Whole-genome SNP association in the horse: identification of a deletion in myosin Va responsible for Lavender Foal Syndrome

Abstract

Lavender Foal Syndrome (LFS) is a lethal inherited disease of horses with a suspected autosomal recessive mode of inheritance. LFS has been primarily diagnosed in a subgroup of the Arabian breed, the Egyptian Arabian horse. The condition is characterized by multiple neurological abnormalities and a dilute coat color. Candidate genes based on comparative phenotypes in mice and humans include the ras-associated protein RAB27a (RAB27A) and myosin Va (MYO5A). Here we report mapping of the locus responsible for LFS using a small set of 36 horses segregating for LFS. These horses were genotyped using a newly available single nucleotide polymorphism (SNP) chip containing 56,402 discriminatory elements. The whole genome scan identified an associated region containing these two functional candidate genes. Exon sequencing of the MYO5A gene from an affected foal revealed a single base deletion in exon 30 that changes the reading frame and introduces a premature stop codon. A PCR-based Restriction Fragment Length Polymorphism (PCR-RFLP) assay was designed and used to investigate the frequency of the mutant gene. All affected horses tested were homozygous for this mutation. Heterozygous carriers were detected in high frequency in families segregating for this trait, and the frequency of carriers in unrelated Egyptian Arabians was 10.3%. The mapping and discovery of the LFS mutation represents the first successful use of whole-genome SNP scanning in the horse for any trait. The RFLP assay can be used to assist breeders in avoiding carrier-to-carrier matings and thus in preventing the birth of affected foals.

Figure 1. A foal with Lavender Foal Syndrome demonstrating opisthotonus, one cardinal neurological sign of the disorder.

(Photo courtesy of Dr. Yael Giora).

Figure 2. P-values (<0.05) for SNP association with Lavender Foal Syndrome.

Individual chromosomes are represented with various colors in numerical order. The region with the most significant P-values (highlighted with a yellow bar) falls on the p arm of ECA1.

Figure 3. Linkage disequilibrium plot of the homozygous region associated with LFS.

Plotted at the top are the corresponding p-values for these 27 SNPs. The yellow shaded box highlights the SNP closest to MYO5A. Red diamonds represent D' values equal to 1, lower values of D' are given in within the boxes in shades of pink to white, while non-significant associations are blue.

Figure 4. Discovery of the Lavender Foal Syndrome–associated single base deletion by sequencing.

Pictured are aligned chromatograms from horses with each of the three genotypes. The deletion occurs at the base marked with the vertical line, causing a mixed sequence from this point forward in the carrier.