SNP fine-mapping by assessment of linked molecular markers in the UCD-Coloboma.003 genetic line resulted in a reduction in the size of the causative region.

Samples were assessed for their 60 K SNP genotyping pattern to identify recombination events thereby reducing the size of the linked region. Genotypes in bold, italics indicate a region which is no longer linked to the coloboma mutation in the particular sample. This region decreased due to recombination and replacement with wildtype (UCD-003) sequence.ASamples genotyped with Illumina 60 K SNP array [4].BA total of 197 mutant embryos were collected following the 60 K SNP analysis [4] and these were genotyped using the ten 60 K informative SNPs (Table S1). Two samples, co-275F and co-276F (superscripts H and G, respectively), were utilized in the CA/NGS technology [32]. Note that co-275F has a minimum and maximum causative region (CRmin and CRmax) of 494,598 and 994,599 bp, respectively.CA total of 66 heterozygous chicks were hatched post-60 K SNP analysis and were genotyped using the ten 60 K SNPs (Table S1); only three chicks exhibited evidence of recombination events.DOverall reduced SNP genotype profile based upon compiled genotyping results from both the mutant and heterozygous samples.ESNP genotype observed in normal, control samples.FNumber of samples analyzed which display each genotype.GGenotype of sample co-276F, a sample used in the capture array technology.HGenotype of sample co-275F, a sample used in the capture array technology, which shows a significantly reduced linked region.IChromosomal coordinate (bp) of SNP on GGA Z; positions are based on the November 2011 Gallus gallus assembly (galGal4).JMinimum and maximum causative region (candidate gene region) identified for each unique SNP genotype.研究对所有样本的60K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型模式进行评估，以识别重组事件，从而缩小连锁区域的规模。以粗体、斜体标注的基因型，代表该样本中不再与脉络膜缺损（coloboma）突变连锁的区域。该区域因重组事件以及野生型（UCD-003）序列的替换而发生缩减。 A 采用Illumina 60K SNP芯片完成基因分型的样本[4]。 B 经60K SNP分析后共收集到197枚突变胚胎[4]，并使用10个信息性60K SNP对其进行基因分型（补充表S1）。选取样本co-275F与co-276F（分别标注上标H与G）用于捕获阵列（Capture Array, CA）/下一代测序（Next-Generation Sequencing, NGS）技术分析[32]。需说明的是，样本co-275F的最小致病区域（CRmin）与最大致病区域（CRmax）分别为494598 bp与994599 bp。 C 经60K SNP分析后共孵化出66只杂合子雏鸡，使用10个60K SNP完成基因分型（补充表S1）；其中仅3只雏鸡检测到重组事件。 D 整合突变样本与杂合子样本的基因分型结果后得到的简化SNP基因型图谱。 E 正常对照样本中检测到的SNP基因型。 F 显示各基因型的分析样本数量。 G 样本co-276F的基因型，该样本被用于捕获阵列技术分析。 H 样本co-275F的基因型，该样本被用于捕获阵列技术分析，其连锁区域出现显著缩减。 I 鸡Z染色体（GGA Z）上SNP的染色体坐标（bp），坐标基于2011年11月发布的家鸡基因组组装版本（galGal4）。 J 针对各独特SNP基因型所确定的最小与最大致病区域（候选基因区域）。