title: Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.
abstract: BACKGROUND
  The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century.
  
  
  RESULTS
  We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses.
  
  
  CONCLUSIONS
  Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
authors.forename: JeHoon
authors.initials: J
authors.lastname: Jun
authors.forename: Yun Sung
authors.initials: YS
authors.lastname: Cho
authors.forename: Haejin
authors.initials: H
authors.lastname: Hu
authors.forename: Hak-Min
authors.initials: HM
authors.lastname: Kim
authors.forename: Sungwoong
authors.initials: S
authors.lastname: Jho
authors.forename: Priyvrat
authors.initials: P
authors.lastname: Gadhvi
authors.forename: Kyung Mi
authors.initials: KM
authors.lastname: Park
authors.forename: Jeongheui
authors.initials: J
authors.lastname: Lim
authors.forename: Woon Kee
authors.initials: WK
authors.lastname: Paek
authors.forename: Kyudong
authors.initials: K
authors.lastname: Han
authors.forename: Andrea
authors.initials: A
authors.lastname: Manica
authors.forename: Jeremy S
authors.initials: JS
authors.lastname: Edwards
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D006736:Horses / Q000235:genetics*; D006801:Humans; D006824:Hybridization, Genetic; D008297:Male; D008969:Molecular Sequence Data; D010641:Phenotype; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity