GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00001375
Main curator
Prigent
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Rice ; O. s. japonica ; Nipponbare ; low nitrate absorption
Trait State in Taxon B
Rice- O. s. indica ; IR24 ; high nitrate absorption
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
rice
Synonyms
rice; red rice; Oryza sativa L.
Rank
species
Lineage
Show more ... ytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
Rice ; O. s. japonica ; Nipponbare ; low nitrate absorption
Taxon B
Latin Name
Common Name
rice
Synonyms
rice; red rice; Oryza sativa L.
Rank
species
Lineage
Show more ... ytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
Rice- O. s. indica ; IR24 ; high nitrate absorption
GENOTYPIC CHANGE
Generic Gene Name
NPF6.3
Synonyms
ARABIDOPSIS THALIANA NITRATE TRANSPORTER 1; AtNPF6.3; ATNRT1; ATNRT1.1; B-1; CHL1; CHL1-1; CHLORATE/NITRATE TRANSPORTER; CHLORINA 1; F12F1.1; F12F1_1; NITRATE TRANSPORTER 1; nitrate transporter 1.1; NITRATE/CHLORATE TRANSPORTER; NPF6.3; NRT1; NRT1/ PTR family 6.3; NRT1.1; At1g12110; T28K15_13
Sequence Similarities
Belongs to the PTR2/POT transporter (TC 2.A.17) family.
UniProtKB
Arabidopsis thaliana
GenebankID or UniProtKB
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
c.980C>T p.Met327Thr
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid - - -
Authors
Hu B; Wang W; Ou S; Tang J; Li H; Che R; Zhang Z; Chai X; et al. ... show more
Abstract
Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.
Additional References
RELATED GEPHE
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
Wild ancestors are O. rufipogon-I and O. rufipogon-III in which the SNP was polymorphic ; the variant of indica has probably been selected during domestication
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