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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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CS3227 carries modifiers that suppress gi-induced petiole and hypocotyl elongation. (A) Mean hypocotyl length for Col-0, CS3227, and several gi alleles grown for 6 d in short days at 23°. (B) Distribution of hypocotyl length in an F2 population derived from a cross between CS3227 and Col-0. (C) Representative adult Col-0, gi-1, and CS3227 plants grown for 8 wk in short days at 23°.
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fig5: CS3227 carries modifiers that suppress gi-induced petiole and hypocotyl elongation. (A) Mean hypocotyl length for Col-0, CS3227, and several gi alleles grown for 6 d in short days at 23°. (B) Distribution of hypocotyl length in an F2 population derived from a cross between CS3227 and Col-0. (C) Representative adult Col-0, gi-1, and CS3227 plants grown for 8 wk in short days at 23°.

Mentions: Not all aspects of CS3227 aligned with the phenotypes described for gi-1. GI loss of function alleles are characterized by elongated hypocotyls in red light and white light. We therefore measured hypocotyl length in Col-0, CS3227, and several gi alleles when grown in white light and short days. As expected, all gi alleles (gi-1, gi-2, and gi-201) had long hypocotyls under these conditions (mean length ~6 mm; with the Col-0 wild-type strain being about 3 mm in length) but remained slightly shorter than the red light photoreceptor mutant phyB-9 (Figure 5A). In contrast, CS3227 displayed a shortened hypocotyl that was comparable to Col-0. The long hypocotyl characteristic of a gi-1 mutant was recovered in an F2 population derived from a cross between CS3227 and Col-0, indicating that CS3227 also carried a modifier locus (or loci) that suppressed the long hypocotyl resulting from loss of GI function (Figure 5B).Figure 5


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

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

CS3227 carries modifiers that suppress gi-induced petiole and hypocotyl elongation. (A) Mean hypocotyl length for Col-0, CS3227, and several gi alleles grown for 6 d in short days at 23°. (B) Distribution of hypocotyl length in an F2 population derived from a cross between CS3227 and Col-0. (C) Representative adult Col-0, gi-1, and CS3227 plants grown for 8 wk in short days at 23°.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: CS3227 carries modifiers that suppress gi-induced petiole and hypocotyl elongation. (A) Mean hypocotyl length for Col-0, CS3227, and several gi alleles grown for 6 d in short days at 23°. (B) Distribution of hypocotyl length in an F2 population derived from a cross between CS3227 and Col-0. (C) Representative adult Col-0, gi-1, and CS3227 plants grown for 8 wk in short days at 23°.
Mentions: Not all aspects of CS3227 aligned with the phenotypes described for gi-1. GI loss of function alleles are characterized by elongated hypocotyls in red light and white light. We therefore measured hypocotyl length in Col-0, CS3227, and several gi alleles when grown in white light and short days. As expected, all gi alleles (gi-1, gi-2, and gi-201) had long hypocotyls under these conditions (mean length ~6 mm; with the Col-0 wild-type strain being about 3 mm in length) but remained slightly shorter than the red light photoreceptor mutant phyB-9 (Figure 5A). In contrast, CS3227 displayed a shortened hypocotyl that was comparable to Col-0. The long hypocotyl characteristic of a gi-1 mutant was recovered in an F2 population derived from a cross between CS3227 and Col-0, indicating that CS3227 also carried a modifier locus (or loci) that suppressed the long hypocotyl resulting from loss of GI function (Figure 5B).Figure 5

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
Related in: MedlinePlus