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

Handle URI:
http://hdl.handle.net/10754/596832
Title:
Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.
Authors:
Doan, Ryan; Cohen, Noah D; Sawyer, Jason; Ghaffari, Noushin; Johnson, Charlie D; Dindot, Scott V
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.
Citation:
Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, et al. (2012) Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare. BMC Genomics 13: 78. Available: http://dx.doi.org/10.1186/1471-2164-13-78.
Publisher:
Springer Nature
Journal:
BMC Genomics
KAUST Grant Number:
KUS-C1-016-04
Issue Date:
17-Feb-2012
DOI:
10.1186/1471-2164-13-78
PubMed ID:
22340285
PubMed Central ID:
PMC3309927
Type:
Article
ISSN:
1471-2164
Sponsors:
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).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorDoan, Ryanen
dc.contributor.authorCohen, Noah Den
dc.contributor.authorSawyer, Jasonen
dc.contributor.authorGhaffari, Noushinen
dc.contributor.authorJohnson, Charlie Den
dc.contributor.authorDindot, Scott Ven
dc.date.accessioned2016-02-21T08:51:31Zen
dc.date.available2016-02-21T08:51:31Zen
dc.date.issued2012-02-17en
dc.identifier.citationDoan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, et al. (2012) Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare. BMC Genomics 13: 78. Available: http://dx.doi.org/10.1186/1471-2164-13-78.en
dc.identifier.issn1471-2164en
dc.identifier.pmid22340285en
dc.identifier.doi10.1186/1471-2164-13-78en
dc.identifier.urihttp://hdl.handle.net/10754/596832en
dc.description.abstractBACKGROUND: 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.en
dc.description.sponsorshipWe 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).en
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subject.meshSequence Analysis, DNAen
dc.subject.meshPolymorphism, Single Nucleotideen
dc.subject.meshGenomeen
dc.titleWhole-genome sequencing and genetic variant analysis of a Quarter Horse mare.en
dc.typeArticleen
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC3309927en
dc.contributor.institutionTexas A and M University, College Station, United Statesen
dc.contributor.institutionTexas A and M University, College Station, United Statesen
dc.contributor.institutionTexas AgriLife Research Center, El Paso, United Statesen
dc.contributor.institutionTexas A and M University, College Station, United Statesen
dc.contributor.institutionAgriLife Genomics and Bioinformatics Center, College Station, United Statesen
dc.contributor.institutionTexas A&M Health Science Center, College of Medicine, College Station, United Statesen
kaust.grant.numberKUS-C1-016-04en

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