A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern

Area of Science:

• Genetics
• Animal Breeding
• Molecular Biology

Background:

• White spotting, or finching, is a distinct coat phenotype observed in Pinzgauer cattle and occasionally in Tux-Zillertaler cattle.
• This spotting pattern is inherited as an autosomal incompletely dominant trait.

Purpose of the Study:

• To identify the genetic basis of the white spotting phenotype in Pinzgauer and Tux-Zillertaler cattle.
• To investigate the evolutionary history and introgression of the causative genetic variant across different cattle breeds.

Main Methods:

• Genome-wide association study (GWAS) using SNP data.
• Whole-genome sequencing of affected cattle.
• Development of a diagnostic PCR assay for genotyping.

Main Results:

• A strong association signal was detected at the KIT locus on chromosome 6.
• A complex structural variant (KIT^PINZ), involving deletion and duplication, was identified downstream of the KIT gene.
• The KIT^PINZ variant was present in Pinzgauer, most white spotted Tux-Zillertaler, and several other European cattle breeds with similar spotting patterns.

Conclusions:

• The KIT^PINZ variant is the likely cause of the observed white spotting phenotype.
• The presence of KIT^PINZ in various breeds suggests historical admixture and an ancient mutation event predating modern breed formation.