The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip.

This research looked at identifying potential inaccurately placed single nucleotide polymorphisms (SNPs) on the genome map of 1201 Thoroughbred horses using the Illumina Equine SNP50 BeadChip. The misplacement of these SNPs could cause problems in applying genomic methods that rely on SNP order.

Linkage Disequilibrium and Illumina Equine SNP50 BeadChip

• The research utilized Linkage Disequilibrium (LD), a measure of the non-random association of alleles at different loci, to scrutinize the SNPs on the genome map identified by Illumina Equine SNP50 BeadChip. The chip is an equine-specific, highly multiplexed, genome-wide SNP genotyping tool.
• The LD was assessed in a pairwise fashion among all autosomal SNPs, studying both within chromosomes and across different chromosomes.

Identification of Misplaced SNPs

• Applying filters to the data helped in identifying the SNPs that might have been wrongly mapped. Filters included looking for SNPs that may have been assigned to the incorrect chromosome and SNPs incorrectly positioned within chromosomes.
• The researchers discovered one SNP on ECA28 displaying low LD with nearby SNPs but considerable LD with a set of SNPs on ECA10. This suggests it may have been misplaced within the genome map.
• Apart from this, a cluster of SNPs on ECA5 demonstrated uncommonly low LD with surrounding SNPs.
• Overall, 39 SNPs met the criteria set for unusual LD within chromosomes, potentially pointing towards their misplacement.

Significance of Findings

• Misplaced SNPs can create obstacles in applying genomic methods, such as homozygosity mapping wherein the accurate placement of SNPs is crucial for identifying regions in the genome where individuals are homozygous.
• These findings will help to refine the genome map of Thoroughbred horses and could contribute to the accuracy of future genomic analyses.