GEPHE SUMMARY Print
Entry Status
Published
GepheID
GP00001280
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Arabidopsis thaliana- Ler0
Trait State in Taxon B
Arabidopsis thaliana- Shahdara
Ancestral State
Taxon A
Taxonomic Status
Taxon A
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 A an Infraspecies?
Yes
Taxon A Description
Arabidopsis thaliana- Ler0
Taxon B
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?
Yes
Taxon B Description
Arabidopsis thaliana- Shahdara
GENOTYPIC CHANGE
UniProtKB
Arabidopsis thaliana
GenebankID or UniProtKB
Mutation #1
Presumptive Null
Yes
Molecular Type
Aberration Type
Insertion Size
1-9 bp
Molecular Details of the Mutation
insertion of three or four TA repeats in intron 2 - together with the G>T mutation it causes frequent exon 3 skipping
Experimental Evidence
Authors
Kesari R; Lasky JR; Villamor JG; Des Marais DL; Chen YJ; Liu TW; Lin W; Juenger TE; et al. ... show more
Abstract
Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the Arabidopsis accession Shakdara (Sha) was threefold less than that of Landsberg erecta (Ler) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme Δ(1)-pyrroline-5-carboxylate synthetase1 (P5CS1) as a basis for the lower proline of Sha. Sha P5CS1 had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip P5CS1). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip P5CS1 splice variant constituted as much as half of the total P5CS1 transcript. In a larger panel of Arabidopsis accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip P5CS1 among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that P5CS1 may have evolved under positive selection, and more extensive correlation of exon 3-skip P5CS1 production than proline abundance with climate conditions of natural accessions also suggest a role of P5CS1 in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip P5CS1 in natural variation of proline metabolism, and suggest an association of P5CS1 and its alternative splicing with environmental adaptation.
Additional References
Mutation #2
Presumptive Null
No
Molecular Type
Aberration Type
SNP
SNP Coding Change
-
Molecular Details of the Mutation
G-to-T in intron 3 causing alternative splicing
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid - - -
Authors
Kesari R; Lasky JR; Villamor JG; Des Marais DL; Chen YJ; Liu TW; Lin W; Juenger TE; et al. ... show more
Abstract
Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the Arabidopsis accession Shakdara (Sha) was threefold less than that of Landsberg erecta (Ler) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme Δ(1)-pyrroline-5-carboxylate synthetase1 (P5CS1) as a basis for the lower proline of Sha. Sha P5CS1 had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip P5CS1). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip P5CS1 splice variant constituted as much as half of the total P5CS1 transcript. In a larger panel of Arabidopsis accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip P5CS1 among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that P5CS1 may have evolved under positive selection, and more extensive correlation of exon 3-skip P5CS1 production than proline abundance with climate conditions of natural accessions also suggest a role of P5CS1 in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip P5CS1 in natural variation of proline metabolism, and suggest an association of P5CS1 and its alternative splicing with environmental adaptation.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
COMMENTS
@Splicing neither the small intron 2 TA-insertion nor the intron 3 polymorphism by itself are sufficient to cause frequent exon 3-skip transcript formation. The high exon 3-skip P5CS1 accessions (with exception of Pt-0) all have both the intron 3 G-to-T transition and insertion of three or four TA repeats in intron 2. Arabidopsis thaliana- Shahdara allele is a reduced functional allele
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