A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers.
A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers.
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DOI：
10.1186/1471-2164-9-223
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发表时间：
2008-05-15
期刊：
影响因子：
4.4
通讯作者：
Lien, Sigbjorn
中科院分区：
文献类型：
--
作者：
Moen, Thomas;Hayes, Ben;Baranski, Matthew;Berg, Paul R.;Kjoglum, Sissel;Koop, Ben F.;Davidson, Willie S.;Omholt, Stig W.;Lien, Sigbjorn
大西洋鲑鱼是一种具有商业和生态意义的物种。与其他鲑科鱼类一样，该物种显示出残留的四体和性别间较大的重组率差异。基因组学的进步需要包含I型和II型标记的全基因组覆盖的连锁图谱。此外，估计物种中的连锁不平衡(LD)水平也很重要。在本研究中，我们开发了数百个大西洋鲑鱼的单核苷酸多态(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谱。我们还进一步研究了男性和女性重组事件在整个基因组中的分布，并估计了标记对之间的LD水平。雄性图谱有29个连锁群，全长390 cM。雌性图谱有30个连锁群，长达1983 cM。总体而言，这些图谱包含138个微卫星标记和304个位于基因内的SNP，其中大多数都被成功地注释。雄性和雌性重组事件的比率要么接近于零，要么非常大，这表明发生雄性和雌性交叉的区域之间几乎没有重叠。雌性图谱可能接近全基因组覆盖，而大多数雄性连锁群可能在发生雄性重组事件的端粒区域缺乏标记。R2水平随标记间距离的减小呈双峰增加，从~60 cM开始缓慢增加，从~12 cM开始增加较快。长期的LD可能是最近种群混合的结果，种群是一个来自几条不同河流的“合成”繁殖种群。在标记间距离小于5 cM时，R2水平在15 cM内降至最大值(高于基线)的一半，而对于非连锁标记(‘有用LD’)则高于基线0.2。本文提供的连锁图谱是进行大西洋鲑鱼遗传、比较和物理图谱绘制的重要资源。雌性地图的地图覆盖率可能并不是很完整，而男性地图的长度可能比真正的地图短得多，这是因为发生雄性交叉的明显较小的物理区域的标记覆盖率不是最优的。在标记间距离小于5 cM处发现了‘有用的LD’。
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. 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. 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.
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影响因子：
2.9
作者：
Moen T;Sonesson AK;Hayes B;Lien S;Munck H;Meuwissen TH
通讯作者：
Meuwissen TH
影响因子：
4.5
作者：
GJEDREM, T;GJOEN, HM;GJERDE, B
通讯作者：
GJERDE, B
影响因子：
1.6
作者：
HARTLEY, SE;HORNE, MT
通讯作者：
HORNE, MT
影响因子：
5.8
作者：
Hayes, Ben J.;Nilsen, Kjetil;Lien, Sigbjorn
通讯作者：
Lien, Sigbjorn
影响因子：
3.1
作者：
Danzmann, RG;Cairney, M;Woram, RA
通讯作者：
Woram, RA