Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.

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“…; Wang et al . ). The comparison of the CNVRs was implemented according to our previous paper (Dong et al .…”

Section: Methodsmentioning

confidence: 97%

“…; Wang et al . ). Although these studies provide a basis to understanding the role of CNVs in equine biology, the current information is still insufficient for the efficient discovery of variants affecting phenotypes in horses.…”

Section: Introductionmentioning

confidence: 97%

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

et al. 2016

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“…Functional annotation of these 246 regions revealed large gene families involved in olfactory reception and immunity. The same 247 observation was made by array CGH in the horse [33] and corresponding findings were also 248 obtained in the human genome [35].…”

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confidence: 53%

“…Our functional CNVs annotation revealed a copy number gain in a gene cluster that 250 includes Latherin (LATH) (ENSEMBL Gene Symbol: ENSECAG00000009747.1). The 251 reference genome assembly indicates just one copy of this gene, yet a copy-number gain was 252 previously reported in a Quarter Horse using NGS data [7], and using array CGH a copy 253 number loss was observed in the same region [33] (ECA 22:23893194-24009882). LATH (also 254 known as BPIFA4) is a member of the palate lung and nasal epithelium clone (PLUNC) family 255 of proteins that is common in the oral cavity and saliva of mammals [36,37].…”

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confidence: 88%

Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses

Al-Abri

Holl

Kalla

et al. 2019

Preprint

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AbstractThe domesticated horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of horse. To enrich the current collection of genetic variants in the horse, we sequenced whole genomes from six horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six horses with coverage between 15x to 24x per horse. After applying rigorous filtration, we identified and functionally annotated 8,128,658 Single Nucleotide Polymorphisms (SNPs), and 830,370 Insertions/Deletions (INDELs), as well as novel Copy Number Variations (CNVs) and Structural Variations (SVs). Our results revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature horse. We detected a copy number gain in the Latherin gene that may be the result of evolutionary selection for thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the horse.Author SummaryThe domesticated horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the horse reference genome yielded the discovery of many genetic variants, the remarkable diversity across breeds of horse calls for additional effort in quantification of the breadth of genetic polymorphism within this unique species. Here, we present genome re-sequencing and variant detection analysis for six horses belonging to geographically and physiologically diverse breeds. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also large insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number gain in the Latherin gene that could be the result of an evolutionary selection for thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.

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“…[67][68][69] Several studies have used technologies other than SNP arrays to identify CNVs in horses, such as next generation sequencing (NGS) and comparative genomic hybridization arrays (aCGH). 52,[70][71][72][73][74] Arrays for CGH are designed by tiling oligonucleotide probes across the genome to which DNA of interest then can be hybridized for the identification of CNVs (Fig 2). Use of aCGH also has limitations for the identification of CNVs, principally related to probe placement and density.…”

Section: Copy Number Variantsmentioning

confidence: 99%

Genetic Susceptibility to Rhodococcus equi

McQueen

Dindot

2015

Veterinary Internal Medicne

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Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).

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Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Cited by 35 publications

References 41 publications

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses

Genetic Susceptibility to Rhodococcus equi

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