Abstract
BackgroundMeiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify. In this study, we developed a parent-sibling tracing (PST) approach from previously reported methods to identify meiotic crossover sites of GEO GSE6754 data set. This approach requires only the single nucleotide polymorphism (SNP) data of the pedigrees of both parents and at least two of children.ResultsCompared to other SNP-based algorithms (identity by descent or pediSNP), fewer uninformative SNPs were derived with the use of PST. Analysis of a GEO GSE6754 data set containing 2,145 maternal and paternal meiotic events revealed that the pattern and distribution of paternal and maternal recombination sites vary along the chromosomes. Lower crossover rates near the centromeres were more prominent in males than in females. Based on analysis of repetitive sequences, we also showed that recombination hotspots are positively correlated with SINE/MIR repetitive elements and negatively correlated with LINE/L1 elements. The number of meiotic recombination events was positively correlated with the number of shorter tandem repeat sequences.ConclusionsThe advantages of the PST approach include the ability to use only two-generation pedigrees with two siblings and the ability to perform gender-specific analyses of repetitive elements and tandem repeat sequences while including fewer uninformative SNP regions in the results.
Highlights
Meiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify
While variation in recombination rates is a ubiquitous feature of the human genome [1], the mechanisms governing the distribution of crossovers along meiotic chromosomes remain largely unclear, with the exception of the recent discovery that Prdm9 is involved in the activation of mammalian recombination hotspots [2,3,4,5]
Using chromosome 1 as an example, identity by descent (IBD) analysis in both children could define the sites of meiotic recombination for paternal gametes
Summary
Meiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify. We developed a parent-sibling tracing (PST) approach from previously reported methods to identify meiotic crossover sites of GEO GSE6754 data set. This approach requires only the single nucleotide polymorphism (SNP) data of the pedigrees of both parents and at least two of children. While variation in recombination rates is a ubiquitous feature of the human genome [1], the mechanisms governing the distribution of crossovers along meiotic chromosomes remain largely unclear, with the exception of the recent discovery that Prdm is involved in the activation of mammalian recombination hotspots [2,3,4,5]. Crossover rates in males are 5-fold lower near
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