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Modulating crossover positioning by introducing large structural changes in chromosomes.

Ederveen A, Lai Y, van Driel MA, Gerats T, Peters JL - BMC Genomics (2015)

Bottom Line: Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2.In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes.When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Plant Physiology, Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. a.ederveen@science.ru.nl.

ABSTRACT

Background: Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation present in offspring. Crossovers are not uniformly distributed along chromosomes; rather there are preferred locations where they may take place. The positioning of crossovers is known to be influenced by both exogenous and endogenous factors as well as structural features inherent to the chromosome itself. We have introduced large structural changes into Arabidopsis chromosomes and report their effects on crossover positioning.

Results: The introduction of large deletions and putative inversions silenced recombination over the length of the structural change. In the majority of cases analyzed, the total recombination frequency over the chromosomes was unchanged. The loss of crossovers at the sites of structural change was compensated for by increases in recombination frequencies elsewhere on the chromosomes, mostly in single intervals of one to three megabases in size. Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2. In both cases, compensatory increases in recombination frequencies were of similar strength and took place in the same chromosome region. In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes.

Conclusions: When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome. Moreover, different reactions to induced structural changes are observed between and within chromosomes. However, the similarity in reaction observed when looking at chromosomes carrying similar changes suggests a direct causal relation between induced change and observed reaction.

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Related in: MedlinePlus

Crossing scheme of the experiment. Flowering individuals of Arabidopsis thaliana ecotype Ler-0 were subjected to γ-irradiation to induce Double Stranded DNA Breaks (DSBs). Four groups of plants were irradiated at 0 (Controls), 150, 300 and 600 Gray. Repair of DSBs resulted in the omission or inversion of interstitial fragments, so creating large chromosomal deletions and putative inversions in the gametes of these plants (M1 generation). Crossing of these plants to ecotype Col-0 was performed on the same day. The resulting offspring (M2) were analyzed on Ler-0 and Col-0 SNP presence at 2100 markers spread over the genome. Regions of Loss of Heterozygosity (LOH) indicating deletions (Δ) were readily observed and 16 promising M2Δ individuals carrying deletions of varying sizes spread over the five chromosomes were backcrossed to ecotype Ler-0 for recombination analyses following SNP detection.
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Fig1: Crossing scheme of the experiment. Flowering individuals of Arabidopsis thaliana ecotype Ler-0 were subjected to γ-irradiation to induce Double Stranded DNA Breaks (DSBs). Four groups of plants were irradiated at 0 (Controls), 150, 300 and 600 Gray. Repair of DSBs resulted in the omission or inversion of interstitial fragments, so creating large chromosomal deletions and putative inversions in the gametes of these plants (M1 generation). Crossing of these plants to ecotype Col-0 was performed on the same day. The resulting offspring (M2) were analyzed on Ler-0 and Col-0 SNP presence at 2100 markers spread over the genome. Regions of Loss of Heterozygosity (LOH) indicating deletions (Δ) were readily observed and 16 promising M2Δ individuals carrying deletions of varying sizes spread over the five chromosomes were backcrossed to ecotype Ler-0 for recombination analyses following SNP detection.

Mentions: To study the effects of large structural changes in chromosomes on the distribution of COs during male meiosis within those chromosomes, mature pollen of Arabidopsis thaliana ecotype Ler-0 was irradiated with γ-rays emitted from a Cobalt60 source at 150, 300 and 600 Gray. Within eight hours of irradiation the treated pollen (M1) was used to fertilize Col-0 plants. Of each resulting group of seeds (M2), ~50 were grown, their DNA was collected and subjected to Illumina GA2-based SNP-detection for deletion identification and their pollen was used to backcross to the Ler-0 ecotype for later recombination analysis (Figure 1). Chromosomal deletions, inversions and translocations were expected to be readily induced in the pollen as a result of the three irradiation treatments.Figure 1


Modulating crossover positioning by introducing large structural changes in chromosomes.

Ederveen A, Lai Y, van Driel MA, Gerats T, Peters JL - BMC Genomics (2015)

Crossing scheme of the experiment. Flowering individuals of Arabidopsis thaliana ecotype Ler-0 were subjected to γ-irradiation to induce Double Stranded DNA Breaks (DSBs). Four groups of plants were irradiated at 0 (Controls), 150, 300 and 600 Gray. Repair of DSBs resulted in the omission or inversion of interstitial fragments, so creating large chromosomal deletions and putative inversions in the gametes of these plants (M1 generation). Crossing of these plants to ecotype Col-0 was performed on the same day. The resulting offspring (M2) were analyzed on Ler-0 and Col-0 SNP presence at 2100 markers spread over the genome. Regions of Loss of Heterozygosity (LOH) indicating deletions (Δ) were readily observed and 16 promising M2Δ individuals carrying deletions of varying sizes spread over the five chromosomes were backcrossed to ecotype Ler-0 for recombination analyses following SNP detection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4359564&req=5

Fig1: Crossing scheme of the experiment. Flowering individuals of Arabidopsis thaliana ecotype Ler-0 were subjected to γ-irradiation to induce Double Stranded DNA Breaks (DSBs). Four groups of plants were irradiated at 0 (Controls), 150, 300 and 600 Gray. Repair of DSBs resulted in the omission or inversion of interstitial fragments, so creating large chromosomal deletions and putative inversions in the gametes of these plants (M1 generation). Crossing of these plants to ecotype Col-0 was performed on the same day. The resulting offspring (M2) were analyzed on Ler-0 and Col-0 SNP presence at 2100 markers spread over the genome. Regions of Loss of Heterozygosity (LOH) indicating deletions (Δ) were readily observed and 16 promising M2Δ individuals carrying deletions of varying sizes spread over the five chromosomes were backcrossed to ecotype Ler-0 for recombination analyses following SNP detection.
Mentions: To study the effects of large structural changes in chromosomes on the distribution of COs during male meiosis within those chromosomes, mature pollen of Arabidopsis thaliana ecotype Ler-0 was irradiated with γ-rays emitted from a Cobalt60 source at 150, 300 and 600 Gray. Within eight hours of irradiation the treated pollen (M1) was used to fertilize Col-0 plants. Of each resulting group of seeds (M2), ~50 were grown, their DNA was collected and subjected to Illumina GA2-based SNP-detection for deletion identification and their pollen was used to backcross to the Ler-0 ecotype for later recombination analysis (Figure 1). Chromosomal deletions, inversions and translocations were expected to be readily induced in the pollen as a result of the three irradiation treatments.Figure 1

Bottom Line: Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2.In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes.When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Plant Physiology, Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. a.ederveen@science.ru.nl.

ABSTRACT

Background: Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation present in offspring. Crossovers are not uniformly distributed along chromosomes; rather there are preferred locations where they may take place. The positioning of crossovers is known to be influenced by both exogenous and endogenous factors as well as structural features inherent to the chromosome itself. We have introduced large structural changes into Arabidopsis chromosomes and report their effects on crossover positioning.

Results: The introduction of large deletions and putative inversions silenced recombination over the length of the structural change. In the majority of cases analyzed, the total recombination frequency over the chromosomes was unchanged. The loss of crossovers at the sites of structural change was compensated for by increases in recombination frequencies elsewhere on the chromosomes, mostly in single intervals of one to three megabases in size. Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2. In both cases, compensatory increases in recombination frequencies were of similar strength and took place in the same chromosome region. In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes.

Conclusions: When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome. Moreover, different reactions to induced structural changes are observed between and within chromosomes. However, the similarity in reaction observed when looking at chromosomes carrying similar changes suggests a direct causal relation between induced change and observed reaction.

Show MeSH
Related in: MedlinePlus