Gn1a (GRAIN NUMBER 1A) : Os01g0197700


Locus ID: Os01g0197700
Transcript ID: Os01t0197700-01 (chr01:5270449-5275585)
Description: Cytokinin oxidase/dehydrogenase, Regulation of grain production
RAP-DB Gene symbol: Gn1a, OsCKX2
RAP-DB Gene name: Cytokinin oxidase/dehydrogenase 2
Gene Ontolgy: catalytic activity (GO:0003824)
cytokinin metabolic process (GO:0009690)
oxidoreductase activity (GO:0016491)
cytokinin dehydrogenase activity (GO:0019139)
flavin adenine dinucleotide binding (GO:0050660)
oxidation-reduction process (GO:0055114)
Links: TASUKE (for RAP-DB), GBrowse


CGSNL Gene symbol: GN1A
Oryzabase Gene symbol: Gn1a, OsCKX2, CKX2, ckx2, Gn1a/OsCKX2, Os CKX2, CKX2/Gn1a
Oryzabase Gene name: Cytokinin oxidase/dehydrogenase 2, grain number 1a, cytokinin oxidase 2, Grain number 1a/Cytokinin oxidase 2, Grain number 1 a
Gene Ontolgy: catalytic activity (GO:0003824)
response to salt stress (GO:0009651)
cytokinin metabolic process (GO:0009690)
inflorescence development (GO:0010229)
cytoplasmic membrane-bounded vesicle (GO:0016023)
oxidoreductase activity (GO:0016491)
cytokinin dehydrogenase activity (GO:0019139)
electron transport chain (GO:0022900)
secretion by cell (GO:0032940)
flavin adenine dinucleotide binding (GO:0050660)
oxidation-reduction process (GO:0055114)
Trait Ontolgy: inflorescence branching (TO:0000050)
primary branching of inflorescence (TO:0000052)
harvest index (TO:0000128)
relative water content (TO:0000136)
secondary branching of inflorescence (TO:0000142)
panicle number (TO:0000152)
plant height (TO:0000207)
vegetative vigor (TO:0000296)
photosynthetic ability (TO:0000316)
1000-seed weight (TO:0000382)
grain yield (TO:0000396)
grain number per plant (TO:0000440)
spikelet number (TO:0000456)
cell membrane stability (TO:0000467)
chlorophyll content (TO:0000495)
carotenoid content (TO:0000496)
grain weight (TO:0000590)
inflorescence development trait (TO:0000621)
cytokinin content (TO:0002660)
grain number (TO:0002759)
salt tolerance (TO:0006001)
Plant Ontolgy : inflorescence meristem (PO:0000230)
inflorescence development stage (PO:0001083)
Links: Oryzabase

Gene information from literatures

Gene function

  • Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an important role in regulating rice grain yield. Gn1a, a QTL for number of grain per panicle. The enzyme degrades the phytohormone cytokinin. Reduced expression of Gn1a causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield.

Functional variations

Representative variations
Var# Cultivar 1 Cultivar 2 HGVS Description References
V1 NPB, Koshihikari Kasalath, Habataki1 g.5275544_5275529del
Habataki and Kasalath showed more grain number than NPB and Koshihikari.
This 16-bp deletion in 5’UTR is common in indica rice varieties.
V2 NPB, Koshihikari, KY1312 Kasalath, Habataki, GKBR3 g.5276186_5276189del
Habataki, Kasalath and KY131 showed more grain number than NPB, Koshihikari and GKBR. PMID:26677125
V3 NPB, Koshihikari, KY131 Kasalath, Habataki, GKBR g.5276224_5276227del
Habataki, Kasalath and KY131 showed more grain number than NPB, Koshihikari and GKBR. PMID:26677125
V4 NPB, Koshihikari, KY131 Kasalath, Habataki, GKBR g.5270928T>G
The substitution of amino acid 537 in Gn1a exerted a critical function on determining the number of grains of panicles.
p.Asn537Lys in papers, but p.Asn535Lys in TASUKE.
V5 NPB, Koshihikari, KY131 Kasalath, Habataki, GKBR g.5275362G>C
V6 NPB, Koshihikari, KY131 Kasalath, Habataki, GKBR g.5275282_5275287del
V7 NPB, Koshihikari, R3551 Shuhui498 (R498), 51504, wild rice accessions 11-bp deletion in the 3rd exon (coding regions) A 11-bp deletion in the 3rd exon, causing a premature termination codon, results in a large panicles in 5150. PMID:26677125

1High-yielding rice variety, 2An elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability, 3A big panicle indica rice variety, 4High-yielding rice varieties from China reported in PMID:15976269.

Other variations
  • Three SNPs in the promoter region which are presumed to associate with Gn1a expression level, are summarized in Fig. 1. Allele specific markers were represented in Table 2 (PMID:26987543).

Gene expression

  • Gn1a was preferentially expressed in leaves, culms, inflorescence meristems, and flowers. The highest levels of Gn1a expression in inflorescence meristems were found in Koshihikari. Expression was observed mainly in the vascular tissue in developing culms, inflorescence meristems, and young flowers.
  • Down-regulation of cytokinin Oxidase 2 expression increases tiller number and improves rice yield (PMID:26643073).

Other information

  • The Habataki Gn1 allele is expected to produce ~92 more grains per main panicle than the Koshihikari allele, Gn1 explains 44% of the difference in grain number between Habataki and Koshihikari (PMID:15976269).
  • Shuhui498 (R498) is an elite parent of heavy panicle hybrid rice by pyramiding the rare gn1a and null gs3 alleles. This finding reveals the genetic basis and great potential application in future breeding of R498 (PMID:29546444).


  • Ashikari M et al. 2005 Cytokinin oxidase regulates rice grain production. Science PMID:15976269
  • Yeh SY et al. 2015 Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield. Rice PMID:26643073
  • Wang J et al. 2015 Artificial Selection of Gn1a Plays an Important role in Improving Rice Yields Across Different Ecological Regions. Rice PMID:26677125
  • Kim SR et al. 2016 Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L. Rice PMID:26987543
  • Feng X et al. 2017 Updating the elite rice variety Kongyu 131 by improving the Gn1a locus. Rice PMID:28730413
  • Wang S et al. 2018 Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes. Theor Appl Genet. PMID:29546444