Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or “SNP chips”, enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.

中文翻译：

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一种50 K SNP芯片的设计与应用 新西兰受威胁的新西兰雀形目hihi

下一代测序通过允许经济有效地识别全基因组变异，改变了生态和进化遗传学领域。单核苷酸多态性 (SNP) 阵列或“SNP 芯片”使大量个体能够在选定的一组这些已识别标记上进行一致的基因分型，并且还具有能够分析不同 DNA 质量的样本的优势。我们使用了 31 只受威胁的hihi ( Notiomystis cincta; stitchbird) 和其中 10 只鸟的低覆盖全基因组测序 (WGS) 以开发 Affymetrix 50 K SNP 芯片。我们通过对 10 只 WGS 鸟类中的每只进行单独和合并的从头组装，克服了没有 hihi 参考基因组和少量序列数据的局限性。来自所有个体的读取被映射回这些从头组装以识别 SNP。选择 RAD-seq 和 WGS SNP 的子集包含在芯片中，优先考虑具有最高质量分数的 SNP，其侧翼序列与斑胸草雀（Taeniopygia guttata) 基因组。在芯片上制造的 58,466 个 SNP 中，72% 通过了过滤指标并且是多态的。通过对阵列上的 1,536 hihi 进行基因分型，我们发现在多个组件中检测到的 SNP 更有可能成功进行基因分型，这代表了一种具有成本效益的方法来识别用于基因分型的 SNP。在这里，我们通过描述 hihi 基因组中连锁不平衡的高比率来证明 SNP 芯片的效用，反映了该物种种群瓶颈的历史。