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

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 - BMC Genomics (2014)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

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.

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Multidimensional scaling plot derived from a Marwari horse and other horse breeds. Black arrow indicates the Marwari horse.
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Figure 1: Multidimensional scaling plot derived from a Marwari horse and other horse breeds. Black arrow indicates the Marwari horse.

Mentions: To further explore the relationships among breeds, we compared the Marwari horse genome data with SNP array data from 729 individual horses belonging to 32 domestic breeds [13]. A total of 54,330 nucleotide positions were shared across all individuals including the Marwari horse. After pruning as described above, 10,554 nucleotide positions were used for the comparative analyses. We calculated pairwise genetic distances and conducted multidimensional scaling (MDS) to visualize the relationships among the horse breeds (Figure 1). The Marwari horse fell together with Iberian-lineage breeds, such as the Andalusian, Mangalarga Paulista, Peruvian Paso, and Morgan horse breeds, all of which are known to have an Arabian ancestry [19-22]. Additionally, we found that the Marwari horse fell between Arabian and Mongolian horses, indicating their dual genetic influences on the Marwari horse as previously suggested [8-10].


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

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 - BMC Genomics (2014)

Multidimensional scaling plot derived from a Marwari horse and other horse breeds. Black arrow indicates the Marwari horse.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4290615&req=5

Figure 1: Multidimensional scaling plot derived from a Marwari horse and other horse breeds. Black arrow indicates the Marwari horse.
Mentions: To further explore the relationships among breeds, we compared the Marwari horse genome data with SNP array data from 729 individual horses belonging to 32 domestic breeds [13]. A total of 54,330 nucleotide positions were shared across all individuals including the Marwari horse. After pruning as described above, 10,554 nucleotide positions were used for the comparative analyses. We calculated pairwise genetic distances and conducted multidimensional scaling (MDS) to visualize the relationships among the horse breeds (Figure 1). The Marwari horse fell together with Iberian-lineage breeds, such as the Andalusian, Mangalarga Paulista, Peruvian Paso, and Morgan horse breeds, all of which are known to have an Arabian ancestry [19-22]. Additionally, we found that the Marwari horse fell between Arabian and Mongolian horses, indicating their dual genetic influences on the Marwari horse as previously suggested [8-10].

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

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.

Show MeSH