Abstract
High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
Highlights
IntroductionMany studies have attempted cataloging the nature and pattern of genomic alterations in population (e.g.[1])
Over the past decade, many studies have attempted cataloging the nature and pattern of genomic alterations in population (e.g.[1])
Similar read mapping rates were obtained in other bovine whole-genome sequencing studies
Summary
Many studies have attempted cataloging the nature and pattern of genomic alterations in population (e.g.[1]). With new advances in high-throughput sequencing technologies, the operational spectrum of SVs has widened to include much smaller genomic alteration events (> 50 bp in size) [8]. During its pilot phase, the 1000 Genomes Project Consortium has sequenced 185 human wholegenomes and has identified more than 22,025 deletions and 6,000 additional SVs [17]. Some of those SVs are associated with disease susceptibility, such as autism [18,19,20] or schizophrenia [21,22,23] in humans
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