Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1,878,727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions; 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10,000 SNPs were selected for the construction of a 12k Infinium BeadChip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5 to 7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

本研究针对覆盖西欧全境的51株欧洲黑杨（Populus nigra L.）个体开展全基因组重测序，测序采用Illumina平台。共计在欧洲黑杨参考基因组序列上鉴定得到1,878,727个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP）。SNP分型的准确性通过桑格测序得以验证。研究人员从三类区域中筛选SNP位点：14个已报道的数量性状基因座（Quantitative Trait Locus, QTL）区域、2916个与锈病抗性、木材性状、水分利用效率及芽物候相关的表达候选基因区域，以及全基因组随机分布的1732个基因区域。最终筛选得到超过10,000个SNP位点，用于构建专为关联作图设计的12k Infinium BeadChip基因分型芯片。使用该芯片对888株欧洲黑杨个体开展SNP基因分型实验，分型成功率达91%。本次高成功率得益于SNP发现面板的合理设计，以及SNP识别与筛选过程中采用的严格参数。在同一套欧洲黑杨基因型材料中，全基因组连锁不平衡（Linkage Disequilibrium, LD）平均在5至7kb范围内衰减至最大值的一半。作为应用验证，研究人员选取全基因组分布的600个SNP位点，以及采自12个流域的706个个体开展ADMIXTURE群体结构分析，所得群体遗传结构模式与中性标记揭示的遗传多样性及种群地理分布格局高度一致。本研究开发的新型SNP资源与基因分型芯片，可为欧洲黑杨的群体遗传学研究，以及基于自然种群的遗传关联分析以鉴定数量性状基因座提供极具价值的研究工具。