Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations

Finding Predictors of Leg Defects in Pigs Using CNV-GWAS

One of the most important areas of modern genome research is the search for meaningful relationships between genetic variants and phenotypes. In the livestock field, there has been research demonstrating the influence of copy number variants (CNVs) on phenotypic variation. Despite the wide range in the number and size of detected CNVs, a significant proportion differ between breeds and their functional effects are underestimated in the pig industry. In this work, we focused on the problem of leg defects in pigs (lumps/growths in the area of the hock joint on the hind legs) and focused on searching for molecular genetic predictors associated with this trait for the selection of breeding stock. The study was conducted on Large White pigs using three CNV calling tools (PennCNV, QuantiSNP and R-GADA) and the CNVRanger association analysis tool (CNV-GWAS). As a result, the analysis identified three candidate CNVRs associated with the formation of limb defects. Subsequent functional analysis suggested that all identified CNVs may act as potential predictors of the hock joint phenotype of pigs. It should be noted that the results obtained indicate that all significant regions are localized in genes (CTH, SRSF11, MAN1A1 and LPIN1) responsible for the metabolism of amino acids, fatty acids, glycerolipids and glycerophospholipids, thereby related to the immune response, liver functions, content intramuscular fat and animal fatness. These results are consistent with previously published studies, according to which a predisposition to the formation of leg defects can be realized through genetic variants associated with the functions of the liver, kidneys and hematological characteristics.

Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data

Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75-2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, β-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle

Copy number variants (CNVs), which are a class of structural variant, can be important in relating genomic variation to phenotype. The primary aims of this study were to discover the common CNV regions (CNVRs) in the dual-purpose XinJiang-Brown cattle population and to detect differences between CNVs inferred using the ARS-UCD 1.2 (ARS) or the UMD 3.1 (UMD) genome assemblies based on the 150K SNP (Single Nucleotide Polymorphisms) Chip. PennCNV and CNVPartition methods were applied to calculate the deviation of the standardized signal intensity of SNPs markers to detect CNV status. Following the discovery of CNVs, we used the R package HandyCNV to generate and visualize CNVRs, compare CNVs and CNVRs between genome assemblies, and identify consensus genes using annotation resources. We identified 38 consensus CNVRs using the ARS assembly with 1.95% whole genome coverage, and 33 consensus CNVRs using the UMD assembly with 1.46% whole genome coverage using PennCNV and CNVPartition. We identified 37 genes that intersected 13 common CNVs (>5% frequency), these included functionally interesting genes such as GBP4 for which an increased copy number has been negatively associated with cattle stature, and the BoLA gene family which has been linked to the immune response and adaption of cattle. The ARS map file of the GGP Bovine 150K Bead Chip maps the genomic position of more SNPs with increased accuracy compared to the UMD map file. Comparison of the CNVRs identified between the two reference assemblies suggests the newly released ARS reference assembly is better for CNV detection. In spite of this, different CNV detection methods can complement each other to generate a larger number of CNVRs than using a single approach and can highlight more genes of interest.

Comparative analyses of copy number variations between Bos taurus and Bos indicus

Background

Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied.

Results

Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on F_ST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage.

Conclusions

This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays

Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp-4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle

Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip

Background

Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks.

Results

A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5.53 kb to 1148.45 kb, with an average size of 170.31 kb. Eight out of nine randomly chosen CNVRs were successfully validated by qPCR. A functional enrichment analysis of the CNVR-associated genes indicated their relationship to a number of molecular adaptations that enable yaks to thrive at high altitudes. One third of the detected CNVRs were mapped to QTLs associated with six classes of economically important traits, indicating that these CNVRs may play an important role in variations of these traits.

Conclusions

Our genome-wide yak CNV map may thus provide valuable insights into both the molecular mechanisms of high altitude adaptation and the potential genomic basis of economically important traits in yak.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5759-1) contains supplementary material, which is available to authorized users.

Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins

BACKGROUND

Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock.

RESULTS

We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs were simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results.

CONCLUSION

To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.

Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis )

Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to the UMD3.1 cattle genome, we identified 1,038 segmental duplications comprising 44.6 Mb (equivalent to ~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the buffalo genome. We experimentally validated 70.3% (71/101) of these duplications using fluorescent in situ hybridization. We also detected a total of 1,344 CNV regions across 14 additional water buffaloes, amounting to 59.8 Mb of variable sequence or the equivalent of 2.2% of the cattle genome. The CNV regions overlap 1,245 genes that are significantly enriched for specific biological functions including immune response, oxygen transport, sensory system and signal transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffaloes as test samples and Olimpia as the reference. Using a linear regression model, a high Pearson correlation (r = 0.781) was observed between the log₂ ratios between copy number estimates and the log₂ ratios of aCGH probes. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions. These results confirm sub-chromosome-scale structural rearrangements present in the cattle and water buffalo. The information on genome variation that will be of value for evolutionary and phenotypic studies, and may be useful for selective breeding of both species.

Diversity of copy number variation in the worldwide goat population

Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.

Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances

Background

Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle.

Methods

ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses.

Results

In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR.

Conclusions

Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0414-x) contains supplementary material, which is available to authorized users.

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.

Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

BACKGROUND

Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for genome-wide association study (GWAS). Recently, GWAS analysis using CNV has been applied in livestock, although few studies have focused on Holstein cattle.

RESULTS

We describe 191 CNV detected using intensity data from over 700,000 SNP genotypes generated with the BovineHD Genotyping BeadChip (Illumina, San Diego, CA) in 528 Holstein cows. The CNV were used for GWAS analysis of 10 important production traits of 473 cattle related to feed intake, milk quality, and female fertility, as well as 2 composite traits of net merit and productive life. In total, we detected 57 CNV associated (P < 0.05 after false discovery rate correction) with at least one of the 10 phenotypes. Focusing on feed efficiency and intake-related phenotypes of residual feed intake and dry matter intake, we detected a single CNV associated with both traits which overlaps a predicted olfactory receptor gene OR2A2 (LOC787786). Additionally, 2 CNV within the RXFP4 (relaxin/insulin like family peptide receptor 4) and 2 additional olfactory receptor gene regions, respectively, were associated with residual feed intake. The RXFP4 gene encodes a receptor for an orexigenic peptide, insulin-like peptide 5 produced by intestinal L cells, which is expressed by enteric neurons. Olfactory receptors are critical for transmitting the effects of odorants, contributing to the sense of smell, and have been implicated in participating in appetite regulation.

CONCLUSIONS

Our results identify CNV for genomic evaluation in Holstein cattle, and provide candidate genes, such as RXFP4, contributing to variation in feed efficiency and feed intake-related traits. These results indicate potential novel targets for manipulating feed intake-related traits of livestock.

Distribution and Functionality of Copy Number Variation across European Cattle Populations

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.