A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.
A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.
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DOI：
10.1186/s12863-016-0445-7
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发表时间：
2016-10-13
期刊：
影响因子：
2.9
通讯作者：
Ebert D
中科院分区：
文献类型：
--
作者：
Dukić M;Berner D;Roesti M;Haag CR;Ebert D
重组率是许多遗传分析的重要参数。重组率在物种、种群、个体和不同基因组区域之间存在很大差异。由于重组对种内多样性和种间差异产生深远影响，重组率变异的表征成为群体基因组研究的关键资源，并强调了高密度遗传图谱作为研究基因组生物学工具的重要性。在这里，我们展示了大型溞的高密度遗传图谱，并分析了整个基因组的重组率模式。通过限制性位点相关 DNA 测序对 F2 杂交组进行基因分型，以构建 D. magna 第三代连锁图谱。生成的高密度图谱包括 4037 个标记，覆盖 813 个支架和重叠群，总计占当前可用基因组草图序列 (v2.4) 的 77% 和估计基因组大小 (238 Mb) 的 55%。这里展示的图谱总遗传长度为 1614.5 cM，全基因组重组率估计为 6.78 cM/Mb。合并遗传和物理信息，我们一致发现，染色体外围部分的重组率估计值较高，而 D. magna 中含有着丝粒的染色体中心则显示出非常低的重组率估计值。由于其高密度，D. magna 的第三代连锁图谱可以与基因组草图组装结合起来，为该模式生物的基因组研究提供了重要的工具。因此，我们的连锁图谱可用于基因组组装的持续改进，但更重要的是，它使我们首次能够表征 D. magna 基因组重组率的变化。这些新见解可以为未来的基因组进化研究、数量性状绘图和群体遗传学研究提供宝贵的帮助。本文的在线版本 (doi:10.1186/s12863-016-0445-7) 包含补充材料，可供授权用户使用。
Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies. The online version of this article (doi:10.1186/s12863-016-0445-7) contains supplementary material, which is available to authorized users.
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