Locus ID: Os06g0133000
Transcript ID: Os06t0133000-01 (chr06:1765622-1770653)
Description: Granule-bound starch synthase, Synthesis of amylose in endosperm
RAP-DB Gene symbol: Wx
RAP-DB Gene name: waxy, Waxy
Gene Ontolgy: glycogen (starch) synthase activity (GO:0004373)
starch synthase activity (GO:0009011)
biosynthetic process (GO:0009058)
glucan biosynthetic process (GO:0009250)
Links: TASUKE (for RAP-DB), GBrowse


CGSNL Gene symbol: WX1
Oryzabase Gene symbol: wx (Wx(am)), Wx, WX-B, GBSS-I, GBSS, OsGBSSI, GBSS1, OsGBSS1, GBSSI, GSS
Oryzabase Gene name: glutinous endosperm, waxy, Waxy, WAXY, “Granule-bound starch synthase 1, chloroplastic/amyloplastic”, Granule-bound starch synthase I, UDP-glycogen synthase, “Granule-bound starch synthase, chloroplast precursor”, glycogen [starch] synthase, Granule-bound glycogen synthase, UDPG-glycogen transglucosylase, uridine diphosphoglucose-glycogen glucosyltransferase, glycogen [starch] synthetase, Granule-bound glycogen [starch] synthase, UDPG-glycogen synthetase, granule bound starch synthase I, granule-bound starch synthase 1, granule-bound starch synthase I
Gene Ontolgy: glycogen (starch) synthase activity (GO:0004373)
starch metabolic process (GO:0005982)
starch synthase activity (GO:0009011)
biosynthetic process (GO:0009058)
glucan biosynthetic process (GO:0009250)
response to water (GO:0009415)
amyloplast (GO:0009501)
chloroplast (GO:0009507)
plastid (GO:0009536)
amyloplast starch grain (GO:0009568)
response to salt stress (GO:0009651)
seed germination (GO:0009845)
starch biosynthetic process (GO:0019252)
NDP-glucose-starch glucosyltransferase activity (GO:0033840)
seed development (GO:0048316)
Trait Ontolgy: glutinous endosperm (TO:0000098)
seed quality (TO:0000162)
amylose content (TO:0000196)
water stress trait (TO:0000237)
seed development trait (TO:0000653)
salt tolerance (TO:0006001)
Plant Ontolgy : seed development stage (PO:0001170)
seed imbibition stage (PO:0007022)
0 seed germination stage (PO:0007057)
seed (PO:0009010)
endosperm (PO:0009089)
Links: Oryzabase

Gene information from literatures

Gene function

  • The rice waxy (Wx) gene encodes a granule-bound starch synthase for the amylose synthesis in endosperm. In cultivated rice, two wild-type alleles Wxa and Wxb, are known. The protein level of Wxa is 10-fold higher than that of Wxb. The low-level expression of Wxb was the result from the inefficient splicing of intron 1 present in the untranslated leader region due to a G-to-T mutation at the 5' splice site. Wxa is widely distributed in indica, a subspecies with higher amylose content, whereas Wxb mainly in japonica, a subspecies with intermediate amylose content. Predominantly, the glutinous rice strains have Wxb-derived alleles.

Functional variations

Representative variations
#Var Cultivar 1 Cultivar 2 HGVS Description References
V1 NPB, Kinuhikari, Kinmaze, Notohikari, Toride1, Taichung 65, Norin 8 IR58, Labelle, Bluebonnet 50, TKM1, IR57311, O. rufipogon, O. glaberrima g.1765761T>G
G>T ( (Wxa>Wxb) mutation at the 5' splice junction of the 1st intron of the Wx locus is the major reason for the reduction of amylose content of the seed (from 24.7% for the G allele to 14.6% for the T allele). PMID:9744101
V2 \

Other variations
  • (No information)

Gene expression

  • The Wx gene is regulated in a tissue-specific manner and the Wx transcript is expressed only in the endosperm and pollen. Three distinct patterns of Wx transcripts in different cultivars and changes in Wx transcripts during seed development were reported. The three groups were group I (indica rice, Wxa, 2.3 kb Wx mRNA), group II (indica and japonica rice, intermediate amylose content, Wxa with Wxb, 2.3 kb Wx mRNA and 3.4 kb Wx mRNA) and group III (the glutinous cultivars, Wxb; only the 3.3 kb pre-mRNA)(PMID:7742858).
  • High amylose varieties accumulated high amounts of completely processed GBSS (granule-bound starch synthase) mRNA. In contrast, all the low amylose varieties accumulated both completely processed GBSS mRNA and partially processed transcript containing the leader intron, whereas glutinous varieties contained only incompletely processed GBSS transcripts (PMID:9670561).
  • The authors reported that the expression of the rice Wx gene was activated in response to a cool temperature (18°C) and that a large amount of Wx protein was produced. The increase in the amylose content in response to a cool temperature is presumably caused by an accumulation of the Wx protein, since the positive correlation between the relative amount of Wx protein and the amylose content was observed. DOI:10.1093/oxfordjournals.pcp.a029438

Other information

  • (No information)


  • Wang ZY et al. 1995 The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J. PMID:7742858
  • Isshiki M et al. 1998 A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5' splice site of the first intron. Plant J. PMID:9744101
  • Hirano HY et al. 1998 A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol Biol Evol. PMID:9718725
  • Cai XL et al. 1998 Aberrant splicing of intron 1 leads to the heterogeneous 5' UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J. PMID:9670561
  • Yamanaka S et al. 2004 Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet. PMID:14740088
  • Zhao Q et al. 2018 Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet. PMID:29335547