Horses (Equus caballus) hold a special place among farm animals. Horses have long served humans and become valuable companions in agriculture, warfare, and transportation. Humans have selectively bred horses based on performance characteristics (speed, endurance, strength, gait), appearance (size, color, conformation), and temperament, resulting in 400-500 different breeds. Varieties derived through selective breeding and the inclusion of only individuals with breed-defining characteristics result in differences in genomic characteristics between different populations. In addition, genetic traits (e.g., muscle diseases, allergies, asthma) in over 130 horse breeds can serve as valuable models for studying similar human conditions. The sequencing and assembly of the equine reference genome have important implications for studying equine health and performance, increasing the scope and resolution of understanding the genetic basis of equine physiology and disease pathology.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable equine genome sequencing services to support research and breeding efforts in the field of equine genomics for clients worldwide. Our services help identify functional genomic features common to all mammals and will serve as a tool for researchers to better understand diseases affecting horses. Additionally, using horse populations to genetically map disease may in turn benefit human health.

Our equine genome sequencing service

CD Genomics offers comprehensive and customizable genome sequencing services for equine. We utilize advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools to perform whole genome sequencing on different equine breeds to provide reliable data support for genomic and other research on equine genome structure, organization, and function. We provide the following equine genome sequencing information with sufficient coverage to confidently identify unique variations in individual horses in a single run.

• Whole-genome sequencing
• Exome sequencing
• Targeted sequencing
• Epigenetic sequencing
• DNA-protein interactions
• Transcriptome sequencing
• Gene expression profiling
• Small RNA sequencing

Our services cover all stages of the sequencing process, from library preparation to data analysis. Strict quality control measures are adopted to ensure the accuracy and reliability of sequencing results, providing researchers with reliable horse genome sequences. In addition to sequencing the genome of purebred horses, we can also examine the DNA of a variety of other horse breeds, including the American quarter horse, Andalusian, Arabian, Belgian draft horse, Hanoverian, Hakkaido, Icelandic horse, Norwegian fjord horse, and Standardbred breeds, etc.

Applications of equine genome sequencing

Our equine genome sequencing can be used for a wide range of research in equine genetics and veterinary medicine. By deciphering the equine genome, we help you gain information on the genetic basis of various traits, diseases, and adaptations in horses.

• Identification of disease-associated variants

Equine whole-genome sequencing helps identify genetic variants that cause various equine diseases. For example, equine genome sequencing has identified missense variants that cause lavender foal syndrome, immune-mediated myositis, hydrocephalus, dwarfism, and occipital-atlantoaxial malformations.

• Genomic risk assessment

Equine genome sequencing can identify specific genetic markers associated with increased risk of certain diseases. By analyzing each horse's genome, veterinarians and breeders can assess its susceptibility to various diseases, allowing for early intervention and preventive measures.

• Genomic breeding

Equine genome sequencing has revolutionized breeding programs by providing efficient information on the genetic basis of traits related to performance, health, and conformation. By selectively breeding horses based on their genomic profiles, breeders can enhance desired traits and minimize the risk of genetic disease, ultimately producing healthier, more competitive offspring.

• Gene annotation and expression profiling

We offer RNA sequencing (RNA-seq) to analyze equine gene expression patterns and improve gene annotation. By quantifying transcript abundance and identifying differential expression between treatments or disease states, RNA-seq can provide insights into the molecular mechanisms of various equine diseases. In addition, CD Genomics utilizes stranded RNA libraries to differentiate antisense transcripts and identify novel regulatory elements involved in gene expression.

• Epigenetic modifications and genome activity

DNA methylation is an epigenetic mechanism involved in gene silencing and can be analyzed using next-generation sequencing technologies such as MeDIP-seq. This method can be used to characterize exercise-induced changes in genomic methylation in equine skeletal muscle, providing insights into the epigenetic regulation of equine physiology.

• Protein-DNA and protein-RNA interactions

By employing chromatin immunoprecipitation (ChIP-seq) and cross-link immunoprecipitation (CLIP-seq) techniques, we were able to identify genomic regions involved in protein-DNA and protein-RNA interactions. CD Genomics can leverage these methods to study the function of genomic variants and uncover the molecular mechanisms of equine disease.

Case study of equine genome sequencing

The sequencing and assembly of the equine genome is a great achievement in the fields of equine genomics and veterinary medicine, as this information has broad potential applications in improving health and performance and understanding differences between species. Sequencing the Quarter Horse's genome was considered important for a number of reasons. The Quarter Horse is by far the largest contributor to the U.S. horse population. In addition, Quarter Horses also suffer from single-gene diseases such as polysaccharide storage myopathy (PSSM), hyperkalemic periodic paralysis (HYPP), glycogen branching enzyme deficiency (GBED), and hereditary equine disease localized skin weakness ( HERDA). Most diseases and traits are complex, involve multiple genes, and may be modulated by environmental factors. Therefore, the identification of genetic variation in individual Quarter Horse genomes will provide rich information for future equid genomic studies. Researchers used massively parallel paired-end sequencing to sequence the whole genome of a Quarter Horse mare.

Fig. 1. Overview of genome-wide variation analysis pipeline by next generation sequencing. (Doan et al., 2012)

• Genetic variation, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variations (CNVs), were identified in the genome of Quarter Horse mares by next-generation sequencing.
• Sequence reads were mapped to reference purebred nuclear and mitochondrial genomes.
• Researchers annotate genetic variants to determine their impact on gene structure and function.
• The researchers also genotyped Quarter Horses for known disease mutations and variants associated with specific traits. Functional cluster analysis of genetic variation revealed that the majority of genetic variation in the equine genome was enriched in sensory perception, signal transduction, immune and defense pathway sequence reads mapped to reference purebred nuclear and mitochondrial genomes.​

CD Genomics is committed to providing reliable equine genome sequencing services. We provide high-quality equine reference genomes, combining unprecedented advances in genomics technology with global collaborations among researchers, clinicians, breeders, and owners from diverse disciplines to advance equine genomic research. If you are interested, please feel free to contact us.

Reference

1. Doan, Ryan, et al. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC genomics. 13 (2012): 1-12.