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BMC genomics2014; 15 Suppl 9(Suppl 9); S4; doi: 10.1186/1471-2164-15-S9-S4

Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.

Abstract: 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.
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Publication Date: 2014-12-08 PubMed ID: 25521865PubMed Central: PMC4290615DOI: 10.1186/1471-2164-15-S9-S4Google Scholar: Lookup
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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 research article focuses on analyzing the genome of the Marwari horse breed, a unique breed originating from crossbreeding of local Indian ponies with Arabian horses. Genetic components from both Arabian and Mongolian breeds were identified in the Marwari genome. The study also identified variants related to olfactory functions and suggested a potential genetic variant linked to the breed’s signature inward-turning ear tip shape.

Characterizing the Marwari Horse Genome

The scientists in this study sought to examine the genome of the Marwari horse breed known for its distinctive inward-turned ear tips. This was done by generating about 101 Gb of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. They were able to:

  • Map the sequences they generated to the reference genome of horses at an approximate mapping rate of 98%.
  • Achieve a coverage of roughly 95% for the genome, with at least 10 times coverage.

Identified Genetic Variations in the Marwari Breed

The study successfully identified several genetic variations. These include:

  • Approximately 5.9 million single nucleotide variations. These are changes in a single nucleotide, the basic building blocks of DNA.
  • About 0.6 million small insertions or deletions. These are removals or additions of small chunks of DNA sequences.
  • 2,569 copy number variation blocks. These are sections of the genome where the number of copies varies between individuals in a species.

Tracing the Genetic Origin of the Marwari Breed

The researchers reported that the Marwari genome displayed a strong Arabian and Mongolian genetic component, tracing back to its believed historical origins from crossbreeding of local Indian ponies with Arabian horses.

Annotation of Variants, Their Possible Functions and Traits

The team went further to annotate the novel variants they discovered in the Marwari sequences. This helped in understanding the roles these variations may play in the breed. They found out that the variants show enrichment in olfactory functions. The researchers also identified a potential functional genetic variant in the TSHZ1 gene, which they suggest could be associated with the characteristic inward-turning ear tip shape of the Marwari horses.

Significance of the Study

This study is the first to present genomic data for an Asian breed. The findings serve as a valuable resource for future research aiming to explore genetic variation associated with phenotypes and diseases in horses.

Cite This Article

APA
Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. (2014). Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics, 15 Suppl 9(Suppl 9), S4. https://doi.org/10.1186/1471-2164-15-S9-S4

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 15 Suppl 9
Issue: Suppl 9
Pages: S4

Researcher Affiliations

Jun, JeHoon
    Cho, Yun Sung
      Hu, Haejin
        Kim, Hak-Min
          Jho, Sungwoong
            Gadhvi, Priyvrat
              Park, Kyung Mi
                Lim, Jeongheui
                  Paek, Woon Kee
                    Han, Kyudong
                      Manica, Andrea
                        Edwards, Jeremy S
                          Bhak, Jong

                            MeSH Terms

                            • Amino Acid Sequence
                            • Animals
                            • Evolution, Molecular
                            • Genetic Variation
                            • Genome / genetics
                            • Genomics
                            • Genotype
                            • Horses / genetics
                            • Humans
                            • Hybridization, Genetic
                            • Male
                            • Molecular Sequence Data
                            • Phenotype
                            • Selection, Genetic
                            • Sequence Analysis, DNA
                            • Species Specificity

                            Grant Funding

                            • R01 HG006876 / NHGRI NIH HHS

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