Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

BMC Genomics
Ryan DoanScott V Dindot

Abstract

The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was e...Continue Reading

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Datasets Mentioned

BETA
SRX110702

Methods Mentioned

BETA
PCR
electrophoresis
Illumina sequencing

Software Mentioned

Ensembl
Galaxy
BLAST
Control
BLAT
ANNOVAR
- ( FREEC )
Ensembl Biomart
CLC Genomics Workbench
DAVID Functional Annotation Tool

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