FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Genomics / A human-horse comparative map based on equine BAC end sequen...
Genomics2006; 87(6); 772-776; doi: 10.1016/j.ygeno.2006.03.002

A human-horse comparative map based on equine BAC end sequences.

Abstract: In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E <or= 10(-5)) in the human genome that provide useful markers for the human-horse comparative map. The 4036 BLASTN hits allowed the anchoring of 3079 BAC clones to the human genome, on average one corresponding equine BAC clone per megabase of human DNA. We used the BLASTN anchored BESs for an in silico prediction of the gene content and chromosome assignment of comparatively mapped equine BAC clones. As a first verification of our in silico mapping strategy we placed 19 equine BESs with matches to HSA6 onto the RH map. All markers were assigned to the predicted localizations on ECA10, ECA20, and ECA31, respectively.
Get Full Text
Publication Date: 2006-04-17 PubMed ID: 16603334DOI: 10.1016/j.ygeno.2006.03.002Google 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.
LinkedInCopy
  • Comparative Study
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study aimed to enhance the availability of sequence-based markers for the horse genome, generating 9473 BAC end sequences from the CHORI-241 BAC library and successfully anchoring 3079 BAC clones to the human genome. The results also provided an in silico prediction of the gene content and chromosome assignment, proven accurate through the successful placement of 19 equine BESs with matches to HSA6 onto the RH map.

Overview of the Research

  • The objective of the research was to augment the density of sequence-based markers for the horse genome, aiming to facilitate better genetic mapping and genomic studies in horses.
  • Researchers achieved this by generating Bacterial Artificial Chromosome (BAC) end sequences – a technique used to clone DNA fragments in bacterial hosts.
  • Their strategy relied on the CHORI-241 BAC library, a rich source for generating these sequences.

Findings from the Research

  • A total of 9473 BAC end sequences (BESs) were generated with an average read length of 677 base pairs.
  • BLASTN searches – a bioinformatics algorithm used to compare primary biological sequence information – were done and meaningful hits were noted in the human genome that proved to be useful markers for comparative mapping between humans and horses.
  • Out of these, 4036 BESs could be ‘anchored’ or mapped to the human genome, enabling researchers to match one corresponding equine BAC clone for approximately every megabase of human DNA.
  • They used these anchored BESs for an in silico (computer-based) prediction of the gene content and chromosome assignment of the comparable mapped equine BAC clones.

Confirmation of the Findings

  • To verify the accuracy of the in silico mapping, researchers successfully placed 19 equine BESs with corresponding matches to the human chromosome 6 (HSA6) onto the RH map.
  • All markers were correctly assigned to their expected locations on the equine chromosomes 10, 20, and 31 (ECA10, ECA20, and ECA31, respectively).
  • This successful assignment verified the accuracy of the researchers’s in silico mapping strategy and confirmed that their technique can be used to accurately predict the location of equine genes and chromosomes based on their human counterparts.

Cite This Article

APA
Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, Blöcker H. (2006). A human-horse comparative map based on equine BAC end sequences. Genomics, 87(6), 772-776. https://doi.org/10.1016/j.ygeno.2006.03.002

Publication

Genomics
ISSN: 0888-7543
NlmUniqueID: 8800135
Country: United States
Language: English
Volume: 87
Issue: 6
Pages: 772-776

Researcher Affiliations

Leeb, Tosso
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany. Tosso.Leeb@itz.unibe.ch
Vogl, Claus
    Zhu, Baoli
      de Jong, Pieter J
        Binns, Matthew M
          Chowdhary, Bhanu P
            Scharfe, Maren
              Jarek, Michael
                Nordsiek, Gabriele
                  Schrader, Frank
                    Blöcker, Helmut

                      MeSH Terms

                      • Animals
                      • Base Sequence
                      • Chromosomes, Artificial, Bacterial / genetics
                      • DNA Primers / genetics
                      • Gene Library
                      • Genetic Markers
                      • Genome, Human
                      • Horses / genetics
                      • Humans
                      • Radiation Hybrid Mapping / methods
                      • Species Specificity

                      Citations

                      This article has been cited 22 times.
                      1. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity.. Genes (Basel) 2022 Dec 2;13(12).
                        doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
                      2. Kingsley NB, Hamilton NA, Lindgren G, Orlando L, Bailey E, Brooks S, McCue M, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. "Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare.. Front Genet 2021;12:649959.
                        doi: 10.3389/fgene.2021.649959pubmed: 33841506google scholar: lookup
                      3. Bugno-Poniewierska M, Raudsepp T. Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings.. Animals (Basel) 2021 Mar 16;11(3).
                        doi: 10.3390/ani11030831pubmed: 33809432google scholar: lookup
                      4. 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
                      5. Roberti A, Bensi M, Mazzagatti A, Piras FM, Nergadze SG, Giulotto E, Raimondi E. Satellite DNA at the Centromere is Dispensable for Segregation Fidelity.. Genes (Basel) 2019 Jun 20;10(6).
                        doi: 10.3390/genes10060469pubmed: 31226862google scholar: lookup
                      6. Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F, McCarter JGW, Cappelletti E, Gozzo F, Harman RM, Antczak DF, Miller D, Scharfe M, Pavesi G, Raimondi E, Sullivan KF, Giulotto E. Birth, evolution, and transmission of satellite-free mammalian centromeric domains.. Genome Res 2018 Jun;28(6):789-799.
                        doi: 10.1101/gr.231159.117pubmed: 29712753google scholar: lookup
                      7. Purgato S, Belloni E, Piras FM, Zoli M, Badiale C, Cerutti F, Mazzagatti A, Perini G, Della Valle G, Nergadze SG, Sullivan KF, Raimondi E, Rocchi M, Giulotto E. Centromere sliding on a mammalian chromosome.. Chromosoma 2015 Jun;124(2):277-87.
                        doi: 10.1007/s00412-014-0493-6pubmed: 25413176google scholar: lookup
                      8. Finno CJ, Bannasch DL. Applied equine genetics.. Equine Vet J 2014 Sep;46(5):538-44.
                        doi: 10.1111/evj.12294pubmed: 24802051google scholar: lookup
                      9. Jiang Y, Gao X, Liu S, Zhang Y, Liu H, Sun F, Bao L, Waldbieser G, Liu Z. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.. BMC Genomics 2013 Nov 11;14:780.
                        doi: 10.1186/1471-2164-14-780pubmed: 24215161google scholar: lookup
                      10. Detournay O, Morrison DA, Wagner B, Zarnegar B, Wattrang E. Genomic analysis and mRNA expression of equine type I interferon genes.. J Interferon Cytokine Res 2013 Dec;33(12):746-59.
                        doi: 10.1089/jir.2012.0130pubmed: 23772953google scholar: lookup
                      11. Zhang Y, Liu S, Lu J, Jiang Y, Gao X, Ninwichian P, Li C, Waldbieser G, Liu Z. Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements.. BMC Genomics 2013 Jun 10;14:387.
                        doi: 10.1186/1471-2164-14-387pubmed: 23758806google scholar: lookup
                      12. Liu C, Guo Y, Lu T, Wu H, Na R, Li X, Guan W, Ma Y. Construction and preliminary characterization analysis of Wuzhishan miniature pig bacterial artificial chromosome library with approximately 8-fold genome equivalent coverage.. Biomed Res Int 2013;2013:587493.
                        doi: 10.1155/2013/587493pubmed: 23691508google scholar: lookup
                      13. Musilova P, Kubickova S, Vahala J, Rubes J. Subchromosomal karyotype evolution in Equidae.. Chromosome Res 2013 Apr;21(2):175-87.
                        doi: 10.1007/s10577-013-9346-zpubmed: 23532666google scholar: lookup
                      14. Anistoroaei R, ten Hallers B, Nefedov M, Christensen K, de Jong P. Construction of an American mink bacterial artificial chromosome (BAC) library and sequencing candidate genes important for the fur industry.. BMC Genomics 2011 Jul 8;12:354.
                        doi: 10.1186/1471-2164-12-354pubmed: 21740547google scholar: lookup
                      15. Li Y, Xu P, Zhao Z, Wang J, Zhang Y, Sun XW. Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio.. Mar Biotechnol (NY) 2011 Aug;13(4):706-12.
                        doi: 10.1007/s10126-010-9332-9pubmed: 21088980google scholar: lookup
                      16. Liu H, Jiang Y, Wang S, Ninwichian P, Somridhivej B, Xu P, Abernathy J, Kucuktas H, Liu Z. Comparative analysis of catfish BAC end sequences with the zebrafish genome.. BMC Genomics 2009 Dec 10;10:592.
                        doi: 10.1186/1471-2164-10-592pubmed: 20003258google scholar: lookup
                      17. Raudsepp T, Gustafson-Seabury A, Durkin K, Wagner ML, Goh G, Seabury CM, Brinkmeyer-Langford C, Lee EJ, Agarwala R, Stallknecht-Rice E, Schäffer AA, Skow LC, Tozaki T, Yasue H, Penedo MC, Lyons LA, Khazanehdari KA, Binns MM, MacLeod JN, Distl O, Guérin G, Leeb T, Mickelson JR, Chowdhary BP. A 4,103 marker integrated physical and comparative map of the horse genome.. Cytogenet Genome Res 2008;122(1):28-36.
                        doi: 10.1159/000151313pubmed: 18931483google scholar: lookup
                      18. Chowdhary BP, Raudsepp T. The horse genome derby: racing from map to whole genome sequence.. Chromosome Res 2008;16(1):109-27.
                        doi: 10.1007/s10577-008-1204-zpubmed: 18274866google scholar: lookup
                      19. Wu X, Zhong G, Findley SD, Cregan P, Stacey G, Nguyen HT. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map.. BMC Genomics 2008 Jan 22;9:28.
                        doi: 10.1186/1471-2164-9-28pubmed: 18211698google scholar: lookup
                      20. Haase B, Brooks SA, Schlumbaum A, Azor PJ, Bailey E, Alaeddine F, Mevissen M, Burger D, Poncet PA, Rieder S, Leeb T. Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.. PLoS Genet 2007 Nov;3(11):e195.
                        doi: 10.1371/journal.pgen.0030195pubmed: 17997609google scholar: lookup
                      21. Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O'Grady M, Nicholas F, Crawford AM, Smith T, de Jong PJ, McEwan J, Oddy VH, Cockett NE. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.. Genome Biol 2007;8(7):R152.
                        doi: 10.1186/gb-2007-8-7-r152pubmed: 17663790google scholar: lookup
                      22. Tozaki T, Hirota K, Hasegawa T, Ishida N, Tobe T. Whole-genome linkage disequilibrium screening for complex traits in horses.. Mol Genet Genomics 2007 Jun;277(6):663-72.
                        doi: 10.1007/s00438-007-0216-2pubmed: 17318585google scholar: lookup
                      Subscribe to our newsletter
                      Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.