Identification of copy number variations and common deletion polymorphisms in cattle

The Identification of Goat KCNJ15 Gene Copy Number Variation and Its Association with Growth Traits

(1) Background: Copy number variation (CNV) is a critical component of genome structural variation and has garnered significant attention. High-throughput screening of the KCNJ15 gene has revealed a correlation between the CNV region and the growth traits of goats. We aimed to identify the CNV of the KCNJ15 gene in five goat breeds and analyze its association with growth characteristics. (2) Methods: We utilized 706 goats from five breeds: Guizhou black goat (GZB), Guizhou white goat (GZW), Bohuai goat (BH), Huai goat (HH), and Taihang goat (TH). To evaluate the number of copies of the KCNJ15 gene using qPCR, we analyzed the correlation between the CNV and growth characteristics and then used a universal linear model. The findings revealed variations in the distribution of different copy number types among the different goat breeds. (3) Results: Association analysis revealed a positive influence of the CNV in the KCNJ15 gene on goat growth. In GZB, individuals with duplication types exhibited superior performance in terms of cannon bone circumference (p < 0.05). In HH, individuals with duplication types exhibited superior performance in terms of body slanting length (p < 0.05). Conversely, normal TH demonstrated better body height and body weight (p < 0.05), while in GZW, when CN = 3, it performed better than other types in terms of body weight and chest circumference (p < 0.05). However, in BH, it had no significant effect on growth traits. (4) Conclusions: We confirmed that the CNV in the KCNJ15 gene significantly influences the growth characteristics of four distinct goat breeds. The correlation between KCNJ15 gene CNVs and goat growth traits offers valuable insights to breeders, enabling them to employ precise and efficient breeding methods that enhance livestock welfare, productivity, and overall economic benefits in the industry.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows

Milk production traits are the most important quantitative economic traits in dairy cow production; improving the yield and quality of milk is an important way to ensure the production efficiency of the dairy industry. This study carried out a series of in-depth statistical genetics studies and molecular analyses on the Chinese Holstein cows in the Jiangsu Province, such as descriptive statistics and copy number variation analysis. A genetic correlation, phenotypic correlation, and descriptive statistical analysis of five milk production traits (milk yield, milk fat percentage, milk fat yield, milk protein percentage, and milk protein yield) of the dairy cows were analyzed using the SPSS and DMU software. Through quality control, 4173 cows and their genomes were used for genomic study. Then, SNPs were detected using DNA chips, and a copy number variation (CNV) analysis was carried out to locate the quantitative trait loci (QTL) of the milk production traits by Perl program software Penn CNV and hidden Markov model (HMM). The phenotypic means of the milk yield, milk fat percentage, milk fat mass, milk protein percentage, and milk protein mass at the first trimester were lower than those at the other trimesters by 8.821%, 1.031%, 0.930%, 0.003%, and 0.826%, respectively. The five milk production traits showed a significant phenotypic positive correlation (p < 0.01) and a high genetic positive correlation among the three parities. Based on the GGPBovine 100 K SNP data, QTL-detecting research on the fist-parity milk performance of dairy cows was carried out via the CNV. We identified 1731 CNVs and 236 CNVRs in the 29 autosomes of 984 Holstein dairy cows, and 19 CNVRs were significantly associated with the milk production traits (p < 0.05). These CNVRs were analyzed via a bioinformatics analysis; a total of 13 gene ontology (GO) terms and 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to lipid metabolism, amino acid metabolism, and cellular catabolic processes. This study provided a theoretical basis for the molecular-marker-assisted selection of dairy cows by developing descriptive statistics on the milk production traits of dairy cows and by locating the QTL and functional genes that affect the milk production traits of first-born dairy cows. The results describe the basic status of the milk production traits of the Chinese Holstein cows in Jiangsu and locate the QTL and functional genes that affect the milk production traits of the first-born cows, providing a theoretical basis for the molecular-marker-assisted selection of dairy cows.

Copy number variations of LRRFIP1 gene and the relationship with growth traits in four Chinese sheep

CNVs (copy number variations) are the novel and common structural variants that could cover entire genes found in plenty of species. CNV may influence economically important traits or disease susceptibility in livestock species. Based on the whole genome resequencing results, we found that there was a CNV region on the LRRFIP1 gene. Then we used qPCR to detect the copy number type distribution in 553 individuals of four sheep breeds and used them for association analysis. The results showed that: (1) In the CKS, the sheep with gain type had a larger heart girth (p = 0.049). (2) For the HS, the CNV could significantly affect rump breadth (p = 0.037) and circumference of the cannon (p = 0.035). And the sheep with median type showed better performance in rump breadth and circumference of cannon. (3) At the STHS, the CNV was significantly correlated with chest width (p = 0.000) with loss type as the most favorable CNV type. Meanwhile, the best was the loss type, and the lowest was the median. (4) This CNV had no significant effect on the LTHS. So, the CNV of LRRFIP1 was related to the growth traits of these three sheep breeds and it may be used as a molecular marker for sheep.

Association between copy number variation of SERPINA3-1 gene and growth traits in Chinese cattle

Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 (SERPINA3) belongs to the serine protease inhibitor family A subtype, and contains 8 genes from SERPINA3-1 to SERPINA3-8. Although the regulatory effects of these 8 genes have been revealed one by one in recent years, the related effects of SERPINA3-1 gene on cattle growth is still unclear. This study used quantitative Real time PCR (qPCR) to detect the type of copy number variation (CNV) of SERPINA3-1 gene in a total of 542 Chinese cattle, and expression of SERPINA3-1 gene in different tissues of Qinchuan cattles (adult) on mRNA level. Then association analysis was conducted between the detection results and cattle growth traits. The results showed that the Duplication type in SERPINA3-1 gene performed better on the growth traits and the CNV was significantly correlated with multiple growth traits (p < 0.05). In addition, SERPINA3-1 gene has different expression conditions in different tissues, results showed that SERPINA3-1 gene has a low expression in muscle. In conclusion, we speculate that the SERPINA3-1 gene can be used as a molecular marker and the result of this study could be a basic material for candidate functional genes for beef cattle growth and development.

Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep

Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.

Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak

Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

Genome-wide elucidation of CNV regions and their association with production and reproduction traits in composite Vrindavani cattle

The present study was aimed to analyze the genome-wide copy number variations (CNVs) in Vrindavani composite cattle and concatenate them into CNV regions (CNVRs), and finally test the association of CNVRs with different production and reproduction traits. Genotypic data, generated on BovineSNP50 Beadchip (v3) array for 96 Vrindavani animals, was used to elucidate the CNVs at the genome level. Intensity data covering over 53,218 SNP genotypes on bovine genome was used. Algorithm based on Hidden Markov Model was employed in PennCNV program to detect, normalize and filter CNVs across the genome. 252 putative CNVs, detected via PennCNV program, in different individuals were concatenated into 71 CNV regions (CNVRs) using CNVRuler program. Association of CNVRs with important (re)production traits in Vrindavani animals was assessed using linear regression. Five CNVRs were found to be significantly associated with ten important (re)production traits. The genes harbored in these regions provided useful insights into the association of CNVRs with genes and ultimately the variation at phenotype level. Important genes that overlapped with CNVRs included WASHC4, HS6ST3, MBNL2, TOLLIP, PIDD1 and TSPAN4. Furthermore, the CNVRs were found to overlap with important QTLs available in AnimalQTL database which affect milk yield and composition along with reproduction and immune function traits. The copy number states of three enes were validated using digital droplet PCR technique. The results from the present study significantly enhance the understanding about CNVs in Vrindavani cattle and should help establish its CNV map. The study will also enable further investigation on association of these variants with important traits of economic interest including disease incidence.

Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits

Copy number variation (CNV) is a structural variant with significant impact on genetic diversity. CNV has been widely used in breeding for growth traits, meat production or quality, and coat color. SRY-like box genes (SOXs) are a class of transcription factors that play a regulatory role in cell fate specification and differentiation. SOX5 and SOX8 belong to subgroups D and E of the SOXs, respectively. Previous studies have shown that SOX5 and SOX8 are essential in the development of bones. In this study, we explored the association between the growth traits and CNVs of SOX5 and SOX8 in 326 Ashidan yaks and detected mRNA expression levels in different tissues. Our results illustrated that CNVs of SOX5 and SOX8 were significantly associated with withers height at 18 months of age and chest girth at 30 months of age (p < 0.05). The CNV combination of SOX5 and SOX8 was significantly associated with withers height at 18 months of age (p < 0.01). SOX5 expression in the lung was significantly higher than in the heart, spleen, kidney, and muscle (p < 0.05). SOX8 expression in the lung was significantly higher than in the liver and muscle (p < 0.05). Our results provide evidence that the CNVs of SOX5 and SOX8 genes could be used as new markers for the selection of yak growth traits.

Copy number variation (CNV) of the AHR gene in the Ashidan yak and its association with growth traits

Copy number variation (CNV) is a principal genomic structure variation affecting the gene expression through the dose-effect and change of gene regulatory region. It plays an important role in regulating the various complex traits of vertebrates. The aromatic hydrocarbon receptor (AHR) is a member of ligand-dependent transcription factors which belong to the alkaline helix-loop-helix PASS family. It is used as a conservative environmental sensor during biological evolution. This study, tracked the growth data (body weight, withers height, body length, chest girth) of 332 yaks in four stages (6, 12, 18, and 30 months) were tracked. The CNV of the yaks was analyzed using real-time quantitative PCR, and the correlation between CNV of AHR and yak growth traits was analyzed using the SPSS and R software. The AHR gene expression profiles were assessed in different tissues of the 18-month-old yak. The statistical analysis indicated the AHR-CNV of the Ashidan yak to significantly correlate with the body length (P < 0.05), and was found to be correlated with the withers height at 18 months old (P < 0.01) with extreme significance. To sum up, this study for the first time discussed the relationship between AHR-CNV and the growth traits of the Ashidan yak. The results indicated that the AHR gene might become a new molecular marker in the breeding yak.

Detection of InDel and CNV of SPAG17 gene and their associations with bovine growth traits

Sperm-associated antigen 17 (SPAG17) gene encodes a central pair protein, which is involved in flagellar motility, male fertility and skeletal growth in ruminants. The insertions/deletions (indels) and copy number variations (CNVs) influence phenotypic traits by altering the sequences and copy numbers of functional genes, respectively. This study identified a novel 8-bp indel of SPAG17 gene in 1520 individuals from eight different cattle breeds, as well as a novel CNV region in 355 animals. The correlation analysis of indel showed that the individuals of ID genotype had superior performance traits such as body height (p = 0.038) and body slanting length (p = 0.041) as compared to other genotypes in Xianan cattle. For the CNV, different copy numbers were closely related to the body height in Qinchuan (p = 0.045) and body weight in Xianan (p = 0.036) breeds. Importantly, significant difference was observed between the 8-bp indel and the copy number loss in Xianan breed (p < 0.01). These findings indicated that the variations within the bovine SPAG17 gene can be considered as an effective DNA molecular marker for beef cattle breeding.

Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds

Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.

Genome-wide detection of copy number variations in Tharparkar cattle

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome.

A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle

BACKGROUND

Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, whereas genetic factors affecting the susceptibility of calves to death are not well known. To identify variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait with a threshold model and performed a genome-wide copy number variation (CNV) association study on calf mortality.

RESULTS

We identified a 44-kb deleted-type CNV ranging from 103,317,687 to 103,361,802 bp on chromosome 5, which was associated with the mortality of 1-180-day-old calves. The CNV harbored C1RL, a pseudogene, and an IncRNA localized in the C1R and C1S gene cluster, which is a component of the classical complement activation pathway for immune complexes for infectious pathogens. The average complement activity in CNVR_221 homozygotes at postnatal day 7 was significantly lower than that of wild-type animals and heterozygotes. The frequency of the risk allele in dead calves suffering from diarrhea and pneumonia and in healthy cows was 0.35 and 0.28, respectively (odds ratio = 2.2, P = 0.016), suggesting that CNVR_221 was associated with the mortality of Japanese Black calves suffering from an infectious disease.

CONCLUSIONS

This study identified a deleted-type CNV associated with the mortality of 1-180-day-old calves. The complement activity in CNVR_221 homozygotes was significantly lower than that in heterozygotes and wild type animals. The frequency of the risk allele was higher in dead calves suffering from an infectious disease than in healthy cows. These results suggest that the existence of CNVR_221 in calves could be attributed to a reduction in complement activity, which in turn leads to susceptibility to infections. Thus, the risk allele could serve as a useful marker to reduce the mortality of infected Japanese Black calves.

Genome-wide association study between copy number variation regions and carcass- and meat-quality traits in Nellore cattle

Context Indicine breeds are the main source of beef products in tropical and subtropical regions. However, genetic improvement for carcass- and meat-quality traits in zebu cattle have been limited and genomics studies concerning structural variations that influence these traits are essential. Aim The aim of this study was to perform a genome-wide association study between copy number variation regions (CNVRs) and carcass- and meat quality-traits in Nellore cattle. Methods In total, 3794 animals, males and females included, were genotyped using a 777962 single-nucleotide polymorphism platform of BovineHD BeadChip (777k; Illumina Inc.). Of these, 1751 Nellore bulls were slaughtered at 24 months of age for further carcass beef analysis. The following traits were studied: beef tenderness, marbling, rib-eye area, backfat thickness and meat colour (lightness, redness and yellowness). The CNV detection was conducted through PennCNV software. The association analyses were performed using CNVRuler software. Key results Several identified genomic regions were linked to quantitative trait loci associated with fat deposition (FABP7) and lipid metabolism (PPARA; PLA2 family; BCHE), extracellular matrix (INS; COL10A1), contraction (SLC34A3; TRDN) and muscle development (CAPZP). The gene-enrichment analyses highlighted biological mechanisms directly related to the metabolism and synthesis of lipids and fatty acids. Conclusions The large number of potential candidate genes identified within the CNVRs, as well as the functions and pathways identified, should help better elucidate the genetic mechanisms involved in the expression of beef and carcass traits in Nellore cattle. Several CNVRs harboured genes that might have a functional impact to improve the beef and carcass traits. Implications The results obtained contribute to upgrade the sensorial and organoleptic attributes of Nellore cattle and make feasible the genetic improvement of carcass- and meat-quality traits.

Copy number variation of the HPGDS gene in the Ashidan yak and its associations with growth traits

Copy number variation (CNV) is a structural variation at the submicroscopic level of the genome, which can affect gene-related phenotypes by changing genes dosage and transcript structure. Hematopoietic prostaglandin D synthase (HPGDS) is a member whose functions are closely related to weight gain and inflammatory diseases of the glutathione S-transferase (GSTs) family. In this study, the growth characteristics (body weight, withers height, body length, and chest girth) of 336 Ashidan yaks were monitored at four stages (6 months, 12 months, 18 months, and 30 months). In addition, CNV of the HPGDS gene was detected, discovered relationships of CNV with growth traits, and explored the level of gene expression. Based on the statistical analysis by IBM SPSS software, significant correlations were observed between HPGDS-CNV and body weight in 12-month-old yak (P < 0.01), 18-month-old yak (P < 0.001) and 30-month-old yak (P < 0.001) and body length in 18-month-old yak (P < 0.05) and 30-month-old yak (P < 0.05), respectively. Additionally, the individuals with gain copy number type performed better in body weight and body length than those with normal or loss copy number type. To our best of knowledge, this is the first time to make efforts to probe into the role of HPGDS-CNV and its interaction with livestock growth traits. Our results suggested that the CNV of the HPGDS gene may be an active candidate gene for the marker-assisted selection (MAS) of yaks.

Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle

Copy number variation (CNV) represents a major source of genetic variation, which may have potentially large effects, including alternating gene regulation and dosage, as well as contributing to gene expression and risk for normal phenotypic variability. We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. Totally, we found 9313 deletion and 234 duplication events, covering 147.5 Mb autosomal regions. Within them, 257 deletion events of high frequency overlapped with 193 known RefGenes. Among these genes, we observed several genes were related to economically important traits, like residual feed intake, immune responding, pregnancy rate and muscle differentiation. Using a locus-based analysis, we identified 11 deletions and 1 duplication, which were significantly associated with three traits including carcass weight, tenderloin and longissimus muscle area. Our sequencing-based study provided important insights into investigating the association of CNVs with important traits in beef cattle.

Goat sperm associated antigen 17 protein gene (SPAG17): Small and large fragment genetic variation detection, association analysis, and mRNA expression in gonads

Transcriptome sequencing analyses have suggested that sperm associated antigen 17 protein gene (SPAG17) may play important regulating roles in litter size. In this study, the expression profiles and genetic variations of the SPAG17 were studied in Shaanbei White Cashmere (SBWC) goats (n=1567). SPAG17 was highly expressed in testis and ovary of SBWC goats. At different developmental stages, it also continued to be highly expressed in testis. In addition, two variations of SPAG17, one indel locus and one copy number variation locus, were significantly associated with first-born litter size. Joint analysis results suggested that two polymorphic loci of the SPAG17 gene may regulate host gene expression in goat ovary and testis. Overall, the results indicated the important role of SPAG17 in the reproductive process of goats.

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Simple Summary

The PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) gene is a member of the PIG gene family and encodes the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex. It initiates the biosynthesis of GPI and plays an important role in cell–cell interactions. Sequencing has revealed a 3600 bp copy number variation (CNV) in exon 2 of the PIGY gene in sheep, potentially altering a functional part of the protein. The CNV overlaps 28 quantitative trait loci that are relevant to some economic traits like muscle density and carcass weight. We screened for this CNV of the PIGY gene in 569 individuals, namely, 240 Chaka sheep (CKS), 168 Hu sheep (HS), and 161 small-tailed Han sheep (STHS), and analyzed the association between the presence of this CNV and sheep body size traits. The results showed that the loss-type CNV was more prevalent than other types in these three breeds, and there were significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of cannon bone of sheep. The results showed that sheep with gain-type CNV had better growth traits than those with other types. The findings reveal the relationship between the CNV of the PIGY gene and growth traits of sheep, suggesting that CNV could be utilized for improved molecular breeding of sheep.

Abstract

Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601–36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

Copy Number Variations and Expression Levels of Guanylate-Binding Protein 6 Gene Associated with Growth Traits of Chinese Cattle

Association studies have indicated profound effects of copy number variations (CNVs) on various phenotypes in different species. In this study, we identified the CNV distributions and expression levels of guanylate-binding protein 6 (GBP6) associated with the growth traits of Chinese cattle. The results showed that the phenotypic values of body size and weight of Xianan (XN) cattle were higher than those of Nanyang (NY) cattle. The medium CNV types were mostly identified in the XN and NY breeds, but their CNV distributions were significantly different (adjusted p < 0.05). The association analysis revealed that the body weight, cannon circumference and chest circumference of XN cattle had significantly different values in different CNV types (p < 0.05), with CNV gain types (Log22-ΔΔCt > 0.5) displaying superior phenotypic values. We also found that transcription levels varied in different tissues (p < 0.001) and the CNV gain types showed the highest relative gene expression levels in the muscle tissue, consistent with the highest phenotypic values of body weight and cannon circumference among the three CNV types. Consequently, our results suggested that CNV gain types of GBP6 could be used as the candidate markers in the cattle-breeding program for growth traits.

Novel copy number variation of the BAG4 gene is associated with growth traits in three Chinese sheep populations

Copy number variation (CNV) as an important source of genetic phenotypic and variation is related to complex phenotypic traits. The aim of this study was to investigate the potential associations of BAG4 (Bcl-2-associated athanogene 4) copy numbers variations with sheep growth traits in three Chinese sheep breeds (CKS, STHS, and HS). BAG4 is located within the stature and udder attachment quantitative trait loci (QTL) in sheep. Expression profiling revealed that the BAG4 gene was widely expressed in the tissues of sheep. The distribution of BAG4 gene copy number showed that the loss of copy number was more dominant in CKS and HS which was different from that in STHS. Statistical analysis revealed that the BAG4 CNV was significantly associated with body height in CKS (p < 0.05), with body slanting length in HS (p < 0.05), and with body height and hip cross height in STHS (p < 0.05). The χ² values showed significant differences in the BAG4 CNV distribution frequency between varieties. In conclusion, the results establish the association between BAG4 CNV and sheep traits and suggest that BAG4 CNV may be a promising marker for the molecular breeding of Chinese sheep.

A large interactive visual database of copy number variants discovered in taurine cattle

BACKGROUND

Copy number variants (CNVs) contribute to genetic diversity and phenotypic variation. We aimed to discover CNVs in taurine cattle using a large collection of whole-genome sequences and to provide an interactive database of the identified CNV regions (CNVRs) that includes visualizations of sequence read alignments, CNV boundaries, and genome annotations.

RESULTS

CNVs were identified in each of 4 whole-genome sequencing datasets, which together represent >500 bulls from 17 breeds, using a popular multi-sample read-depth-based algorithm, cn.MOPS. Quality control and CNVR construction, performed dataset-wise to avoid batch effects, resulted in 26,223 CNVRs covering 107.75 unique Mb (4.05%) of the bovine genome. Hierarchical clustering of samples by CNVR genotypes indicated clear separation by breeds. An interactive HTML database was created that allows data filtering options, provides graphical and tabular data summaries including Hardy-Weinberg equilibrium tests on genotype proportions, and displays genes and quantitative trait loci at each CNVR. Notably, the database provides sequence read alignments at each CNVR genotype and the boundaries of constituent CNVs in individual samples. Besides numerous novel discoveries, we corroborated the genotypes reported for a CNVR at the KIT locus known to be associated with the piebald coat colour phenotype in Hereford and some Simmental cattle.

CONCLUSIONS

We present a large comprehensive collection of taurine cattle CNVs in a novel interactive visual database that displays CNV boundaries, read depths, and genome features for individual CNVRs, thus providing users with a powerful means to explore and scrutinize CNVRs of interest more thoroughly.

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Simple Summary

Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss- or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects.

Abstract

Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.

Associations of ORMDL1 gene copy number variations with growth traits in four Chinese sheep breeds

Copy number variations (CNVs) are gains and losses of genomic sequence of more than 50 bp between two individuals of a species. Also, CNV is considered to be one of the main elements affecting the phenotypic diversity and evolutionary adaptation of animals. ORMDL sphingolipid biosynthesis regulator 1 (ORMDL1) is a protein-coding gene associated with diseases and development. In our study, the polymorphism of ORMDL1 gene copy numbers in four Chinese sheep breeds (abbreviated CK, HU, STH, and LTH) was detected. In addition, we analyzed the transcriptional expression level of ORMDL1 gene in different tissues of sheep and examined the association of ORMDL1 CNV with growth traits. The statistical analysis revealed that ORMDL1 CNV was remarkably correlated with body height, heart girth, and circumference of cannon bone in HU sheep (P<0.05), and there are significant effects on body weight, body height, body length, chest depth, and height of hip cross in STH sheep (P<0.05). In conclusion, our results provide a basis for the relationship between CNV of ORMDL1 gene and sheep growth traits, suggesting that ORMDL1 CNV may be considered a promising marker for the molecular breeding of Chinese sheep.

Copy Number Variation of the SHE Gene in Sheep and Its Association with Economic Traits

Simple Summary

Src Homology 2 Domain Containing E (SHE) is a protein coding gene, and member of the SH2 domain-containing family. Sequencing revealed a 2000 bp copy number variation in the SHE gene. There is overlap between SHE copy number variation (CNV) and quantitative trait loci related to milk fat percentage and bone density. A total of 750 sheep, including Chaka sheep (CKS), Hu sheep (HS), Small Tail Han sheep (STHS) and Large Tail Han sheep (LTHS) were available to detect the CNV of the SHE gene and correlate these gene variations with economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS. Association analysis showed that gain and normal copy number types performed better in body length (p < 0.05), circumference of cannon bone (p < 0.05), heart girth (p < 0.05), chest width (p < 0.05) and high at the cross (p < 0.05) in CKS, HS and STHS. Chi-square analyses found significant variation in the CNV of the SHE gene, so it varies greatly between varieties. These findings clarified the relationship between the CNV of the SHE gene and the economic traits in these four kinds of sheep, and provide a reference for sheep breeding.

Abstract

Copy number variation (CNV) caused by gene rearrangement is an important part of genomic structural variation. We found that the copy number variation region of the Src Homology 2 Domain Containing E (SHE) gene correlates with a quantitative trait locus of sheep related to milk fat percentage and bone density. The aim of our study was to detect the copy number variation of the SHE gene in four sheep breeds and to conduct a correlation analysis with economic traits, hoping to provide some reference for sheep breeding. In this study, we examined 750 sheep from four Chinese breeds: Chaka sheep (CKS), Hu sheep (HS), Large Tail Han sheep (LTHS) and Small Tail Han sheep (STHS). We used qPCR to evaluate the copy number of the SHE gene, and then used general linear models to analyze the associations between CNV and economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS individuals. Association analyses showed that gain and normal copy number types were correlated to body length, circumference of cannon bone, heart girth, chest width and high at the cross in CKS, HS and STHS (p < 0.05), but this association was not observed for LTHS. Chi-square values (χ²) found prominent differences in CNV distribution among the studied breeds. Overall, the CNV of the SHE gene may be an important consideration for sheep molecular breeding.

Copy number variation of MYLK4 gene and its growth traits of Capra hircus (goat)

Copy number variation (CNV) is a form of genetic variation caused by genome rearrangement, with abnormal fragments ranging from 50 bp to Mb. And, CNV is closely related to disease, growth and reproductive shape of livestock. As a member of myosin light chain kinase (MYLK) family with serine/threonine specificity, MYLK4 belongs to an enzyme encoded by MYLK4 gene. Although MYLK4 is a recognized kinase, its function has yet to be revealed in subsequent studies. This study aims to analyze CNV and genetic effects of MYLK4 gene in goats. We used qPCR to detect CNV of MYLK4 gene in African Nubian goat (n = 32), Guizhou black goat (n = 196) and Guizhou white goat (n = 95), respectively, and correlated CNV data of MYLK4 gene with goat growth traits in Chinese goats. The results showed that the effect of MYLK4 gene CNV on body weight, body length and body height of goats had significantly different (p < 0.05, Q < 0.05), in which CNV showed better growth traits in type of deletion. Therefore, CNV of MYLK4 gene can be used as a molecular marker for assisted selection of goat growth traits, which provides a theoretical basis for the genetic improvement of goat breeds in China.

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.

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.

Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle

Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak and dairy cattle, the beef cattle like Luxi and Xianan breed had significantly higher median copy numbers, suggesting the diversity of SHH-CNV in beef cattle selections. The negative correlation of SHH-CNV with SHH transcriptional level in adult adipose tissue (P < 0.01) indicated the dosage effects of SHH-CNV related to bovine fat formation. Association analysis of SHH-CNV and body size traits was conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significantly better chest depth in 24 months old Qinchuan cattle, and better body weight, body length, and chest girth in 18 months old Nanyang cattle, whereas the normal copy number had superior chest girth and body weight in adult Jinnan cattle (P < 0.05 or P < 0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expression and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.

Copy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traits

The insulin-like growth factor 1 receptor (IGF1R) plays a vital role in immunomodulation and muscle and bone growth. The copy number variation (CNV) is believed to the reason for many complex phenotypic variations. In this paper, we statistically analyzed the copy number and the expression profiling in different tissue types of the IGF1R gene using the 422 samples from four Chinese beef cattle breeds, and the mRNA of IGF1R was widely expressed in nine tissue types of adult cattle (heart, liver, kidney, muscle, fat, stomach, spleen, lung and testis). Results of CNV and growth traits indicated that the IGF1R CNV was significantly associated with body weight and body height of Jinnan (JN) cattle and was significantly associated with body height and hucklebone width of Qinchuan (QC) cattle, making IGF1R CNV a promising molecular marker to improve meat production in beef cattle breeding. Bioinformatics predictions show that the CNV region is highly similar to the human genome, and there are a large number of transcription factors, DNase I hypersensitive sites, and high levels of histone acetylation, suggesting that this region may play a role in transcriptional regulation, providing directions for further study of the role of bovine CNV and economic traits.

Genome-wide detection of copy-number variations in local cattle breeds

The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.

Detection of copy number variations in brown and white layers based on genotyping panels with different densities

Background

Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis for 18,719 individuals from four pure lines and one commercial cross of layer chickens. Samples were genotyped on four single nucleotide polymorphism (SNP) genotyping platforms, i.e. the Illumina 42K, Affymetrix 600K, and two different customized Affymetrix 50K chips. CNV recovered from the Affymetrix chips were identified by using the Axiom^® CNV Summary Tools and PennCNV software and those from the Illumina chip were identified by using the cnvPartition in the Genome Studio software.

Results

The mean number of CNV per individual varied from 0.50 to 4.87 according to line or cross and size of the SNP genotyping set. The length of the detected CNV across all datasets ranged from 1.2 kb to 3.2 Mb. The number of duplications exceeded the number of deletions for most lines. Between the lines, there were considerable differences in the number of detected CNV and their distribution. Most of the detected CNV had a low frequency, but 19 CNV were identified with a frequency higher than 5% in birds that were genotyped on the 600K panel, with the most common CNV being detected in 734 birds from three lines.

Conclusions

Commonly used SNP genotyping platforms can be used to detect segregating CNV in chicken layer lines. The sample sizes for this study enabled a detailed characterization of the CNV landscape within commercially relevant lines. The size of the SNP panel used affected detection efficiency, with more CNV detected per individual on the higher density 600K panel. In spite of the high level of inter-individual diversity and a large number of CNV observed within individuals, we were able to detect 19 frequent CNV, of which, 57.9% overlapped with annotated genes and 89% overlapped with known quantitative trait loci.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0428-4) contains supplementary material, which is available to authorized users.

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.

Copy Number Variations of KLF6 Modulate Gene Transcription and Growth Traits in Chinese Datong Yak (Bos Grunniens)

Copy number variation (CNV) is a significant marker of the genetic and phenotypic diversity among individuals that accounts for complex quantitative traits of phenotype and diseases via modulating gene dosage and disrupting coding regions in the genome. Biochemically, Kruppel-like factor 6 (KLF6) genes plays a significant role in the regulation of cell differentiation and proliferation and muscle development. The aim of this study was to detect the distributions of KLF6 copy number variations (CNVs) in five breeds of domestic yak and to explore their effect on growth traits and gene expression. The data were analyzed by real-time quantitative PCR (qPCR). Our results elucidated that a decreased CNV in the KLF6 gene is more highly associated (p < 0.05) with various growth traits than increased or normal CNVs in six-month-old and five-year-old Datong yak. Nevertheless, negative correlations between the DNA copy number and KLF6 gene expression were observed in the skeletal muscle of adult Datong yak. These results suggest that CNVs of the KLF6 gene could be crucial genomic markers for growth phenotypes of Chinese Datong yak breeds and this finding constitutes the first evidence of the biological role of KLF6 CNVs in Chinese Datong yak breeds.

Landscape of copy number variations in Bos taurus: individual - and inter-breed variability

Background

The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence.

Results

A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10⁻¹⁵) and in the number of deletions (P < 10⁻¹⁵). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10⁻¹⁵) and deletions (P < 10⁻¹⁵). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals was found in the coding sequence of a novel gene ENSBTAG00000000688 on chromosome 18. In Brown Swiss, Norwegian Red and Simmental breed-specific deletions were located within KIT and MC1R genes, which are responsible for a coat colour. The functional annotation of coding regions underlying the breed-specific CNVs showed that in Norwegian Red, Guernsey, and Simmental significantly under- and overrepresented GO terms were related to chemical stimulus involved in sensory perception of smell and the KEGG pathways for olfactory transduction. In addition, specifically for the Norwegian Red breed, the dopaminergic synapse KEGG pathway was significantly enriched within deleted parts of the genome.

Conclusions

The CNV landscape in Bos taurus genome revealed by this study was highly complex, with inter-breed differences, but also a significant variation within breeds. The former, may explain some of the phenotypic differences among analysed breeds, and the latter contributes to within-breed variation available for selection.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4815-6) contains supplementary material, which is available to authorized users.

Copy number variation in livestock: A mini review

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle

Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds. Though the GBP2 gene copy number presented no correlation with the transcriptional expression of JX (P > .05), but the transcriptional expression in heart is higher than other tissues, and the copy number in muscles and fat of JX is higher than others breeds. Statistical analysis revealed that the GBP2 gene CNV1 and CNV2 were significantly associated with growth traits (P < .05). In conclusion, this research established the correlations between CNVs of GBP2 gene and growth traits in different cattle breeds, and our results suggested that the CNVs in GBP2 gene may be considered markers for the molecular breeding of Chinese beef cattle.

Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set

The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.

Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle

Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V _i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V _ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V _i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Background

Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.

Results

We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.

Conclusions

Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.

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.

In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls

We have identified de novo copy number variations (CNVs) generated in bulls as they age. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 and 111, respectively, i.e. 49% and 51%). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 out of 85). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.

CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Background

Copy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle.

Results

In this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2–11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb).

Conclusions

In conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3636-3) contains supplementary material, which is available to authorized users.