Equine recombination map updated to EquCab3.0.
Abstract: No abstract available
Publication Date: 2019-12-30 PubMed ID: 31887785PubMed Central: PMC7054148DOI: 10.1111/age.12898Google Scholar: Lookup
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- Journal Article
Summary
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The researchers updated the recombination map of the domestic horse, making it compatible with the recently completed EquCab3 reference genome assembly. This move allows thousands of specific DNA changes that could previously not be placed on equine chromosomes to be placed accurately, making the recombination map more useful for future equine genome research.
Data Collection
- The dataset used in the study comprised of Single Nucleotide Polymorphism (SNP) genotypes previously generated from 485 horses across 32 breeds.
- The genomic coordinates for these data were originally based on a previous version of the reference build (EquCab2).
- To transfer these data to the latest EquCab3, the researchers performed a procedure known as probe-based remapping which resulted in a final set of 1,820,349 biallelic SNP genotypes.
- These SNP genotypes were then phased using a computational tool known as BEAGLE.
Generating Recombination Maps
- Recombination maps were generated using a technique described in a previous study.
- 40 haplotypes (distinct sets of linked genetic variants) were sampled per chromosome, and the population recombination rates were estimated using another computational tool called LDhat.
- Breed-specific maps were also created following the same procedure for 12 individual breeds.
- Recombination hotspots (areas of the genome where recombination events occur more frequently) were predicted using LDhot.
- Finally, recombination rates were converted from population estimates to centimorgans (a unit of genetic distance) using previous estimates of effective population size.
Updated Recombination Map Data
- The updated equine genome recombination map spans 2,794.81 centimorgans over 2.41 GigaBases (total length of the DNA).
- This results in an average genome-wide recombination rate of 1.16 cM/MegaBases, which is lower than the previous estimate of 1.24 cM/Mb.
- The recombination rate across individual chromosomes is also lower in the updated map than in the previous version.
- Interestingly, the recombination hotspots, which only account for 6% of the equine genome, make up about 50.6% of the genetic map length.
- Although the total number of hotspots and their contribution to the genetic map have decreased, their mean recombination rate is 8 times the genome-wide average.
- Specific data for each breed are included in a supplemental table.
Conclusion
- The differences between the updated recombination map and the previous version likely reflect improvements in the assembly of the equine genome.
- This improved recombination map serves as a more effective resource for investigations into the structure and function of the equine genome.
Cite This Article
APA
Beeson SK, Mickelson JR, McCue ME.
(2019).
Equine recombination map updated to EquCab3.0.
Anim Genet, 51(2), 341-342.
https://doi.org/10.1111/age.12898 Publication
Researcher Affiliations
- Veterinary Population Medicine Department, 225 Veterinary Medical Center, 1365 Gortner Ave, Saint Paul, 55108, Minnesota, USA.
- Veterinary and Biomedical Sciences Department, 301 Veterinary Science Building, 1971 Commonwealth Ave, Saint Paul, Minnesota, 55108, USA.
- Veterinary Population Medicine Department, 225 Veterinary Medical Center, 1365 Gortner Ave, Saint Paul, 55108, Minnesota, USA.
MeSH Terms
- Animals
- Chromosome Mapping
- Chromosomes, Mammalian
- Horses / classification
- Horses / genetics
- Polymorphism, Single Nucleotide
- Recombination, Genetic
Grant Funding
- 5F30OD023369 / NIH Office of the Director
- F30 OD023369 / NIH HHS
- National Animal Genome Project (USDA-NRSP8)
- MIN-62-090 / Minnesota Agricultural Experiment Station
- 2012-67,015-19,432 / National Institute of Food and Agriculture
References
This article includes 8 references
- Beeson SK, Mickelson JR, McCue ME. Exploration of fine-scale recombination rate variation in the domestic horse.. Genome Res 2019 Oct;29(10):1744-1752.
- 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.
- 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.
- Kalbfleisch TS et al. (2018) Commun Biol. 1(1):1–8.
- Beeson SK, Schaefer RJ, Mason VC, McCue ME. Robust remapping of equine SNP array coordinates to Eq쪳.. Anim Genet 2019 Feb;50(1):114-115.
- Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.. Am J Hum Genet 2007 Nov;81(5):1084-97.
- Auton A, McVean G. Recombination rate estimation in the presence of hotspots.. Genome Res 2007 Aug;17(8):1219-27.
- Auton A et al. (2014). arXiv Prepr. 2014:2–4. doi:arXiv:1403.4264v1
Citations
This article has been cited 5 times.- Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023 Jul 21;26(7):107104.
- Szmatoła T, Gurgul A, Jasielczuk I, Oclon E, Ropka-Molik K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types. Animals (Basel) 2022 Nov 25;12(23).
- Patterson Rosa L, Martin K, Vierra M, Lundquist E, Foster G, Brooks SA, Lafayette C. A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus). Animals (Basel) 2022 Aug 2;12(15).
- Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024 Jul;631(8022):819-825.
- Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023 Sep 1;40(9).
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