qSH1 (Shattering (QTL)-1) : Os01g0848400


Locus ID: Os01g0848400
Transcript ID: Os01t0848400-01 (chr01:36445456-36449951)
Description: BEL1-type homeobox family, Seed shattering
RAP-DB Gene symbol: qSH1, qSH1, qsh1, qSH-1
RAP-DB Gene name: Shattering (QTL)-1, QTL of seed shattering in chromosome 1
Gene Ontolgy: DNA binding (GO:0003677)
sequence-specific DNA binding transcription factor activity (GO:0003700)
protein binding (GO:0005515)
nucleus (GO:0005634)
sequence-specific DNA binding (GO:0043565)
Links: TASUKE (for RAP-DB), GBrowse


CGSNL Gene symbol: qSH1
CGSNL Gene name: Shattering (QTL)-1
Oryzabase Gene symbol: qSH1, qsh1, qSH-1
Oryzabase Gene name: QTL of seed shattering in chromosome 1
Gene Ontolgy: DNA binding (GO:0003677)
sequence-specific DNA binding transcription factor activity (GO:0003700)
protein binding (GO:0005515)
nucleus (GO:0005634)
regulation of transcription, DNA-dependent (GO:0006355)
sequence-specific DNA binding (GO:0043565)
Trait Ontolgy: grain shattering (TO:0000473)
Plant Ontolgy: -
Links: Oryzabase

Gene information from literatures

Gene function

  • qSH1 encodes a BEL1-type homeobox gene and regulates pedicel AZ (abscission zone) formation, and an single nucleotide polymorphism (SNP) in the 5′ regulatory region of the qSH1 gene causes loss of seed shattering owing to the absence of abscission layer formation. The role of qSH1 in rice evolution is now considered to be important during the improvement of japonica varieties.

Functional variations

Representative variations
Var# Cultivar 1 Cultivar 2 HGVS Description References
V1 NPB Kasalath, IR261 g.36461792A>C
This FNP causes loss of seed shattering owing to the absence of abscission layer formation. Functional in cultivated O.sativa, but non-functional in weedy rice or O. rufipogon. PMID:16614172
V2 NPB, Jiucaiqing2 IR26 g.36451344_36451345InsTAAG
V3 NPB, Jiucaiqing IR26 g.36451290A>G
V4 NPB, Jiucaiqing IR26 g.36450765_36450766delinsTG
Putative functional SNP in promoter region, causing a CAAT box contained, that might change the expression pattern of shattering related genes with seed development. PMID:27902802
V5 NPB, Jiucaiqing IR26 g.36449883C>T
SNP on a putative SORLIP1AT domain PMID:27902802

1Indica variety, easy shattering, 2Nonshattering japonica rice landrace Jiucaiqing (JCQ) from Taihu Lake valley in China. Jiucaiqing is a good source of genes for salt tolerance, seed germination, and seed vigor.

  • One single-nucleotide polymorphism (V1), located at 12-kb upstream region of qSH1 ORF, was highly associated with the degree of seed shattering among temperate japonica rice cultivars (PMID:16614172).
  • Nucleotide substitution of C with A at the 12 kb ahead of qSH1 position was associated with the nonshattering phenotype. The nucleotide sequences at the 12 kb ahead of qSH1 were identical (C) between Jiucaiqing and IR26, while the nonshattering A allele was present in Nipponbare. The promoter of qSH1 were identical between Jiucaiqing and Nipponbare, while IR26 differed from others, having a TAAG insertion at position −1845 (V2) and nucleotide changes, A to G, GC to TG and C to T, at position −1787 (V3), −1262 (V4), and −380 (V5), respectively (PMID:27902802).

Gene expression

  • In situ hybridization analysis revealed that in the NIL the ORF was expressed at the inflorescence meristem in the stage of rachis meristem establishment. It was also expressed at both the anther region and the provisional abscission layer at the base of the spikelet in the stage of floral organ differentiation (PMID:16614172).

Other information

  • A SNP in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication (PMID:16614172).
  • qSH1 and SH5 have a role in maintaining the expression of Sh4 and SHAT1. The BEL1-type homeobox gene SH5, a homolog of qSH1, was shown to inhibit lignin biosynthesis and enhance abscission layer development qSH1 functions downstream of SHAT1 and SH4 in maintaining their expression in the abscission zone (AZ), thus promoting AZ differentiation (DOI:10.1111/aab.12159).
  • qSH1 in Japonica and Sh4 in Indica rice are major genes governing seed shattering trait (DOI:10.1111/aab.12159).
  • As a consequence of domestication, qSH1 shows a change in the spatial pattern of its expression. In the genetic background of cultivated rice, the wild qSH1 allele has stronger effect on seed shattering than that of sh4. In addition, the wild alleles at both qSH1 and sh4 loci showed semi-dominant effects. On the other hand, in the genetic background of wild rice, the non-shattering behavior was not obtained by a single mutation. Probably, some other minor genes are still associated with the formation or activation of abscission layer, which enhance the seed shattering (PMID:21178306).
  • qSH1JCQ can significantly decrease the expression of shattering related genes (qSH1, OsCPL1, Sh4, SH5, and SHAT1) especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease.PMID:27902802


  • Konishi S et al. 2006 An SNP caused loss of seed shattering during rice domestication. Science PMID:16614172
  • Ishikawa R et al. 2010 Allelic interaction at seed-shattering loci in the genetic backgrounds of wild and cultivated rice species. Genes Genet Syst. PMID:21178306
  • Nunes AL et al. 2014 Nucleotide variability and gene expression reveal new putative genes related to seed shattering in weedy rice. Annals of Applied Biology DOI:10.1111/aab.12159
  • Cheng J et al. 2016 Identification and Characterization of Quantitative Trait Loci for Shattering in Rice Landrace Jiucaiqing from Taihu Lake Valley, China. Plant Genome PMID:27902802