Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Wallner, Barbara ^a   Vogl, Claus ^a   Shukla, Priyank ^a   Burgstaller, Joerg P ^a   Druml, Thomas ^a   Brem, Gottfried ^a  

^a UNIVERSITY OF VETERINARY MEDICINE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MITOCHONDRIAL DNA;

ANIMAL TISSUE; ARTICLE; CHROMOSOMAL LOCALIZATION; CHROMOSOME ANALYSIS; CHROMOSOME IDENTIFICATION; CHROMOSOME VARIANT; CONTROLLED STUDY; DNA SEQUENCE; DOMESTICATION; EQUUS PRZEWALSKII; FEMALE; GENE FLOW; GENE FREQUENCY; GENE MUTATION; GENETIC MARKER; GENETIC VARIABILITY; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HORSE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATERNITY; PEDIGREE; PHYLOGENY; PHYLOGEOGRAPHY; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME;

ANIMALS; BREEDING; EUROPE; FOUNDER EFFECT; GENE FREQUENCY; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HORSES; MALE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PEDIGREE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; Y CHROMOSOME;

EQUIDAE; EQUUS CABALLUS; EQUUS PRZEWALSKII;

EID: 84875717186     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060015     Document Type: Article

References (54)

1. Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, et al. (2009) Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol 19: 1453-1457.
2. Repping S, van Daalen SK, Brown LG, Korver CM, Lange J, et al. (2006) High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat Genet 38: 463-467.
3. Jobling MA, Samara V, Pandya A, Fretwell N, Bernasconi B, et al. (1996) Recurrent duplication and deletion polymorphisms on the long arm of the Y chromosome in normal males. Hum Mol Genet 5: 1767-1775.
4. Trombetta B, Cruciani F, Underhill PA, Sellitto D, Scozzari R, (2009) Footprints of X-to-Y gene conversion in recent human evolution. Mol Biol Evol 27: 714-725.
5. Ellegren H, (2011) Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nat Rev Genet 12: 157-166.
6. Underhill PA, Kivisild T, (2007) Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41: 539-564.
7. King T, Jobling M, (2009) What's in a name? Y chromosomes, surnames and the genetic genealogy revolution. Trends Genet 25: 351-360.
8. Ding ZL, Oskarsson M, Ardalan A, Angleby H, Dahlgren LG, Tepeli C, Kirkness E, Savolainen P, Zhang YP, (2012) Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA. Heredity 108: 507-514.
9. Brown SK, Pedersen NC, Jafarishorijeh S, Bannasch DL, Ahrens KD, et al. (2011) Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins. PLoS One 6: e28496.
10. Sundqvist A, Björnerfeldt S, Leonard J, Hailer F, Hedhammar A, et al. (2006) Unequal contribution of sexes in the origin of dog breeds. Genetics 172: 1121-1128.
11. Ramirez O, Ojeda A, Tomas A, Gallardo D, Huang L, et al. (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Mol Biol Evol 26: 2061-2072.
12. Cliffe KM, Day AE, Bagga M, Siggens K, Quilter CR, et al. (2010) Analysis of the non-recombining Y chromosome defines polymorphisms in domestic pig breeds: ancestral bases identified by comparative sequencing. Anim Genet 41: 619-629.
13. Meadows J, Hanotte O, Drögemüller C, Calvo J, Godfrey R, et al. (2006) Globally dispersed Y chromosomal haplotypes in wild and domestic sheep. Anim Genet 37: 444-453.
14. Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, et al. (2011) Dual Origins of Dairy Cattle Farming - Evidence from a Comprehensive Survey of European Y-Chromosomal Variation. PLoS ONE 6(1): e15922.
15. Vila C, Leonard J, Gotherstrom A, Marklund S, Sandberg K, et al. (2001) Widespread origins of domestic horse lineages. Science 291: 474-477.
16. Jansen T, Forster P, Levine M, Oelke H, Hurles M, et al. (2002) Mitochondrial DNA and the origins of the domestic horse. Proc Natl Acad Sci U S A 99: 10905-10910.
17. Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, et al. (2010) Origin and history of mitochondrial DNA lineages in domestic horses. PLoS One 5: e15311.
18. Lippold S, Matzke NJ, Reissmann M, Hofreiter M, (2011) Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol 11: 328.
19. Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, et al. (2012) Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci U S A 109: 2449-2454.
20. Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, et al. (2012) Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc Natl Acad Sci U S A 109: 8202-8206.
21. Lindgren G, Backstroem N, Swinburne J, Hellborg L, Einarsson A, et al. (2004) Limited number of patrilines in horse domestication. Nat Genet 36: 335-336.
22. Wallner B, Brem G, Mueller M, Achmann R, (2003) Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus. Anim Genet 34: 453-456.
23. Wallner B, Piumi F, Brem G, Mueller M, Achmann R, (2004) Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus. J Hered 95: 158-164.
24. Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, et al. (2011) Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat Commun 2: 450.
25. Ling Y, Ma Y, Guan W, Cheng Y, Wang Y, et al. (2010) Identification of y chromosome genetic variations in Chinese indigenous horse breeds. J Hered 101: 639-643.
26. Brem G (2011) Der Lipizzaner im Spiegel der Wissenschaft. Vienna: Austrian Academy of Sciences Press. 338 p.
27. Hamann H, Distl O, (2008) Genetic variability in Hanoverian warmblood horses using pedigree analysis. J Anim Sci 86: 1503-1513.
28. Druml T (2009) Functional Traits in Early Horse Breeds of Mongolia, India and China from the Perspective of Animal Breeding. In: B F, V S, R P, A S, editors. Horses in Asia: History, Trade and Culture. Vienna: Austrian Academy of Sciences. 9-16.
29. Grilz-Seger G and Druml T (2011) Lipizzaner Hengststämme. Graz: Vehling Medienservice und Verlag GmbH. 312 p.
30. Hendricks B (1995) International Encyplopedia of Horse Breeds. Norman: University of Oklahoma Press. 486 p.
31. Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, et al. (2009) Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 30: 1703-1712.
32. Godard S, Schibler L, Oustry A, Cribiu E, Guerin G, (1998) Construction of a horse BAC library and cytogenetical assignment of 20 type I and type II markers. Mamm Genome 9: 633-637.
33. Raudsepp T, Santani A, Wallner B, Kata S, Ren C, et al. (2004) A detailed physical map of the horse Y chromosome. Proc Natl Acad Sci U S A 101: 9321-9326.
34. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5: 1005-1010.
35. Andrews S. (2010) FastQC: a quality control tool for high throughput sequence data. Available: www.bioinformatics.bbsrc.ac.uk/projects/fastqc/Accessed 2012 January.
36. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
37. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
38. Nei M (1987) Molecular evolutionary genetics. New York: Columbia University Press. 512 p.
39. Buggs RJ, Chamala S, Wu W, Gao L, May GD, et al. (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol Ecol 19Suppl 1: 132-146.
40. Paria N, Raudsepp T, Pearks Wilkerson AJ, O'Brien PC, Ferguson-Smith MA, et al. (2011) A gene catalogue of the euchromatic male-specific region of the horse y chromosome: comparison with human and other mammals. PLoS One 6: e21374.
41. Iwase M, Satta Y, Hirai H, Hirai Y, Takahata N, (2010) Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evol Biol 10: 225.
42. Rosser ZH, Balaresque P, Jobling MA, (2009) Gene conversion between the X chromosome and the male-specific region of the Y chromosome at a translocation hotspot. Am J Hum Genet 85: 130-134.
43. Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, et al. (2011) Variation in genome-wide mutation rates within and between human families. Nat Genet 43: 712-714.
44. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639.
45. Clutton-Brock J (1999) A Natural History of Domesticated Mammals. Cambridge, Massachusetts: Cambridge University Press. 248 p.
46. Natanaelsson C, Oskarsson M, Angleby H, Lundeberg J, Kirkness E, et al. (2006) Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery. BMC Genet 7: 45.
47. Cunningham E, Dooley J, Splan R, Bradley D, (2001) Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses. Anim Genet 32: 360-364.
48. Kavar T, Brem G, Habe F, Sölkner J, Dovc P, (2002) History of Lipizzan horse maternal lines as revealed by mtDNA analysis. Genet Sel Evol 34: 635-648.
49. Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, et al. (2011) The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett 7: 316-320.
50. Bower MA, Campana MG, Nisbet RE, Weller R, Whitten M, et al. (2012) Truth in the bones: resolving the identity of the founding elite thoroughbred racehorses. Archaeometry 54: 916-925.
51. Hill EW, Bradley DG, Al-Barody M, Ertugrul O, Splan RK, et al. (2002) History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Anim Genet 33: 287-294.
52. Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, et al. (2012) Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 43: 483-502.
53. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, et al. (2012) A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies. PLoS Genet 8(1): e1002451.
54. Eclipse At New Market With Groom (British racehorses of the 18th century), by Stubbs George (1724-1806); source: Wikimedia Commons, public domain, copyright has expired.