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

Abstract

<jats:title>Abstract</jats:title><jats:p>The 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 <jats:italic>ANKRD1</jats:italic> and <jats:italic>HMGA1</jats:italic> in the very large Percheron and the <jats:italic>ZFAT</jats:italic> gene in the American Miniature horse. We detected a copy number gain in the <jats:italic>Latherin</jats:italic> 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.</jats:p><jats:sec><jats:title>Author Summary</jats:title><jats:p>The 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 <jats:italic>Latherin</jats:italic> 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.</jats:p></jats:sec>

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

“…We retrieved the genetic variants representing the population level polymorphism from the following species and respective available datasets: Equus caballus (EquCab2 assembly in the EVA study PRJEB9799[50]), Canis familiars (CanFam3.1 assembly in the EVA study PRJEB24066[51]), Bos taurus (UMD3.1 assembly in the NextGen project), Ovis aries (Oar v3.1 assembly in the NextGen project), Capra Hircus (CHIR1 assembly in the NextGen project converted to ARS1 assembly with dbSNP identifiers[52]), Chlorocebus sabaeus (ChlSab1.1 assembly in the EVA project PRJEB22989[53]), Homo sapiens (GRCh38 assembly from the 1000-genome project[54, 55]).…”

“…We retrieved the genetic variants representing the population level polymorphism from the following species and respective available datasets: Equus caballus (EquCab2 assembly in the EVA study PRJEB9799 [50]),…”

Cross-matching of allogeneic mesenchymal stromal cells eliminates recipient immune targeting

“…Conversely, the horse has wide genetic diversity with frequent MHC recombination events and is an ideal model to study immune compatibility of allogeneic cell therapy 26‐28 . Additionally, the horse is well‐recognized for its value as a preclinical model for joint injury as the equine articular joint closely mimics that of man in the cartilage thickness and collagen distribution as well as the architecture of subchondral bone 29,30 .…”

Metabogenomics reveals four candidate regions involved in the pathophysiology of Equine Metabolic Syndrome

“…Variant analysis was performed utilizing publicly available sequence data from 16 Arabian horses of diverse backgrounds aligned to EqCab2.0 and EqCab3.0 through the UCSC Variant Annotation Integrator tool [37][38][39][40]. To investigate specific feature correlations to the individual original nine diagnostic phenotypes utilized to build the EMS score [31], we employed an ANOVA in JMP® Pro 14.1.0 (SAS Institute Inc., 2017).…”

“…We chose to focus on the ECA19 candidate region given the strong and well-supported signal of association. Examination of publicly available whole-genome from Arabian horses sequence data found no coding sequence changes or gene-disrupting structural variants [37,38,40]. Gene ontology overrepresentation analysis using PANTHER identified significant terms in biological processes for detection of chemical stimuli involved in "sensory perception of bitter taste" (P = 7.18 x 10 −4 ), as well as "protein insertion into membrane" (P = 1.61 x 10 −3 ).…”