It’s all in the genes: Mutation responsible for filly’s unexpected coloring

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Lucy's coloring has been attributed to a missense mutation in the KIT gene.
Lucy’s coloring has been attributed to a missense mutation in the KIT gene. © Wai Eyre Farm/UC Davis

Scientists in the US have determined that the coloring of an unusually marked standardbred foal in New Zealand was not inherited from her sire or dam but instead occurred as a missense mutation during development.

The standardbred filly was born at Wai Eyre Farm in Canterbury with a sabino-like white spotting pattern. She was tested for parentage through Harness Racing New Zealand by InfogeneNZ at Massey University, which confirmed her pedigree. InfogeneNZ then recommended coat color testing at the Veterinary Genetics Laboratory (VGL) at the UC Davis School of Veterinary Medicine to determine the cause of white patterning.

The breed’s most common coat color is bay, but they can also be born with black, chestnut, or gray coats. There are also skewbald lines in the breed.

The filly has not yet been officially named, but her paddock name is Lucy. She is by Sky Major, a bay stallion, and out of Myex, who is registered as black.

The researchers found that the cause of the coloring was a “de novo” missense mutation in the KIT gene. “De novo” means a change in DNA arising in the individual and not inherited from the parents.

She is the third “de novo” white coat color variant identified in Standardbreds. The first was found in 2017 in an American standardbred, and the second in 2017 in an Italian trotter.

A brief report on the filly by Elizabeth Esdaile and colleagues has appeared in the journal Animal Genetics.

Lucy is by Sky Major and from the Armbro Operative mare Myex.
Lucy is by Sky Major and from the Armbro Operative mare Myex. © Wai Eyre Farm/UC Davis

This coat color can be selected for in subsequent generations, said VGL director Dr Rebecca Bellone, who was part of the study team. VGL intends to track the generational lineage of the filly’s novel coat color, should she be bred.

“Discovering a de novo mutation is always exciting as most of the time as geneticists we are trying to trace the history of genetic variation, not identifying the variation in the generation in which they occur,” Bellone said.

“This discovery shows how breeding remains relevant today for helping us to understand the way that mutations occur and their effects on the living world.”

VGL, which conducts scientific research and also provides commercial genetic analysis services, has unique expertise and technology to determine the novel origin of the filly’s coat.

The laboratory partnered with InfogeneNZ to confirm parentage, using the International Society for Animal Genetics primary and backup panels. VGL then conducted genetic analysis using allele-specific PCR with products resolved on the Applied Biosystems 3730XL DNA Analyzer (Thermo Fisher Scientific), a custom-designed MassARRAY genotyping assay (Agena Bioscience), and Ion Torrent S5 amplicon sequencing (Thermo Fishier Scientific) to investigate known mutations. Ultimately, the Ion Torrent S5 amplicon sequencing experiment is what allowed for the discovery of the novel variant.

Earlier article: Gene mutation behind splashed white pattern found

Reporting: Liza Gershony

A de novo missense mutation in KIT is responsible for dominant white spotting phenotype in a Standardbred horse. Elizabeth Esdaile, Brad Till, Angelica Kallenberg, Michelle Fremeux, Leslie Bickel, Rebecca R. Bellone. https://doi.org/10.1111/age.13222

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