The recombination landscape of the zebra finch Taeniopygia guttata genome
The recombination landscape of the zebra finch Taeniopygia guttata genome
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DOI：
10.1101/gr.101410.109
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发表时间：
2010-04-01
期刊：
影响因子：
7
通讯作者：
Ellegren, Hans
中科院分区：
文献类型：
--
作者：
Backstrom, Niclas;Forstmeier, Wolfgang;Ellegren, Hans
了解重组率变化的原因和后果是必不可少的，因为这个参数被认为会影响遗传变异的水平，选择的有效性，以及关联和连锁作图研究的设计。然而，有有限的知识有关的因素控制重组率的变化。我们对1920个单核苷酸多态性进行了基因分型，在1000多个斑胸草雀（Taeniopygia guttata）的多代系谱中建立了一个遗传连锁图谱，然后我们使用这些图谱数据与最近获得的斑胸草雀基因组序列草图一起估计基因组中1 Mb间隔的重组率。斑胸草雀的平均重组率（1.5 cM/Mb）高于人类，但明显低于鸡。鸡和斑胸草雀的局部重组率只有微弱的相关性，表明鸟类重组景观的进化周转。重组事件的分布严重偏向染色体末端，端粒效应比迄今为止在任何生物体中看到的都要强。事实上，在较大染色体中间长达100 Mb的间隔中，重组率低至0.1 cM/Mb。我们发现重组率和GC含量，以及GC丰富的序列基序之间呈正相关。连锁不平衡（LD）的水平显着较高的低重组的区域，表明重组率的异质性在斑胸草雀种群LD的基因组景观留下了足迹。
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.