Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.
KAUST Grant NumberKUS-C1-016-04
MetadataShow full item record
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.
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.
SponsorsWe 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).
PubMed Central IDPMC3309927
CollectionsPublications Acknowledging KAUST Support
Except where otherwise noted, this item's license is described as This 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.
- Applied equine genetics.
- Authors: Finno CJ, Bannasch DL
- Issue date: 2014 Sep
- Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity.
- Authors: Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, Khen M, Stütz AM, Schlattl A, Lancet D, Korbel JO
- Issue date: 2010 Nov 11
- Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery.
- Authors: Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS
- Issue date: 2011 Nov 15
- Genome-wide patterns of genetic variation in two domestic chickens.
- Authors: Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH
- Issue date: 2013
- Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.
- Authors: Kim RN, Kim DS, Choi SH, Yoon BH, Kang A, Nam SH, Kim DW, Kim JJ, Ha JH, Toyoda A, Fujiyama A, Kim A, Kim MY, Park KH, Lee KS, Park HS
- Issue date: 2012 Jun