Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
Genome Res. 2010 Apr;20(4):485-95. doi: 10.1101/gr.101410.109. Epub 2010 Mar 31.
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.
了解重组率变化的原因和后果至关重要，因为这一参数被认为会影响遗传变异水平、选择的有效性以及关联和连锁作图研究的设计。然而，关于控制重组率变化的因素，我们的了解还很有限。我们对超过 1000 只斑马雀（Taeniopygia guttata）的多世代家系中的 1920 个单核苷酸多态性进行了基因分型，以构建遗传连锁图谱，然后我们利用这些图谱数据和最近获得的斑马雀草图基因组序列，来估计基因组中 1 Mb 间隔的重组率。斑马雀的平均重组率（1.5 cM/Mb）高于人类，但明显低于鸡。鸡和斑马雀的局部重组率相关性很弱，表明鸟类的重组景观发生了进化性更替。重组事件的分布严重偏向染色体的末端，端粒效应比迄今在任何生物中看到的都要强。事实上，在较大染色体的中间长达 100 Mb 的区间内，重组率低至 0.1 cM/Mb。我们发现重组率与 GC 含量以及富含 GC 的序列基序呈正相关。在低重组率的区域，连锁不平衡（LD）水平显著较高，这表明重组率的异质性在斑马雀种群的 LD 基因组景观上留下了痕迹。
