Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data

Abstract

Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to characterize CNVs in a large multibreed population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. All CNVs were classified into either deletions or duplications. The median concordance between PennCNV and QuantiSNP, per animal, was 18.5% for deletions and 0% for duplications. The low concordance rate between PennCNV and QuantiSNP indicated that neither algorithm, by itself, could identify all CNVs in the population. In total, PennCNV and QuantiSNP collectively identified 747,129 deletions and 432,523 duplications; 80.2% of all duplications and 69.1% of all deletions were present only once in the population. Only 0.154% of all CNVs identified were present in more than 50 animals in the population. The distribution of the percentage of the autosomes that were composed of deletions, per animal, was positively skewed, as was the distribution for the percentage of the autosomes that were composed of duplications, per animal. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of deletions were 0.019%, 0.037%, and 0.201%, respectively. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of duplications were 0.013%, 0.028%, and 0.076%, respectively. The distributions of the number of deletions and duplications per animal were both positively skewed. The interquartile range for the number of deletions per animal in the population was between 16 and 117, whereas for duplications it was between 8 and 23. Per animal, there tended to be twice as many deletions as duplications. The distribution of the length of deletions was positively skewed, as was the distribution of the length of duplications. The interquartile range for the length of deletions in the population was between 25 and 101 kb, and for duplications the interquartile range was between 46 and 235 kb. Per animal, duplications tended to be twice as long as deletions. This study provides a description of the characteristics and distribution of CNVs in a large multibreed population of beef and dairy cattle.

Figure 1.

The mean concordance rate (as a percentage) between CNVs called with PennCNV and QuantiSNP with different overlap criterion for concordant CNVs. The CNVs called by PennCNV and QuantiSNP were considered concordant when a certain percentage of their lengths were overlapping. The black bars represent the interquartile range for the rate of concordance. Deletions are represented by red circles and duplications are represented by blue circles.

Figure 2.

Frequency distribution of the number of copy number variants (CNVs) per animal. The distributions are shown separately for deletions and duplications; animals with >150 (n = 751) duplications or >150 deletions (n = 1,219) not included.

Figure 3.

Distribution of the number of times a given copy number variant (CNV) was present in the population. The distributions are shownseparately for deletions and duplications. Deletions present in more than 10 animals in the population (n = 9,358) and duplications present in more than 10 animals in population (n = 3,096) were not included.

Figure 4.

Frequency distribution of the number of copy number variants (CNVs) by length. The distributions of deletions and duplications are shown separately. Duplications longer than 1,000 kb (n = 2,341) and deletions longer than 1,000 kb (n = 10,611) were not included.

Figure 5.

Interaction plot of the number of times copy number variants (CNVs) appear in the population against mean length of CNVs. Duplications are represented by blue triangles and deletions are represented by the red circles. The black error bars give the 95% confidence interval for each point. Deletions (n = 3,427) and duplications (1,051) present in more than 20 animals in the population were not included.

Figure 6.

Frequency distribution of the percentage of the autosomes that were composed of copy number variants (CNVs) per animal in the population. The distributions are shown separately for deletions and duplications. Animals whose a percentage of the autosomes that were composed of deletions was > 0.25% (n = 1,218), or animals whose percentage of the autosomes that were composed of duplications was > 0.25% (n = 953) were not included.