Equine Genotyping Arrays

Robert J. Schaefer; Molly E. McCue

doi:10.1016/j.cveq.2020.03.001

Equine Genotyping Arrays

Robert J. Schaefer, Molly E. McCue

Research output: Contribution to journal › Review article › peer-review

10 Scopus citations

Abstract

High-quality genomic tools have been integral in understanding genomic architecture and function in the modern-day horse. The equine genetics community has a long tradition of pooling resources to develop genomic tools. Since the equine genome was sequenced in 2006, several iterations of high throughput genotyping arrays have been developed and released, enabling rapid and cost-effective genotyping. This review highlights the design considerations of each iteration, focusing on data available during development and outlining considerations in selecting the genetic variants included on each array. Additionally, we outline recent applications of equine genotyping arrays as well as future prospects and applications.

Original language	English (US)
Pages (from-to)	183-193
Number of pages	11
Journal	Veterinary Clinics of North America - Equine Practice
Volume	36
Issue number	2
DOIs	https://doi.org/10.1016/j.cveq.2020.03.001
State	Published - Aug 2020

Bibliographical note

Funding Information:
Development of the first-generation EquineSNP50 array (54,602 SNPs) occurred shortly after the whole genome sequencing of Twilight in 2006 (a female Thoroughbred), funded by the National Human Genome Research Institute and led by the Broad Institute. This massive Sanger sequencing project also incorporated an SNP discovery effort that resequenced 7 individuals at very low coverage, each representing different breeds (Akhal-Teke, Andalusian, Arabian, Icelandic, Quarter Horse, Standardbred, and Thoroughbred). These efforts resulted in a pool of approximately 750,000 SNPs discovered from Twilight in addition to approximately 400,000 SNPs discovered from the low coverage sequencing of the 7 additional horses. The SNP selection criteria for inclusion on the array was performed as a single step process that largely involved assigning scores to each SNP based on their ability to be converted to a reliable oligonucleotide probe for the Illumina Infinium II assay. From the pool of approximately 1.1 million candidate SNPs from Twilight and the 7 additional horses, approximately 60,000 SNPs were suitable for array design based on their ability to be converted to oligonucleotide probes.

Funding Information:
The authors would like to thank Jim Mickelson for his thoughtful input and feedback in writing this article. This work was supported by USDA NIFA project 2012-67015-19432, Minnesota Agricultural Experiment Station Multi-state project MIN-62-090 and the National Animal Genome Project (NRSP8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. The funders had no role in the preparation of this manuscript.

Funding Information:
This work was supported by USDA NIFA project 2012-67015-19432, Minnesota Agricultural Experiment Station Multi-state project MIN-62-090 and the National Animal Genome Project (NRSP8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. The funders had no role in the preparation of this manuscript.

Publisher Copyright:
© 2020 Elsevier Inc.

Keywords

Equine
GWAS
Genotyping array
Imputation
Population genomics
SNP

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title = "Equine Genotyping Arrays",

abstract = "High-quality genomic tools have been integral in understanding genomic architecture and function in the modern-day horse. The equine genetics community has a long tradition of pooling resources to develop genomic tools. Since the equine genome was sequenced in 2006, several iterations of high throughput genotyping arrays have been developed and released, enabling rapid and cost-effective genotyping. This review highlights the design considerations of each iteration, focusing on data available during development and outlining considerations in selecting the genetic variants included on each array. Additionally, we outline recent applications of equine genotyping arrays as well as future prospects and applications.",

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note = "Funding Information: Development of the first-generation EquineSNP50 array (54,602 SNPs) occurred shortly after the whole genome sequencing of Twilight in 2006 (a female Thoroughbred), funded by the National Human Genome Research Institute and led by the Broad Institute. This massive Sanger sequencing project also incorporated an SNP discovery effort that resequenced 7 individuals at very low coverage, each representing different breeds (Akhal-Teke, Andalusian, Arabian, Icelandic, Quarter Horse, Standardbred, and Thoroughbred). These efforts resulted in a pool of approximately 750,000 SNPs discovered from Twilight in addition to approximately 400,000 SNPs discovered from the low coverage sequencing of the 7 additional horses. The SNP selection criteria for inclusion on the array was performed as a single step process that largely involved assigning scores to each SNP based on their ability to be converted to a reliable oligonucleotide probe for the Illumina Infinium II assay. From the pool of approximately 1.1 million candidate SNPs from Twilight and the 7 additional horses, approximately 60,000 SNPs were suitable for array design based on their ability to be converted to oligonucleotide probes. Funding Information: The authors would like to thank Jim Mickelson for his thoughtful input and feedback in writing this article. This work was supported by USDA NIFA project 2012-67015-19432, Minnesota Agricultural Experiment Station Multi-state project MIN-62-090 and the National Animal Genome Project (NRSP8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. The funders had no role in the preparation of this manuscript. Funding Information: This work was supported by USDA NIFA project 2012-67015-19432, Minnesota Agricultural Experiment Station Multi-state project MIN-62-090 and the National Animal Genome Project (NRSP8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. The funders had no role in the preparation of this manuscript. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",

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Equine Genotyping Arrays

Abstract

Bibliographical note

Keywords

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