Characterising regional variation in recombination rates across the genome is critical for understanding the forces that shape patterns of variation in genetic diversity and divergence. The Prdm9 plays a key role for determining positions of meiotic crossovers and demarcating the location of ‘recombination hotspots’ in several mammalian species. However, other vertebrate species without Prdm9, such as birds, also show highly variable recombination rate across the genome, but much less is known about the underlying mechanism.
Here we estimate fine-scale population recombination rate based on the patterns of linkage disequilibrium across the whole genomes of 89 collared flycatchers (Ficedula albicollis). We identified 2,669 recombination hotspots with average recombination rate being more than 10 times higher than the genomic background. These hotspots showed a strong association with gene promoter regions, first exons and CpG islands, although a substantial portion of hotspots was located in intergenic regions. Consistent with this pattern, overall recombination rate was higher at gene promoter regions, first exons and CpG islands than the genomic background. This is in line with the ‘open chromatin hypothesis’, where genomic regions with loosely packed chromatin, such as gene promoters and transcription start sites, are more easily accessible to the recombination machinery. Interestingly, recombination rate was also higher at regions containing LINE and LTR retrotransposons. This may indicate an indirect correlation between retrotransposons and high recombination rate such that highly recombinogenic regions characterised by open chromatin are also targets for the integration of retrotransposons, which also requires an accessible chromatin state. However, CT-rich motifs were significantly enriched in highly recombinogenic LTR retrotransposons, which may indicate a causal relationship between retrotransposons and recombination hotspots. Because similar CT-rich motifs are known to be associated with meiotic crossovers in plants and yeasts, these CT-rich retrotransposons may increase local recombination rate by modifying chromatin marks in bird genomes.