GS3 (GRAIN SIZE 3) : Os03g0407400

RAP-DB

Locus ID: Os03g0407400
Transcript ID: Os03t0407400-01 (chr03:16729501-16735109)
Description: Protein with plant-specific organ size regulation (OSR) domain, transmembrane region, TNFR/NGFR family cysteine-rich domain and VWFC module, Regulator of grain size and organ size
RAP-DB Gene symbol: GS3
RAP-DB Gene name: grain size 3
Gene Ontolgy: signal transducer activity (GO:0004871)
heterotrimeric G-protein complex (GO:0005834)
G-protein coupled receptor signaling pathway (GO:0007186)
Links: TASUKE+ (for RAP-DB), GBrowse

Oryzabase

CGSNL Gene symbol: LK3
CGSNL Gene name: LONG KERNEL 3
Oryzabase Gene symbol: lk3(t), lk3(t)*, SG3, GS3, SG3-GS3, OsGW3, OsGS3
Oryzabase Gene name: long kernel 3, long kernel-3, grain size, grain length and weight protein, GRAIN SIZE 3, G gamma subunit GS3
Gene Ontolgy: signal transducer activity (GO:0004871)
heterotrimeric G-protein complex (GO:0005834)
G-protein coupled receptor protein signaling pathway (GO:0007186)
G-protein coupled receptor signaling pathway (GO:0007186)
multicellular organismal development (GO:0007275)
Trait Ontolgy: panicle length (TO:0000040)
seed length (TO:0000146)
seed quality (TO:0000162)
plant height (TO:0000207)
1000-seed weight (TO:0000382)
seed size (TO:0000391)
grain yield (TO:0000396)
grain size (TO:0000397)
grain width (TO:0000402)
grain weight (TO:0000590)
grain length (TO:0000734)
grain shape (TO:0002730)
grain length to width ratio (TO:0002731)
Plant Ontolgy : seed (PO:0009010)
Links: Oryzabase

Gene information from literatures

Gene function

  • GS3 encodes a protein with several conserved domains, including a transmembrane domain, a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C in the C terminus. The OSR domain is the key negative regulator of grain length, whereas the two C-terminal domains have an inhibitory effect on OSR function. GS3 gene located on chromosome 3 is a major gene for grain size in rice, which has also been under strong selection pressure during domestication.

Functional variations

Representative functional variations
Var# Cultivar 1 Cultivar 2 HGVS Description References
V1 NPB, Pusa Basmati 11211 Sonasal2, Kala Jeera, Kishori, Birui, Jangi Jata, Kalo Bhutia, Vishnu Bhog, Neelabati, Gangabal g.16729672_16730014del
p.Asn134Leufs*VreLeuAspAspAspArgSerSerCysAlaArgThr
Conferred a short seeded phenotype. The deletion was present predominantly in the landraces, while it was absent in long grain genotypes. doi:10.1007/s13562-013-0243-5
V2 NPB JC73-4, JC49, JC157, JC101 and ABRI3 g.16729695_16730014del
p.Asn134Alafs*ArgThr
Deletion in the fifth exon of GS3 coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. PMID:23641184
V3 NPB ARC7291, TAL214 g.16730054_16730057del
p.Ser120Profs*30
Deletion in the fifth exon of GS3 coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. PMID:23641184
V4 NPB Zhenshan974, Chuan75 g.16730056_16730058del
p.Ser119del
Nipponbare had a 3-bp (TCC) insertion at the same site, resulting in an in-frame addition of a serine residue. It is unlikely that this InDel has a large effect on grain size. PMID:20974950
PMID:16453132
V5 NPB, Zhenshan97 Chuan7 g.16730058del
p.Ser120Profs*31
The 1-bp deletion in Chuan 7 causes frameshift from site 120, resulting in the loss of TNFR and VWFC domains. PMID:20974950
V6 NPB H343, Tumo-Tumo g.16730066_16730078del
p.Ala113Hisfs*35
Deletion in the fifth exon of GS3 coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. PMID:23641184
V7 NPB Podiwi, A8 g.16730044_16730046del
g.16730125del
p.Ala97Argfs*53
Deletion in the fifth exon of GS3 coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. PMID:23641184
V8 NPB, Chuan7, Zhenshan97, Asominori, O. rufipogon Minghui636, Jefferson, IR24, AIS22 g.16733441C>A
c.165C>A
p.Cys55*
C: small grain, A: long grain. A substitution of C (small grain group) by A (long grain group) in the second exon results in a premature stop codon. The putative protein encoded by Minghui 63 allele contains no functional domain because of premature termination. PMID:19506305
PMID:20974950
PMID:16453132
PMID:21107518
PMID:23641184

1 Extra long slender grain variety, 2 Short grain aromatic landrace, 3 Short grain variety, 4 Indica variety with short grain, 5: Indica variety with very small grain, 6 long grain variety

  • A major InDel of 342 bp (V1) was found in the GS3 gene of short grain landrace Sonasal, which included a 300 bp deletion from exon-5 followed by a insertion of 12 bp sequence and introduction of a stop codon reducing the CDS to 411 bp coding for 136 aa as compared to the GS3 reference sequence which had CDS length of 699 bp encoding for 232 aa (doi:10.1007/s13562-013-0243-5).
  • A total of 78 SNPs and 26 indels relative to Nipponbare were identified among the selected 10 strains in the sequence analysis of GS3. Of these mutations, only deletion(s) in the fifth exon of GS3 were observed in all 10 strains. JC73-4, JC149, JC157, JC101 and ABRI showed a 320-bp deletion at the 5064-bp downstream from the start codon (V2); H343 and Tumo-Tumo had a 13-bp deletion at the 5000-bp site (V6); ARC7291 and TAL214 had a 4-bp deletion at the 5021-bp site (V3); Podiwi A8 had a 1-bp deletion at the 4953-bp site and a 3-bp deletion at the 5016-bp site (V7) (PMID:23641184 Fig.1).
  • A 1-bp deletion in the fifth exon of GS3, leading to a frameshift mutation at the C terminus, produced a short seeded phenotype due to a truncated protein that lacked the TNFR/NGFR and VWFC domains (V5) (PMID:20974950).
  • Chuan 7 had a 1-bp deletion at 357 bp (C) downstream from the predicted translation start site, which caused a frameshift mutation in the C terminus that yielded a truncated 149-aa protein. Interestingly, Nipponbare had a 3-bp (TCC) insertion at the same site (V4), resulting in an in-frame addition of a serine residue. Therefore, GS3 has at least four different alleles according to the coding sequence: GS3-1 (Zhenshan 97), GS3-2 (Nipponbare), GS3-3 (Minghui 63) and GS3-4 (Chuan 7) (PMID:20974950, PMID:23641184).
  • Rice varieties such as Oryza sativa L. ‘Minghui63’, which have long grains, contain a GS3 allele characterized by a C-to-A substitution (V8) at the 165th nucleotide position that causes premature termination of the protein, resulting in a complete loss of the functional protein domain. This allele is common in rice with long grains. Using genetic transformation, it was demonstrated that the wild-type allele (C) confers short grain and the derived allele (A) confers long grain in natural populations. Other mutations in GS3 gene have also been shown to affect grain length but they occur at low frequency in O. sativa. A C-to-A nonsense mutation in the second exon of GS3 results in a long seeded phenotype (PMID:23641184).
  • Other SNPs/Indels were summarized in Fig. 3. of PMID:23641184 and Table 2 of doi:10.1007/s13562-013-0243-5.

Gene expression

  • GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering. GS3 participates in stigma exsertion as well as seed length in rice (PMID:23641184). A GS3 promoter::GUS fusion construct into Nipponbare, the GUS expression was observed in the basal part of young stigmas, and the strongest GUS expression was found in the basal part of stigmas and the upper part of styles. GUS expression was not detected in the pistil (doi:10.1270/jsbbs.61.244). The expression level and pattern were not the cause of the loss of function of GS3 in Minghui 63.

Other information

  • GS3 is an interesting case because its mutants both positively and negatively regulate seed length (PMID:27457210). The identification of novel, incomplete dominant alleles at GS3 that all confer short seeds. The fifth exon of the GS3 gene is a hotspot for mutation and has been the target of selection by many independent groups of humans during the evolution of O. sativa (PMID:16453132, PMID:23641184).
  • Domestication process has resulted in both extra long and extra short rice grains as compared to the wild rice because of different mutations in the GS3 gene (PMID:20520727, doi:10.1007/s13562-013-0243-5). All the short and medium grains genotypes carry the C-allele and the long and extra-long grains carry the A-allele of the GS3 gene (PMID:19020856). A GS3 haplotype conferring extra short grain was selected by traditional Indian farmers (doi:10.1007/s13562-013-0243-5). Multiple independent origins of short seeded GS3 alleles suggesting that farmers and early breeders forced artificial selection favoring short seeds (PMID:23641184, doi:10.1007/s13562-013-0243-5).
  • It has been repeatedly demonstrated that GS3 can simultaneously increase grain length which improves the appearance quality of indica rice, and grain-weight which increases grain yield. Surprisingly, however, this gene has not been intensively utilized in many rice breeding programs especially in China, as indicated by the high frequency of the medium grain cultivars (PMID:16453132).
  • An InDel marker, aksGS3-12 involving 342 bp deletion specific to Sonasal, a short grain aromatic landrace was developed and validated in a set of diverse rice germplasm varying for grain length. The deletion was present predominantly in the landraces, while it was absent in long grain genotypes and also in the accessions of O. rufipogon and O. nivara, the immediate progenitors of cultivated rice. Hence, the deletion associated with the short grain length might have occurred during the course of domestication of short grain aromatic rice varieties from the progenitor species (doi:10.1007/s13562-013-0243-5).
  • Stigma exsertion is an important trait that contributes to the improvement of seed production in hybrid rice. We demonstrate that GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice (doi:10.1270/jsbbs.61.244).

References

  • Fan C et al. 2006 GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet. PMID:16453132
  • Takano-Kai N et al. 2009 Evolutionary history of GS3, a gene conferring grain length in rice. Genetics PMID:19506305
  • Mao H et al. 2010 Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci U S A. PMID:20974950
  • Zhao K et al. 2010 Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One PMID:20520727
  • Takano-Kai N et al. 2011 GS3 participates in stigma exsertion as well as seed length in rice Breed Sci. doi:10.1270/jsbbs.61.244
  • Wang C et al. 2011 Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet. PMID:21107518
  • Takano-Kai N et al. 2013 Multiple and independent origins of short seeded alleles of GS3 in rice. Breed Sci. PMID:23641184
  • Anand D et al. 2015 Novel InDel variation in GS3 locus and development of InDel based marker for marker assisted breeding of short grain aromatic rices. Journal of Plant Biochemistry and Biotechnology doi:10.1007/s13562-013-0243-5
  • Segami S et al. 2016 Detection of Novel QTLs Regulating Grain Size in Extra-Large Grain Rice (Oryza sativa L.) Lines. Rice PMID:27457210