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.