis-regulatory,
Insertion
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Association Mapping
Si L; Chen J; Huang X ; et al. (2016)
OsSPL13 controls grain size in cultivated rice.
GP00001572
SPL13
Q6Z461
Morphology
a CACTTC tandem repeat sequence in the 5' UTR is causing reduced expression
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
OsSPL13
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
OsSPL14 / WFP
Grain yield
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Jiao Y; Wang Y; Xue D ; et al. (2010)
Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.
1 Additional References
GP00000813
IPA1
D8WJ58
Morphology
Point mutation resulting in altered binding of a micro-RNA
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL14 / WFP
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL16
Grain size
Grain shape
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Wu K; Yuan Q ; et al. (2012)
Control of grain size, shape and quality by OsSPL16 in rice.
1 Additional References
GP00000814
SPL16
L0AP48
Morphology
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL16
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi-ta
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Bryan GT; Wu KS; Farrall L ; et al. (2000)
tA single amino acid difference distinguishes resistant and susceptible alleles of the rice blast re[...]
2 Additional References
GP00000876
Pi-ta
C9E6G5
Physiology
Ala918Ser
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi-ta
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi2 (Nbs4-Pi2)
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhou B; Qu S; Liu G ; et al. (2006)
The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance [...]
GP00000877
PI2
M1EC06
Physiology
eight amino acid changes - exact causing change(s) unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi2 (Nbs4-Pi2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi36
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Liu X; Lin F; Wang L ; et al. (2007)
The in silico map-based cloning of Pi36, a rice coiled-coil nucleotide-binding site leucine-rich rep[...]
GP00000878
Pi36
D5J6W0
Physiology
Asp590Ser
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi36
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi37
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Lin F; Chen S; Que Z ; et al. (2007)
The blast resistance gene Pi37 encodes a nucleotide binding site leucine-rich repeat protein and is [...]
GP00000879
Pi37
Q06AJ9
Physiology
V239A and I247M are the only amino acid substitutions found in all tested resistant strains- the effect of each individual amino acid change has not been tested
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi37
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi5-1 + Pi5-2 cluster
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Lee SK; Song MY; Seo YS ; et al. (2009)
Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleoti[...]
GP00000880
Pi5-1
C3SBK3
Physiology
In genetic transformation experiments of a susceptible rice cultivar neither the Pi5-1 nor the Pi5-2 gene was found to confer resistance to M. oryzae. In contrast transgenic rice plants expressing both of these genes (generated by crossing transgenic lines carrying each gene individually) conferred Pi5-mediated resistance to M. oryzae
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi5-1 + Pi5-2 cluster
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi9 (= Nbs2-Pi9)
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Qu S; Liu G; Zhou B ; et al. (2006)
The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat p[...]
GP00000881
Pi9
Q1WGB0
Physiology
Coding variation; necessary for resistance in completementation assay
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi9 (= Nbs2-Pi9)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pib
Pathogen resistance
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang ZX; Yano M; Yamanouchi U ; et al. (1999)
The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat cla[...]
GP00000882
Pi-b
Q9SSY0
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pib
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pid3
Pathogen resistance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Chen J; Shi Y; Liu W ; et al. (2011)
A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae.
GP00000883
Pid3
C0LMX9
Physiology
1bp deletion resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Pid3
Oryza sativa
rice - (species)
Published - Accepted by Curator
PigmR
Pathogen resistance (plant fungus pathogen)
Unknown,
Unknown
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Deng Y; Zhai K; Xie Z ; et al. (2017)
Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance.
GP00001592
Pigm_GM4.7
A0A1P8CYR1
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
PigmR
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pikm1-TS + Pikm2-TS cluster
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ashikawa I; Hayashi N; Yamane H ; et al. (2008)
Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-spe[...]
1 Additional References
GP00000884
PIKM1-TS
B5UBC1
Physiology
Coding variation in both genes; with alleles of both genes necessary for resistance in completementation assays
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pikm1-TS + Pikm2-TS cluster
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pit
Pathogen resistance (rice blast disease; fungal pathogen; Magnaporthe grisea)
Cis-regulatory,
Insertion
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Hayashi K; Yoshida H (2009)
Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a re[...]
GP00002052
Pit
B9A1G4
Physiology
insertion of a 5.5-kb LTR retrotransposon Renovator upstream of the gene (256‐bp upstream of the predicted start codon for NBSt2K59; in the same orientation as the gene)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Pit
Oryza sativa
rice - (species)
Published - Accepted by Curator
Piz-t
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhou B; Qu S; Liu G ; et al. (2006)
The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance [...]
GP00000895
Piz-t
Q0H213
Physiology
Coding variation in the LRR domain
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Piz-t
Oryza sativa
rice - (species)
Published - Accepted by Curator
PROG1
Plant architecture
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Tan L; Li X; Liu F ; et al. (2008)
Control of a key transition from prostrate to erect growth in rice domestication.
2 Additional References
GP00000925
PROG1
Q69NY0
Morphology
Various
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
PROG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001632
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-2a: L710P missense mutation in the CONSTANS-Co-like and TOC1 domain of the protein N
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001633
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1a: a 8-bp deletion at position 1515 leading to frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001634
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1b: Y704H N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001635
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1c: a premature stop Q705* N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
qPE9-1
Plant architecture
Inflorescence architecture
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhou Y; Zhu J; Li Z ; et al. (2009)
Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant archit[...]
GP00000941
PAY1
B8Y995
Morphology
Morphology
637-bp deletion and 12-bp insertion resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qPE9-1
Oryza sativa
rice - (species)
Published - Accepted by Curator
qSH1
Seed shattering
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Konishi S; Izawa T; Lin SY ; et al. (2006)
An SNP caused loss of seed shattering during rice domestication.
GP00000942
qSH1
Q941S9
Physiology
1bp change
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
qSH1
Oryza sativa
rice - (species)
Published - Accepted by Curator
qSW5
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Shomura A; Izawa T; Ebana K ; et al. (2008)
Deletion in a gene associated with grain size increased yields during rice domestication.
1 Additional References
GP00000944
qSW5
F8SPD1
Morphology
1212bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qSW5
Oryza sativa
rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
GP00000959
Rc
A7J5U6
Morphology
14bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
2 Additional References
GP00000960
Rc
A7J5U6
Morphology
substitution; C->A in exon 6; introduces a premature stop codon (Cys>*) that truncates the protein before the bHLH domain N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
S5
Hybrid incompatibility (F1 female sterility)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Chen J; Ding J; Ouyang Y ; et al. (2008)
A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indi[...]
GP00001020
GRXS5
Q5QLR2
Physiology
2 non-synonymous changes Leu273Phe and Val471Ala segregate perfectly between japonica (Leu-Val) and japonica (Phe-Ala) - the effect of each amino acid chaeg has not been tested
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
S5
Oryza sativa
rice - (species)
Published - Accepted by Curator
S5 (ORF3-ORF4-ORF5 gene complex)
Hybrid incompatibility (sterility)
Coding,
Complex Change
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Yang J; Zhao X; Cheng K ; et al. (2012)
A killer-protector system regulates both hybrid sterility and segregation distortion in rice.
GP00001021
GRXS5
Q5QLR2
Physiology
System of alleles at three linked genes resulting in killer-protector system (hybrid incompabilitites)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
S5 (ORF3-ORF4-ORF5 gene complex)
Oryza sativa
rice - (species)
Published - Accepted by Curator
SaM + SaF
Hybrid incompatibility (F1 male sterility)
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Long Y; Zhao L; Niu B ; et al. (2008)
Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent ge[...]
1 Additional References
GP00001022
SaF+
B6RRX2
Physiology
Intron structure + aa changes on two adjacent coding genes
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
SaM + SaF
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (height)
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Asano K; Yamasaki M; Takuno S ; et al. (2011)
Artificial selection for a green revolution gene during japonica rice domestication.
GP00001027
GA20OX2
Q0JH50
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
3 Additional References
GP00001028
GA20OX2
Q0JH50
Morphology
383bp deletion introducing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001029
GA20OX2
Q0JH50
Morphology
G94V
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001030
GA20OX2
Q0JH50
Morphology
D349H
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001031
GA20OX2
Q0JH50
Morphology
L266F
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
se5
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Izawa T; Oikawa T; Tokutomi S ; et al. (2000)
Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant).
GP00001034
HO1
Q69XJ4
Physiology
1bp deletion in exon 1; causes a frameshift and a premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
se5
Oryza sativa
rice - (species)
Published - Accepted by Curator
Shattering1 - OsSh1
Seed shattering
Unknown,
Insertion
Oryza sativa
rice - (species) D
Domesticated
Association Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
2 Additional References
GP00001039
YAB2
Q10FZ7
Physiology
>4kb insertion in intron (unclear)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Shattering1 - OsSh1
Oryza sativa
rice - (species)
Published - Accepted by Curator
shattering4 - sh4
Seed shattering
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Li C; Zhou A; Sang T (2006)
Rice domestication by reducing shattering.
GP00001046
sh4
Q1PIH9
Physiology
Asn -> Lys
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
shattering4 - sh4
Oryza sativa
rice - (species)
Published - Accepted by Curator
SKC1 =OsHKT1
Salt tolerance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ren ZH; Gao JP; Li LG ; et al. (2005)
A rice quantitative trait locus for salt tolerance encodes a sodium transporter.
GP00001055
HKT8
A2WNZ9
Physiology
several candidate missense mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
SKC1 =OsHKT1
Oryza sativa
rice - (species)
Published - Accepted by Curator
SLB1/2
Pathogen resistance (Root parasitic plant) (root parasitic plant)
Gene Loss,
Deletion
N
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Cardoso C; Zhang Y; Jamil M ; et al. (2014)
Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 ort[...]
GP00001631
Os01g0700900
M9R6D3
Physiology
deletion of 2 cytochrome P450 genes (Os010700900 & Os01g0701400) N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
SLB1/2
Oryza sativa
rice - (species)
Published - Accepted by Curator
Thermo-tolerance 1 (TT1)
Temperature tolerance
Coding,
SNP
Oryza glaberrima
African rice - (species) D
Interspecific
Linkage Mapping
Li XM; Chao DY; Wu Y ; et al. (2015)
Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of Afri[...]
GP00001566
PAB1
Q10KF0
Physiology
p.R99H
Oryza sativa
rice - (species)
Oryza glaberrima
African rice - (species) D
Thermo-tolerance 1 (TT1)
Oryza glaberrima
African rice - (species)
Published - Accepted by Curator
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ishimaru K; Hirotsu N; Madoka Y ; et al. (2013)
Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yie[...]
GP00001126
TGW6
Q69U01
Morphology
-1bp at +313 resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang ZY; Zheng FQ; Shen GZ ; et al. (1995)
The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy [...]
3 Additional References
GP00001204
waxy
Q8L699
Physiology
substitution G->T in the 5' splice site of intron 1
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Hori Y; Fujimoto R; Sato Y ; et al. (2007)
A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]
GP00002069
waxy
Q8L699
Physiology
23-bp duplication in the second exon which causes loss of the function of granule-bound starch synthase (GBSS) encoded by the Wx gene N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Hori Y; Fujimoto R; Sato Y ; et al. (2007)
A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]
GP00002070
waxy
Q8L699
Physiology
insertion of 7764 bp in the ninth exon of the wx gene. Transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and the deduced amino acid sequence of the transcript lacks a motif important for GBSS. The 7,764-bp insertion is a retrotransposon-like sequence with long terminal repeats; a primer binding site and a polypurine tract N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
Xa1
Pathogen resistance
Unknown,
Unknown
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Yoshimura S; Yamanouchi U; Katayose Y ; et al. (1998)
Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation.
GP00001216
XA1
A0A0H5AGW3
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Xa1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Xa21
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Song WY; Wang GL; Chen LL ; et al. (1995)
A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21.
GP00001217
Xa21
A0PIA3
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Xa21
Oryza sativa
rice - (species)
Published - Accepted by Curator
Xa26
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Sun X; Cao Y; Yang Z ; et al. (2004)
Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor[...]
GP00001218
Xa26
Q00KZ8
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Xa26
Oryza sativa
rice - (species)
Published - Accepted by Curator