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首页> 外文期刊>BMC Genomics >A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers
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A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

机译：基于EST衍生SNP标记的大西洋鲑（Salmo salar）连锁图

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Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM. Conclusion The linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.
机译：背景技术大西洋鲑是具有商业和生态意义的物种。像其他鲑鱼一样，该物种显示出残留的四体性，并且两性之间的重组率差异很大。基因组学的进步需要同时包含I型和II型标记的全基因组覆盖图。此外，重要的是估计物种中连锁不平衡（LD）的水平。在这项研究中，我们为大西洋鲑鱼开发了数百个单核苷酸多态性（SNP）标记，并构建了包含SNP和微卫星标记的雄性和雌性连锁图。我们还进一步调查了男性和女性重组事件在整个基因组中的分布，以及标记对之间的LD估计水平。结果男性图有29个连锁群，长390 cM。雌性地图有30个连锁组，长度为1983 cM。总共，这些图包含位于基因内的138个微卫星标记和304个SNP，其中大多数已成功注释。男性和女性重组事件的比率接近于零或非常大，表明发生男性和女性交叉的区域之间几乎没有重叠。女性图谱可能具有接近完整的基因组覆盖范围，而大多数男性连锁基团可能在发生男性重组事件的端粒区域中缺乏标记。 r 2 的水平以双峰方式随着标记间距离的减小而增加;从〜60 cM开始缓慢增加，从〜12 cM开始迅速增加。长期LD可能是近期种群混合的结果，该种群是“合成”繁殖种群，来自数条不同的河流。 r 2 的水平在15 cM内降至其最大值的一半（基线以上），并且在标记间距离小于5 cM时未链接的标记（“有用LD”）高于基线0.2以上。结论此处给出的连锁图是大西洋鲑的遗传，比较和物理作图的重要资源。雌性地图的地图覆盖范围可能不完整，而雄性地图的长度则可能比真实地图短得多，这是由于在发生男性交叉的明显较小的物理区域中标记覆盖率不足。在标记间距离小于5 cM处发现“有用的LD”。

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