GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00000443
Main curator
Martin
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
Arabidopsis thaliana _ cadmium (Cd) tolerant
Trait State in Taxon B
Arabidopsis thaliana _ cadmium (Cd)-sensitive
Ancestral State
Data not curated
Taxonomic Status
Taxon A
Latin Name
Common Name
thale cress
Synonyms
thale cress; mouse-ear cress; thale-cress; Arabidopsis thaliana (L.) Heynh.; Arabidopsis thaliana (thale cress); Arabidopsis_thaliana; Arbisopsis thaliana; thale kress
Rank
species
Lineage
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; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B
Latin Name
Common Name
thale cress
Synonyms
thale cress; mouse-ear cress; thale-cress; Arabidopsis thaliana (L.) Heynh.; Arabidopsis thaliana (thale cress); Arabidopsis_thaliana; Arbisopsis thaliana; thale kress
Rank
species
Lineage
Show more ...
; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
HMA3
Synonyms
-
String
-
Sequence Similarities
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IB subfamily.
GO - Molecular Function
GO:0005524 : ATP binding
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GO - Biological Process
GO - Cellular Component
GO:0016021 : integral component of membrane
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Mutation #1
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
Gln564Met and Tyr480Asp - both seem to affect the protein function - several haplotypes at high-frequency resulting in hypofunctional proteins; associated with hyper-accumulation of cadmium
Experimental Evidence
Taxon A | Taxon B | Position | |
---|---|---|---|
Codon | - | - | - |
Amino-acid | Gln | Met | 564 |
Authors
Chao DY; Silva A; Baxter I; Huang YS; Nordborg M; Danku J; Lahner B; Yakubova E; et al.
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Abstract
Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5-2 µg Cd g(-1) dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.
Additional References
Mutation #2
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
Gln564Met and Tyr480Asp - both seem to affect the protein function - several haplotypes at high-frequency resulting in hypofunctional proteins; associated with hyper-accumulation of cadmium
Experimental Evidence
Taxon A | Taxon B | Position | |
---|---|---|---|
Codon | - | - | - |
Amino-acid | Tyr | Asp | 480 |
Authors
Chao DY; Silva A; Baxter I; Huang YS; Nordborg M; Danku J; Lahner B; Yakubova E; et al.
... show more
Abstract
Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5-2 µg Cd g(-1) dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.
Additional References
RELATED GEPHE
Related Haplotypes
EXTERNAL LINKS
COMMENTS
@GxE @SeveralMutationsWithEffect
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