Pavy Nathalie, Pelgas Betty, Beauseigle Stéphanie, Blais Sylvie, Gagnon France, Gosselin Isabelle, Lamothe Manuel, Isabel Nathalie, Bousquet Jean
Arborea and Canada Research Chair in Forest and Environmental Genomics, Centre d'Etude de la Forêt, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Québec G1V 0A6, Canada.
BMC Genomics. 2008 Jan 18;9:21. doi: 10.1186/1471-2164-9-21.
To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.).
Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity.
The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers.
为了探索高通量基因分型检测在大型复杂基因组分析中的潜在价值，我们使用GoldenGate SNP检测法设计了两种高度多重的Illumina微珠芯片，用于白云杉（Picea glauca [Moench] Voss）和黑云杉（Picea mariana [Mill.] B.S.P.）的基因定位。
每个芯片包含768个单核苷酸多态性（SNP），这些SNP通过对每个作图群体亲本的基因组DNA进行重测序来确定。对于白云杉和黑云杉，分别有69.2%和77.1%的基因分型SNP具有有效的GoldenGate检测分数，并在作图群体中分离。对于这些成功的SNP中的每一个，平均有超过99%的后代获得了有效的基因分型分数。将SNP数据与现有的扩增片段长度多态性（AFLP）、表达序列标签多态性（ESTP）和简单序列重复（SSR）标记整合，构建了白云杉和黑云杉基因组的两个单独的连锁图谱和一个复合图谱。白云杉复合图谱包含821个标记，其中包括348个基因位点。此外，835个标记，包括328个基因位点，定位在黑云杉复合图谱上。两个物种之间总共共享215个锚定标记（主要是基因标记）。考虑到这两种云杉至少在1000万年前的谱系分化，同源连锁群的种间比较显示出显著的共线性和标记共线性。
定制的高度多重Illumina SNP芯片的设计似乎是一种有效的方法，可以加强表达基因的定位，并使连锁图谱在这类基因组了解较少的物种中更具信息性和强大功能。这种基因分型方法将为针叶树中候选基因和数量性状位点（QTL）的共定位、部分基因组测序以及比较作图开辟新途径。
