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Abstract

Whole genome sequencing provides a rich and unprecedented collection of the existing genetic variation in a genome. The development of next generation sequencing (NGS) technologies has enabled a rapid and relatively inexpensive method for whole genome sequencing. The current archive of genetic variations in the horse is mostly based on the Thoroughbred mare used to generate the reference sequence (EquCab2.0). Therefore, we have used Illumina paired-end NGS technology to sequence three horse genomes from diverse breeds; an Arabian, a Percheron and an American Miniature Horse. Our objective is to catalog newly identified variations within these three individuals and in comparison to the reference. After filtering the reads, we used BWA to align them to the reference and the Genome Analysis Tool Kit (GATK) HaplotypeCaller to call Single Nucleotide Polymorphisms (SNPs) and insertion/deletion polymorphisms (In/Dels). We also used ControlFreec to obtain regions predicted to contain copy number variations on each of the three genomes. Finally, we used BreakDancer to detect structural variations like inversions and translocations. These newly detected variations will enrich the database of genetic variations in the horse and could potentially have a phenotypic impact related to the biology of each of the three horse breeds. Here we will be presenting preliminary findings on our analysis and highlight the important steps in our pipeline.

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/content/papers/10.5339/qfarf.2013.BIOSP-040
2013-11-20
2020-07-06
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http://instance.metastore.ingenta.com/content/papers/10.5339/qfarf.2013.BIOSP-040
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