Genome wide landscaping of copy number variations for horse inter-breed variability.

This research study used genotyping arrays to identify and categorize copy number variations (CNVs) in six Indian horse breeds, establishing a new database, EqCNVdb, which catalogs this important genetic information.

Understanding CNVs and Their Importance

• Copy number variations (CNVs) refer to genetic mutations where certain sections of the genome are repeated. They have been recognized as significant contributors to genomic variability and phenotypic diversity (the observable characteristics of an individual).
• Identification of these CNVs and their associated regions (CNVRs) is therefore useful in understanding genetic traits and variations. In the case of horses, these can include disparity in adaptation to different climates and distinct phenotypic characters.

Methodology

• The horse breeds chosen for this study were Manipuri, Zanskari, Bhutia, Spiti, Kathiawari, and Marwari, each having different agro-climatic adaptations and phenotypes.
• An Axiom Equine Genotyping Array was utilized to identify CNVs. This technique is a high-throughput tool that aids in the robust determination of genetic variations.
• The PennCNV tool and DeepCNV, both software packages, were used to identify and re-validate the CNVs and CNVRs. CNVRs were further filtered using DeepCNV.
• Real-time PCR (polymerase chain reaction) was also used to validate three randomly selected CNVRs.

Findings

• A total of 2,668 autosomal CNVs and 381 CNVRs were identified. The term “autosomal” refers to genetic variations that occur on any chromosome other than sex chromosomes (X and Y). After re-validation using DeepCNV, the number of autosomal CNVs was revised to 883.
• Approximately 9.06% of the CNVs analyzed were identified as singleton type, which refers to the CNVs that have only occurred once.
• The length of CNVRs was estimated to be between 3.12 Kb and 4.90 Mb.
• Most of the genes within the CNVRs were found to be associated with sensory perception and olfactory receptor activity.

Outcomes

• An Equine CNVs database, EqCNVdb, was developed, providing detailed information on identified horse CNVs, CNVRs, and gene content within the CNVRs.
• The discovery of these CNVs will help in understanding the genetic makeup of horses and is viewed as groundwork for future CNV association research with significant horse traits.
• This knowledge will lead to better insights into the genetic basis of important traits in horses, potentially facilitating enhanced breeding and selection processes.