Annotating the Equine Genome

Researchers are taking the next step and asking questions about the information the equine genome contains.


The Thoroughbred mare Twilight, whose DNA served as the basis for sequencing the horse genome, achieved world fame in 2009 when an international team of researchers published a paper in the journal Science analyzing her DNA. Determining the whole horse genome sequence was a major leap forward in equine genetics. Now, Matthew S. Hestand, a postdoctoral scholar at the University of Kentucky, is taking the next step and asking about the information the genome contains.

Hestand's research focus is transcriptomics (RNA products of genes that provide templates for cells to synthesize proteins) based on next-generation sequencing of protein-coding RNA, under the supervision of James MacLeod, VMD, PhD, professor of veterinary science at the Gluck Equine Research Center. Hestand's research has continued efforts in MacLeod's lab to identify and characterize gene structures within the horse genome sequence, as well as look for differences in the genome that are found across different horses.

"To put it simply, you can think of the horse genome as a large toolbox full of tools and additional filler," Hestand said. "At first glance, the box is a mess of tools and other items, with the initial challenging step being to identify each individual tool, or gene in our case, from the pile. We found nearly 67,000 structures, some of which represent different structures for the same gene.

"Once we can separate out a tool, we can then look at its shape and begin to learn about its function," he continued. "There may be some genes that exist in multiple copies with small differences between them. These can be viewed as multiple screwdrivers that also have slight differences and hence slightly different performance such as a flathead versus a Phillips screwdriver, to remain in the toolbox analogy."

Hestand said that with new technology that has become available, researchers can now base these structures on evidence using current advanced DNA sequencing technologies. "Originally, most of the gene structures in the equine genome were based on predictions," he explained. "The new experimental data confirms and refines these predictions, while also providing evidence to support 'new' genes in the horse."

Hestand and colleagues identified 488 genes in horses that were similar to those found in dogs, cows, and humans, but were not found in Twilight's genome.

According to Hestand, identifying these gene structures is the first step in characterizing a gene and its function. Variations between horses also provide a list of changes in the genomic alphabet that likely have some phenotypic (physical expression of a genetic trait) affect.

"In our current study we also found approximately 140,000 small changes in the genome, a small subset of which may affect how a gene performs," he said. "This concept can be illustrated by established examples like some of the genes that control coat color, where one variation of a gene might control for a chestnut color and another variation might control for a black color."

As the catalog of gene structures and variations refines and expands, researchers will have an updated reference to identify changes across many different animals that contribute to their appearance, performance, disease, disease resistance, etc., Hestand concluded.

Those involved in this project and their affiliations:

  • Matthew S. Hestand, Stephen J. Coleman, and James N. MacLeod VMD, PhD, Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky
  • Ted Kalbfleisch, PhD, Biochemistry and Molecular Biology Department, School of Medicine, University of Louisville
  • Zheng Zeng and Jinze Liu, PhD, Department of Computer Science, University of Kentucky

Shaila Sigsgaard is a contributing writer for the Bluegrass Equine Digest.

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