Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds

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.

Fig 1. Small indels identified with GATK and Pindel.

Venn diagram summarizing small indels identified by GATK and by Pindel.

Fig 2. Distribution of SVs based on their type and size.

Histogram summarizing the distribution of SVs based on their type and size. Inversions are highlighted in blue, deletions in red and tandem duplications in green.

Fig 3. Chromosomal distribution of large SVs.

Histogram showing the distribution of SVs within bovine chromosomes. Deletions are shown in blue, inversions in red and tandem duplications in green.

Fig 4. SV distribution among the 62 sequenced animals.

Histogram showing the distribution of SVs among all 62 sequenced animals. Frequencies of SVs present in more than 16 sequenced samples were too low to be visualized and were therefore drawn in a separate graph embedded in the first one.

Fig 5. Distribution of SVs found within the three breeds.

Venn diagram showing shared and unique SVs between the 3 breeds.

Fig 6. Results of PCA analysis.

PCA analysis results were shown for the 3 main dairy breeds (Fig 6A) and for the 8 breeds (Fig 6B).

Fig 7. Genetic population structure prediction.

Genetic population structure predicted by STRUCTURE software for the 3 main dairy breeds (Fig 7A) and for the 8 breeds (Fig 7B).