title: Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.
abstract: BACKGROUND
  Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East.
  
  
  RESULTS
  The variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups.
  
  
  CONCLUSIONS
  The whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.
authors.affiliation: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77843-4458, USA. GCothran@cvm.tamu.edu.
authors.forename: Anas M
authors.initials: AM
authors.lastname: Khanshour
authors.forename: Ernest Gus
authors.initials: EG
authors.lastname: Cothran
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D004272:DNA, Mitochondrial / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D006736:Horses / Q000145:classification* / Q000235:genetics*; D008877:Middle East; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
references.citation: Genet Sel Evol. 2004 Nov-Dec;36(6):663-72
references.pmid: 15496286
references.citation: Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10905-10
references.pmid: 12130666
references.citation: Anim Genet. 2010 Dec;41 Suppl 2:176-85
references.pmid: 21070293
references.citation: Genetics. 1995 Oct;141(2):743-53
references.pmid: 8647407
references.citation: Genetics. 1983 Feb;103(2):287-312
references.pmid: 6299878
references.citation: Mol Ecol. 2011 Feb;20(3):573-83
references.pmid: 21199027
references.citation: Genet Sel Evol. 2007 Sep-Oct;39(5):609-19
references.pmid: 17897600
references.citation: Am J Hum Genet. 2004 Nov;75(5):752-70
references.pmid: 15457403
references.citation: Gene. 1994 Oct 21;148(2):357-62
references.pmid: 7958969
references.citation: Genet Mol Res. 2011 Oct 31;10(4):4104-13
references.pmid: 22057995
references.citation: BMC Evol Biol. 2011 Nov 14;11:328
references.pmid: 22082251
references.citation: Nucleic Acids Res. 2012 Oct;40(18):9073-88
references.pmid: 22761406
references.citation: Biochem Genet. 2007 Apr;45(3-4):375-95
references.pmid: 17265183
references.citation: PLoS One. 2010 Dec 20;5(12):e15311
references.pmid: 21187961
references.citation: Anim Genet. 2000 Feb;31(1):1-7
references.pmid: 10690354
references.citation: J Mol Evol. 1980 Dec;16(2):111-20
references.pmid: 7463489
references.citation: Science. 2001 Jan 19;291(5503):474-7
references.pmid: 11161199
references.citation: Anim Genet. 2002 Oct;33(5):356-63
references.pmid: 12354144
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: J Hered. 2011 Nov-Dec;102(6):753-8
references.pmid: 21914666
references.citation: Mol Biol Evol. 1996 Nov;13(9):1167-73
references.pmid: 8896369
references.citation: Proc Natl Acad Sci U S A. 1979 Apr;76(4):1967-71
references.pmid: 109836
references.citation: Anim Genet. 2002 Aug;33(4):287-94
references.pmid: 12139508
references.citation: Hereditas. 1998;129(1):37-43
references.pmid: 9868927
references.citation: Nature. 1974 Oct 11;251(5475):536-8
references.pmid: 4423884
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: Anim Genet. 1999 Dec;30(6):423-30
references.pmid: 10612231
references.citation: Evol Bioinform Online. 2007 Feb 23;1:47-50
references.pmid: 19325852
references.citation: Anim Genet. 1999 Apr;30(2):102-8
references.pmid: 10376300
references.citation: J Anim Breed Genet. 2007 Apr;124(2):94-100
references.pmid: 17488360
references.citation: J Hered. 2013 May-Jun;104(3):386-98
references.pmid: 23450090
references.citation: Mol Biol Evol. 2001 Sep;18(9):1833-7
references.pmid: 11504863
references.citation: Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2449-54
references.pmid: 22308342
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Anim Genet. 1994 Aug;25(4):215-21
references.pmid: 7985837
references.citation: J Hered. 2012 May-Jun;103(3):380-90
references.pmid: 22504109