The challenges and importance of structural variation detection in livestock

Abstract

Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among individuals of each species. Many of these variants have been linked to debilitating diseases in humans, thereby cementing the importance of refining methods for their detection. Despite progress in the field, reliable detection of SVs still remains a problem even for human subjects. Many of the underlying problems that make SVs difficult to detect in humans are amplified in livestock species, whose lower quality genome assemblies and incomplete gene annotation can often give rise to false positive SV discoveries. Regardless of the challenges, SV detection is just as important for livestock researchers as it is for human researchers, given that several productive traits and diseases have been linked to copy number variations (CNVs) in cattle, sheep, and pig. Already, there is evidence that many beneficial SVs have been artificially selected in livestock such as a duplication of the agouti signaling protein gene that causes white coat color in sheep. In this review, we will list current SV and CNV discoveries in livestock and discuss the problems that hinder routine discovery and tracking of these polymorphisms. We will also discuss the impacts of selective breeding on CNV and SV frequencies and mention how SV genotyping could be used in the future to improve genetic selection.

Keywords: CNVs; SV; antimicrobial peptides; coat color genetics; insertions and deletions (indels); livestock genomics; olfaction.

FIGURE 1

The molecular mechanisms of CNV formation. Currently identified mechanisms of copy number variation (CNV) formation include non-allelic homologous recombination (NAHR), fork stalling and template switching (FOSTES), non-homologous end-joining (NHEJ), and mobile element insertion (MEI). (A) NAHR generates CNVs when a genomic segment with high sequence similarity to another, non-allelic locus (blue boxes) recombines. The results of this recombination can generate a duplication of the similar locus on one chromosome, while removing the copy from the other. (B) FOSTES occurs when the DNA replication complex stalls due to DNA lesions or chemical modifications of the nucleoside bases (hatch mark) and the lagging strand of DNA (red dashed line) associates with a different region of the genome with high sequence similarity. The location of the association determines if a duplication (pictured) or deletion occurs. (C) Double stranded breaks in DNA sequence (blue crosses) prompt NHEJ associated proteins to repair and ligate DNA strands together. First, end-repair (red ovals) replaces lost nucleotides on the double strand break and DNA ligase associates broken DNA fragments together. If fragments from different chromosomes ligate together, duplications or deletions of sequence can occur. (D) Retrotransposition involves an RNA intermediate (red dashed lines) that is reverse transcribed into cDNA and is subsequently inserted into the genome, thereby causing a duplication of the original endogenous retrovirus.

FIGURE 2

Examples of phenotypes caused by CNV formation. Selection of different CNVs within animal populations can leave evidence as to the evolutionary origins of the phenotypes they grant. (A) Figure adapted from Rubin et al. (2012). Duplications of regulatory elements upstream and downstream of the KIT gene locus (colored boxes) resulted in a belted phenotype in pigs. Subsequent duplication of this altered KIT gene locus, in addition to a splice site variant that excludes exon17 (not shown), results in the dominant white phenotype. (B) Figure adapted from Durkin et al. (2012). Translocation of the KIT locus, in addition to surrounding regulatory genomic segments, has resulted in distinct coloration phenotypes in cattle. It was discovered that the color-sided phenotypes in Belgian Blue (middle) and Brown Swiss (bottom) cattle were achieved by two translocations of the KIT locus to different cattle chromosomes. The rearrangement of surrounding genomic segments (colored boxes) near the KIT locus at each translocation point suggested that circular intermediates were involved in the movement of this locus.

FIGURE 3

Methods that can be used to track structural variants using genotyping platforms. The ubiquity of SNP chip data for livestock species allows researchers the opportunity to track genomic segments with relative ease. Regardless, the association of SVs with SNP markers has proven to be problematic. Here are three strategies for tracking SVs using SNP genotyping arrays: (A) association of SNP marker genotypes (filled and empty ovals) with the SV; (B) identification of SVs from the logR ratio (LogRR) intensity of SNP probes (X axis tick marks); (C) and association of SVs (duplicated gray boxes) with SNP markers that form haplotypes.