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Development of a Nasonia vitripennis outbred laboratory population for genetic analysis.

van de Zande L, Ferber S, de Haan A, Beukeboom LW, van Heerwaarden J, Pannebakker BA - Mol Ecol Resour (2013)

Bottom Line: As a characterization of its genetic composition, we provide data on the standing genetic variation and estimate the effective population size (N(e)) by microsatellite analysis.A genome-wide description of polymorphism is provided through pooled resequencing, which yielded 417,331 high-quality SNPs spanning all five Nasonia chromosomes.The HVRx population and its characterization are freely available as a community resource for investigators seeking to elucidate the genetic basis of complex trait variation using the Nasonia model system.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, the Netherlands.

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Genome-wide polymorphism pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean estimates of nucleotide diversity (π) in nonoverlapping 100 kb windows, plotted against chromosomal position.
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fig04: Genome-wide polymorphism pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean estimates of nucleotide diversity (π) in nonoverlapping 100 kb windows, plotted against chromosomal position.

Mentions: The mean nucleotide diversity per 100 kb window over all chromosomes was 0.13%, showing significant differentiation by chromosome (one-way aov; F4,155 = 9.97, P = 5.76e-08, Table3), with chromosome 1 showing the lowest nucleotide diversity compared with other chromosomes. The distribution of genomic variation over the chromosomes showed similar patterns for both SNP density as for nucleotide diversity. Both measures were higher towards the tips of the chromosomes than the centres (Figs3 and 4). Estimates of nucleotide diversity were lacking in areas where the read depths were low, such as the near the centre of the chromosomes (Fig. 4).


Development of a Nasonia vitripennis outbred laboratory population for genetic analysis.

van de Zande L, Ferber S, de Haan A, Beukeboom LW, van Heerwaarden J, Pannebakker BA - Mol Ecol Resour (2013)

Genome-wide polymorphism pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean estimates of nucleotide diversity (π) in nonoverlapping 100 kb windows, plotted against chromosomal position.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260118&req=5

fig04: Genome-wide polymorphism pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean estimates of nucleotide diversity (π) in nonoverlapping 100 kb windows, plotted against chromosomal position.
Mentions: The mean nucleotide diversity per 100 kb window over all chromosomes was 0.13%, showing significant differentiation by chromosome (one-way aov; F4,155 = 9.97, P = 5.76e-08, Table3), with chromosome 1 showing the lowest nucleotide diversity compared with other chromosomes. The distribution of genomic variation over the chromosomes showed similar patterns for both SNP density as for nucleotide diversity. Both measures were higher towards the tips of the chromosomes than the centres (Figs3 and 4). Estimates of nucleotide diversity were lacking in areas where the read depths were low, such as the near the centre of the chromosomes (Fig. 4).

Bottom Line: As a characterization of its genetic composition, we provide data on the standing genetic variation and estimate the effective population size (N(e)) by microsatellite analysis.A genome-wide description of polymorphism is provided through pooled resequencing, which yielded 417,331 high-quality SNPs spanning all five Nasonia chromosomes.The HVRx population and its characterization are freely available as a community resource for investigators seeking to elucidate the genetic basis of complex trait variation using the Nasonia model system.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, the Netherlands.

Show MeSH