The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res

Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
Genome Research (Impact Factor: 14.63). 03/2010; 20(4):485-95. DOI: 10.1101/gr.101410.109
Source: PubMed


Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.

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    • "The study concluded that " recombination rate is likely of little importance " in relation to plant domestication (Ross-Ibarra 2004). The study of Burt and Bell (1987), in which chiasmata counts for domestic mammals are reported, is often cited as evidence that domestic animals have higher recombination rate than their wild counterparts (see Schmidt-Hempel and Jokela 2002; Dumont and Payseur 2008; Groenen et al. 2009; Backström et al. 2010; Poissant et al. 2010; Smukowski and Noor 2011). "
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    • "Intrachromosomal rearrangements, which have occurred between the three bird species considered (reviewed by Ellegren 2010, 2014; see also van Oers et al. 2014), should not make the test counterconservative . This is because, for macrochromosomes, shuffling genes between the ends and the central parts is expected to homogenize differences in recombination frequency , whereas for microchromosomes, genetic maps in all species studied to date suggest recombination rates are roughly constant along the length of the chromosome (Backströ m et al. 2010; Stapley et al. 2010; van Oers et al. 2014). There is evidence that GC content is not at statistical equilibrium in multiple avian lineages and that GC-biased gene "
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    • "There are multiple signatures of strong selection in the Ficedula divergence islands – including reduced diversity, a skewed allele frequency spectrum, and higher linkage disequilibrium (LD) – and they largely coincide with centromeres, regions known to have reduced recombination in syntenic bird genomes (e.g. Backstr€ om et al. 2010). Together with the lower values of absolute divergence, the data better support a model in which regions of 50-fold higher 'divergence' instead indicate regions of 50-fold lower polymorphism and that many of these islands have been subject to recurrent selection since before the species split. "
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