Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charlie D Johnson, Scott V Dindot

Research output: Contribution to journalArticlepeer-review

51 Scopus citations

Abstract

BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.
Original languageEnglish (US)
Pages (from-to)78
JournalBMC Genomics
Volume13
Issue number1
DOIs
StatePublished - Feb 17 2012
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUS-C1-016-04
Acknowledgements: We thank Sam Wigington at Texas A&M University, College of Veterinary Medicine and Biomedical Sciences for identification of the mare whose genome we sequenced. Funding for this study was provided by Texas AgriLife Research; the GW & G Pool Large Animal Hospital Endowment at the Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences; the Department of Animal Science; and the Link Equine Research Endowment, Texas A&M University. This publication is based in part on work supported by Award No. KUS-C1-016-04, made by King Abdullah University of Science and Technology (KAUST).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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