Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).
Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).
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DOI：
10.1186/1471-2164-15-90
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发表时间：
2014-02-06
期刊：
影响因子：
4.4
通讯作者：
Hamilton A
中科院分区：
文献类型：
--
作者：
Houston RD;Taggart JB;Cézard T;Bekaert M;Lowe NR;Downing A;Talbot R;Bishop SC;Archibald AL;Bron JE;Penman DJ;Davassi A;Brew F;Tinch AE;Gharbi K;Hamilton A
密集单核苷酸多态(SNP)基因分型阵列提供了有关感兴趣物种基因组的多态变异的广泛信息。这些信息可用于研究数量性状的遗传结构，并在育种计划中提高选择的准确性。在大西洋鲑鱼(Salmo Salar)中，这些目标目前因缺乏高密度SNP基因分型平台而受阻。因此，这项研究的目的是开发和测试密集的大西洋鲑鱼SNP阵列。通过对来自养殖和野生大西洋鲑鱼样品(n=283)的简化表示(RR-Seq)、限制位点相关DNA(RAD-Seq)和信使核糖核酸(RNA-Seq)文库进行广泛的深度测序，发现了>；400K的SNP。我们创建了Affymetrix Axiom®myDesign定制阵列，并在野生和养殖动物样本(n=96)上进行了测试，在我们的样本中总共发现了132,033个多态SNPs，具有高呼叫率、良好的簇分离和稳定的孟德尔遗传。这些SNP中至少有38%来自转录的基因组区域，因此更有可能包括功能变异。利用鲑鱼缺乏雄性重组的连锁分析，可以绘制分布在所有29对染色体上的40,214个SNPs，突出了SNPs在全基因组范围内的广泛覆盖。逐个州的身份聚类分析表明，该阵列可以清楚地区分不同来源的鱼，以及养殖和野生种群之间的鱼。最后，阵列上包含的Y染色体特异探针为性别提供了准确的分子遗传学测试。这篇手稿描述了第一个用于大西洋鲑鱼的高密度SNP基因分型阵列。该阵列将公开提供，并可能被用作高分辨率遗传学研究的平台，以研究鲑科动物具有进化和经济重要性的特征，并通过基因组选择在水产养殖育种计划中使用。
Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
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作者：
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通讯作者：
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Houston RD;Davey JW;Bishop SC;Lowe NR;Mota-Velasco JC;Hamilton A;Guy DR;Tinch AE;Thomson ML;Blaxter ML;Gharbi K;Bron JE;Taggart JB
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