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Copy number variation in the horse genome
Sharmila Ghosh1, Zhipeng Qu2, Pranab J Das1
1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
Plos Genetics
|October 24, 2014
Summary
Researchers mapped copy number variations (CNVs) in horse breeds using a 400K whole-genome tiling oligoarray. This study identified novel CNV regions and potential genetic causes for disorders of sexual development in horses.
Area of Science:
- Genomics
- Animal Genetics
- Comparative Genomics
Background:
- Copy number variations (CNVs) are significant sources of genetic diversity and can impact phenotypic traits.
- Understanding CNVs in horses is crucial for breed improvement and identifying genetic disorders.
Purpose of the Study:
- To construct and apply a 400K whole-genome tiling oligoarray for comprehensive CNV discovery in diverse horse breeds.
- To integrate findings with existing datasets for a more complete genome-wide CNV map.
- To investigate the potential role of CNVs in horses with disorders of sexual development.
Main Methods:
- Development and application of a 400K whole-genome tiling oligoarray for CNV detection.
- Analysis of 38 normal horses from 16 breeds and the Przewalski horse.
- Integration of newly identified CNV regions (CNVRs) with previously published data.
- Pilot study of CNVs in horses with XY disorders of sexual development.
Main Results:
- Identification of 258 novel CNV regions (CNVRs), comprising 1.3% of the horse genome, with chromosome 12 showing the highest enrichment.
- Significant variation in CNV numbers among different breeds, with American Miniature horses having the most and American Quarter Horses the fewest.
- Majority of CNVRs involved genes related to sensory perception, immunity, and reproduction; 20% were in intergenic regions.
- A composite dataset of 1476 CNVRs was generated, with 1174 being novel.
- A homozygous deletion in the AKR1C gene cluster was identified in two horses with XY disorders of sexual development, suggesting a potential causative link.
Conclusions:
- The study provides an expanded and integrated map of horse CNVs, adding 11 new breeds to the analyzed population.
- The identified CNVs and associated genes offer insights into horse evolution, breed diversity, and disease susceptibility.
- Further analysis of more breeds and individuals using standardized methods is necessary for comprehensive discovery of clinically relevant genetic variants.
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