Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 6 4 2015 02 20 Genic Variant Detection of Caspian Horse Using High-throughput Sequencing Technology Genic Variant Detection of Caspian Horse Using High-throughput Sequencing Technology 101 116 1343 10.22103/jab.2015.1343 FA Babak Arefnejad Department of Animal Science, University of Tehran, Karaj, Iran Hamid Kohram Department of Animal Science, University of Tehran, Karaj, Iran Mohammad Moradi Shahrbabak Department of Animal Science, University of Tehran, Karaj, Iran 0000-0002-5255-609X Malak Shakeri Campus of Agriculture and Natural Resources / Faculty of Science and Agricultural Engineering Yang Dong State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Xiaoli Zhang State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Wen Wang State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Ghasem Hoseini Salekdeh Biotechnology Research Institute Journal Article 2014 01 23 Recently, new advanced high-throughput sequencing technology as a novel tool has opened the way to study of genomic variants and functional information stored within farm animals. The Caspian horse is one of the valuable horses ever exist in the world. Hence, propose of this study was to investigate genetic variants of single nucleotide polymorphisms, insertion and deletions and copy number variations within the genome of Caspian horse and their involved biological pathways. Using high-throughput sequencing technology, we generated 108 Gb (Average depth of 45.8) of DNA sequence from three Caspian horse mares resulting in an average of 14.41X coverage and 76.4% covered with reference genome. Using a stringent filtering method, we identified 1666717 single nucleotide polymorphisms, 358020 insertion and deletions, and 3109 copy number variations. Functional clustering analysis of genic variants revealed that most of the genetic variants in the Caspian horse’s genome were enriched in nervous system, GTP-related signal transduction, cellular morphogenesis, cytoskeleton organization, vascular development and cellular movement. Moreover, we have detected structural variations as like as inversion, intra- and inter-chromosomal translocations, large insertion and deletions which could be useful for marker based population genetic investigation Recently, new advanced high-throughput sequencing technology as a novel tool has opened the way to study of genomic variants and functional information stored within farm animals. The Caspian horse is one of the valuable horses ever exist in the world. Hence, propose of this study was to investigate genetic variants of single nucleotide polymorphisms, insertion and deletions and copy number variations within the genome of Caspian horse and their involved biological pathways. Using high-throughput sequencing technology, we generated 108 Gb (Average depth of 45.8) of DNA sequence from three Caspian horse mares resulting in an average of 14.41X coverage and 76.4% covered with reference genome. Using a stringent filtering method, we identified 1666717 single nucleotide polymorphisms, 358020 insertion and deletions, and 3109 copy number variations. Functional clustering analysis of genic variants revealed that most of the genetic variants in the Caspian horse’s genome were enriched in nervous system, GTP-related signal transduction, cellular morphogenesis, cytoskeleton organization, vascular development and cellular movement. Moreover, we have detected structural variations as like as inversion, intra- and inter-chromosomal translocations, large insertion and deletions which could be useful for marker based population genetic investigation https://jab.uk.ac.ir/article_1343_a18ac291149a50ca0ed96346f9e54192.pdf