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Plant genetic archaeology: whole-genome sequencing reveals the pedigree of a classical trisomic line.

Salomé PA, Weigel D - G3 (Bethesda) (2014)

Bottom Line: The circadian oscillator is astonishingly robust to changes in the environment but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication, and homeologous gene loss.While studying the potential effect of aneuploidy on the Arabidopsis thaliana circadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering.With the help of whole-genome sequencing, we uncovered the unexpected complexity of this trisomic stock's history, as its genome shows evidence of past outcrossing with another A. thaliana accession.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany salome@chem.ucla.edu.

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Estland/Estonia (Est) is a likely candidate progenitor for the non−Col-0 genomic regions found in CS3227. The Est accession shared most of its SNPs with the non−Col-0 regions of CS3227, here shown for chromosome 1 but also for chromosomes 2−4. (A) Inter-SNP distance for all SNPs found along chromosome 1 in CS3227 when Col-0 is used as reference. (B) Inter-SNP distance for chromosome 1 of CS3227 with Est as reference genome. (C) Complementary pattern of Col-0−like and Est-like genomic regions along chromosome 1 of CS3227. SNP, single-nucleotide polymorphism.
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fig6: Estland/Estonia (Est) is a likely candidate progenitor for the non−Col-0 genomic regions found in CS3227. The Est accession shared most of its SNPs with the non−Col-0 regions of CS3227, here shown for chromosome 1 but also for chromosomes 2−4. (A) Inter-SNP distance for all SNPs found along chromosome 1 in CS3227 when Col-0 is used as reference. (B) Inter-SNP distance for chromosome 1 of CS3227 with Est as reference genome. (C) Complementary pattern of Col-0−like and Est-like genomic regions along chromosome 1 of CS3227. SNP, single-nucleotide polymorphism.

Mentions: Although most Arabidopsis laboratories currently focus on one of the Col accessions or Ler, initial Arabidopsis research included 10 distinct accessions, all collected and distributed to the community by Friedrich Laibach (Laibach 1943). We therefore compared SNPs of a non−Col-0 portion of chromosome 1 from CS3227 with SNP datasets from seven of the nine non-Col accessions used by George Redeí that have been re-sequenced as part of the 1001 Genomes project (http://1001genomes.org) (Weigel and Mott 2009) and found a match with Est (from Estland/Estonia; Figure S3). Blocks of high similarity between Est and CS3227 coincided with regions with high SNP density relative to Col-0, and were found on all chromosomes except chromosome 5 (Figure 6 and Figure S2).


Plant genetic archaeology: whole-genome sequencing reveals the pedigree of a classical trisomic line.

Salomé PA, Weigel D - G3 (Bethesda) (2014)

Estland/Estonia (Est) is a likely candidate progenitor for the non−Col-0 genomic regions found in CS3227. The Est accession shared most of its SNPs with the non−Col-0 regions of CS3227, here shown for chromosome 1 but also for chromosomes 2−4. (A) Inter-SNP distance for all SNPs found along chromosome 1 in CS3227 when Col-0 is used as reference. (B) Inter-SNP distance for chromosome 1 of CS3227 with Est as reference genome. (C) Complementary pattern of Col-0−like and Est-like genomic regions along chromosome 1 of CS3227. SNP, single-nucleotide polymorphism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321033&req=5

fig6: Estland/Estonia (Est) is a likely candidate progenitor for the non−Col-0 genomic regions found in CS3227. The Est accession shared most of its SNPs with the non−Col-0 regions of CS3227, here shown for chromosome 1 but also for chromosomes 2−4. (A) Inter-SNP distance for all SNPs found along chromosome 1 in CS3227 when Col-0 is used as reference. (B) Inter-SNP distance for chromosome 1 of CS3227 with Est as reference genome. (C) Complementary pattern of Col-0−like and Est-like genomic regions along chromosome 1 of CS3227. SNP, single-nucleotide polymorphism.
Mentions: Although most Arabidopsis laboratories currently focus on one of the Col accessions or Ler, initial Arabidopsis research included 10 distinct accessions, all collected and distributed to the community by Friedrich Laibach (Laibach 1943). We therefore compared SNPs of a non−Col-0 portion of chromosome 1 from CS3227 with SNP datasets from seven of the nine non-Col accessions used by George Redeí that have been re-sequenced as part of the 1001 Genomes project (http://1001genomes.org) (Weigel and Mott 2009) and found a match with Est (from Estland/Estonia; Figure S3). Blocks of high similarity between Est and CS3227 coincided with regions with high SNP density relative to Col-0, and were found on all chromosomes except chromosome 5 (Figure 6 and Figure S2).

Bottom Line: The circadian oscillator is astonishingly robust to changes in the environment but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication, and homeologous gene loss.While studying the potential effect of aneuploidy on the Arabidopsis thaliana circadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering.With the help of whole-genome sequencing, we uncovered the unexpected complexity of this trisomic stock's history, as its genome shows evidence of past outcrossing with another A. thaliana accession.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany salome@chem.ucla.edu.

Show MeSH