Analyze Diet
Animal genetics2018; 50(1); 114-115; doi: 10.1111/age.12745

Robust remapping of equine SNP array coordinates to EquCab3.

Abstract: No abstract available
Publication Date: 2018-11-13 PubMed ID: 30421446PubMed Central: PMC6349531DOI: 10.1111/age.12745Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
  • Journal Article

Cite This Article

APA
Beeson SK, Schaefer RJ, Mason VC, McCue ME. (2018). Robust remapping of equine SNP array coordinates to EquCab3. Anim Genet, 50(1), 114-115. https://doi.org/10.1111/age.12745

Publication

ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 50
Issue: 1
Pages: 114-115

Researcher Affiliations

Beeson, Samantha K
  • Veterinary Population Medicine Department, 225 Veterinary Medical Center, 1365 Gortner Avenue, Saint Paul, MN, 55108, USA.
Schaefer, Robert J
  • Veterinary Population Medicine Department, 225 Veterinary Medical Center, 1365 Gortner Avenue, Saint Paul, MN, 55108, USA.
Mason, Victor C
  • Institute of Genetics, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.
McCue, Molly E
  • Veterinary Population Medicine Department, 225 Veterinary Medical Center, 1365 Gortner Avenue, Saint Paul, MN, 55108, USA.

MeSH Terms

  • Animals
  • Chromosome Mapping / veterinary
  • Genotyping Techniques / veterinary
  • Horses / genetics
  • Polymorphism, Single Nucleotide

Grant Funding

  • 5F30OD023369 / NIH NRSA
  • F30 OD023369 / NIH HHS
  • 2017-67015-26296 / USDA NIFA project
  • ISME (Swiss Institute of Equine Medicine) Research Group
  • MIN-62-090 / Minnesota Agricultural Experiment Station Multistate project

References

This article includes 7 references
  1. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
  2. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.. BMC Genomics 2017 Jul 27;18(1):565.
    pmc: PMC5530493pubmed: 28750625doi: 10.1186/s12864-017-3943-8google scholar: lookup
  3. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
    pmc: PMC3785132pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
  4. Kalbfleisch TS et al. (2018). BioRxiv 306928 [Preprint]. doi:10.1101/306928
    doi: 10.1101/306928google scholar: lookup
  5. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006.. Nucleic Acids Res 2006 Jan 1;34(Database issue):D590-8.
    pmc: PMC1347506pubmed: 16381938doi: 10.1093/nar/gkj144google scholar: lookup
  6. Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies.. Bioinformatics 2014 Apr 1;30(7):1006-7.
  7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool.. J Mol Biol 1990 Oct 5;215(3):403-10.
    pubmed: 2231712doi: 10.1016/s0022-2836(05)80360-2google scholar: lookup

Citations

This article has been cited 14 times.
  1. Peng S, Magdesian KG, Dowd J, Blea J, Carpenter R, Ho W, Finno CJ. Investigation of high gamma-glutamyltransferase syndrome in California Thoroughbred racehorses.. J Vet Intern Med 2022 Nov;36(6):2203-2212.
    doi: 10.1111/jvim.16582pubmed: 36377652google scholar: lookup
  2. Colpitts J, McLoughlin PD, Poissant J. Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds.. BMC Genomics 2022 Jul 12;23(1):501.
    doi: 10.1186/s12864-022-08729-9pubmed: 35820826google scholar: lookup
  3. Criscione A, Mastrangelo S, D'Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S. Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern.. J Anim Breed Genet 2022 Sep;139(5):540-555.
    doi: 10.1111/jbg.12680pubmed: 35445758google scholar: lookup
  4. Laseca N, Molina A, Ramón M, Valera M, Azcona F, Encina A, Demyda-Peyrás S. Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares.. Front Vet Sci 2022;9:754028.
    doi: 10.3389/fvets.2022.754028pubmed: 35252415google scholar: lookup
  5. Santos WB, Schettini GP, Maiorano AM, Bussiman FO, Balieiro JCC, Ferraz GC, Pereira GL, Baldassini WA, Neto ORM, Oliveira HN, Curi RA. Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping.. BMC Genomics 2021 Oct 14;22(1):737.
    doi: 10.1186/s12864-021-08053-8pubmed: 34645387google scholar: lookup
  6. Hisey EA, Hermans H, Lounsberry ZT, Avila F, Grahn RA, Knickelbein KE, Duward-Akhurst SA, McCue ME, Kalbfleisch TS, Lassaline ME, Back W, Bellone RR. Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses.. BMC Genomics 2020 Nov 30;21(1):848.
    doi: 10.1186/s12864-020-07265-8pubmed: 33256610google scholar: lookup
  7. Mancin E, Ablondi M, Mantovani R, Pigozzi G, Sabbioni A, Sartori C. Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information.. Animals (Basel) 2020 Jul 30;10(8).
    doi: 10.3390/ani10081310pubmed: 32751586google scholar: lookup
  8. Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data.. Animals (Basel) 2020 Jun 8;10(6).
    doi: 10.3390/ani10061005pubmed: 32521830google scholar: lookup
  9. Hales EN, Esparza C, Peng S, Dahlgren AR, Peterson JM, Miller AD, Finno CJ. Genome-Wide Association Study and Subsequent Exclusion of ATCAY as a Candidate Gene Involved in Equine Neuroaxonal Dystrophy Using Two Animal Models.. Genes (Basel) 2020 Jan 10;11(1).
    doi: 10.3390/genes11010082pubmed: 31936863google scholar: lookup
  10. Beeson SK, Mickelson JR, McCue ME. Equine recombination map updated to Eq쪳.0.. Anim Genet 2020 Mar;51(2):341-342.
    doi: 10.1111/age.12898pubmed: 31887785google scholar: lookup
  11. Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines.. Genes (Basel) 2019 Nov 27;10(12).
    doi: 10.3390/genes10120976pubmed: 31783652google scholar: lookup
  12. Norton E, Schultz N, Geor R, McFarlane D, Mickelson J, McCue M. Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses.. Genes (Basel) 2019 Nov 6;10(11).
    doi: 10.3390/genes10110893pubmed: 31698676google scholar: lookup
  13. Tanaka J, Leeb T, Rushton J, Famula TR, Mack M, Jagannathan V, Flury C, Bachmann I, Eberth J, McDonnell SM, Penedo MCT, Bellone RR. Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies.. Genes (Basel) 2019 Oct 19;10(10).
    doi: 10.3390/genes10100826pubmed: 31635058google scholar: lookup
  14. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup