Copy number variation in livestock: A mini review

Copy number variations affecting growth curve parameters in a crossbred chicken population

Copy number variations (CNVs) are key structural variations in the genome and may contribute to phenotypic differences. In this study, we used a F2 chicken population created from reciprocal crossing between fast-growing Arian broiler line and Urmia native chickens. The chickens were genotyped by 60 K SNP BeadChip, and PennCNV algorithm was used to detect genome-wide CNVs. The growth curve parameters of W0, k, L, Wf, Wi, ti and average GR were used as phenotypic data. The association between CNV and growth curve parameters was carried out using the CNVRanger R/Bioconductor package. Five CNV regions (CNVRs) were chosen for the validation experiment using qPCR. Gene enrichment analysis was done using WebGestalt. The STRING database was used to search for significant pathways. The results identified 966 CNVs and 600 CNVRs including 468 gains, 67 losses, and 65 both events on autosomal chromosomes. Validation of the CNVRs obtained from the qPCR assay were 79 % consistent with the prediction by PennCNV. A total of 43 significant CNVs were obtained for the seven growth curve parameters. The 416 genes annotated for significant CNVs. Six genes out of 416 genes were most related to growth curve parameters. These genes were LCP2, Dock2, CD80, CYFIP1, NIPA1 and NIPA2. Some of these genes in their biological process were associated with the growth, reproduction and development of cells or organs that ultimately lead to the growth of the body. The results of the study could pave the way for better understanding the molecular process of CNVs and growth curve parameters in birds.

Characterizing Homozygous Variants in Bardet-Biedl Syndrome-Associated Genes Within Iranian Families: Unveiling a Founder Variant in BBS2, c.471G>A

Bardet-Biedl syndrome (BBS) is a rare inherited ciliopathy disorder characterized by a broad spectrum of clinical symptoms such as retinal dystrophy, obesity, polydactyly, genitourinary and kidney anomalies, learning disability, and hypogonadism. The understanding of the variants involved in BBS-causing genes remains incomplete, highlighting the need for further research to develop a molecular diagnostic strategy for this syndrome. Singleton whole-exome sequencing (WES) was performed on sixteen patients. Our study revealed (1) nine patients carried eight homozygous pathogenic variants with four of them being novel (2) Specifically, a synonymous splicing variant (c.471G > A) in BBS2 gene in six patients with Baloch ethnicity. The identification of runs of homozygosity (ROH) calling was performed using the BCFtools/RoH software on WES data of patients harboring c.471G > A variant. The presence of shared homozygous regions containing the identified variant was confirmed in these patients. In-silico analysis predicted the effect of the c.471G > A variants on BBS2 mRNA splicing. This variant results in disrupted wild-type donor site and intron retention in the mature mRNA. (3) And a deletion of exons 14 to 17 in the BBS1 gene was identified in one patient by Copy-Number Variation (CNV) analysis using the ExomeDepth pipeline. Our results identified the founder variant c.471G > A in the BBS2 gene in the Baloch ethnicity of the Iranian population. This finding can guide the diagnostic approach of this syndrome in future studies.

Progress and future perspectives of livestock genomics in India: a mini review

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle

Crossbreeding forms part of Climate-Smart beef production and is one of the strategies to mitigate the effects of climate change. Two Nguni-sired and three Bonsmara-sired crossbred animals underwent whole genome sequencing. Following quality control and file preparation, the sequence data were investigated for genome-wide copy number variation (CNV) using the panelcn.MOPS tool. A total of 355 CNVs were identified in the crossbreds, of which 274 were unique in Bonsmara-sired crossbreds and 81 unique in the Nguni-sired crossbreds. Genes that differed in copy number in both crossbreds included genes related to growth (SCRN2, LOC109572916) and fertility-related factors (RPS28, LOC1098562432, LOC109570037). Genes that were present only in the Bonsmara-sired crossbreds included genes relating to lipid metabolism (MAF1), olfaction (LOC109569114), body size (HES7), immunity (LOC10957335, LOC109877039) and disease (DMBT1). Genes that were present only in the Nguni-sired crossbreds included genes relating to ketosis (HMBOX1) and amino acid transport (LOC109572916). Results of this study indicate that Nguni and Bonsmara cattle can be utilized in crossbreeding programs as they may enhance the presence of economically important traits associated with both breeds. This will produce crossbred animals that are good meat producers, grow faster, have high fertility, strong immunity and a better chance of producing in South Africa's harsh climate conditions. Ultimately, this study provides new genetic insights into the adaptability of Nguni and Bonsmara crossbred cattle.

Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing

BACKGROUND

De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints.

RESULTS

We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data.

CONCLUSIONS

Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.

Goat MyoD1: mRNA expression, InDel and CNV detection and their associations with growth traits

The Myogenic differentiation 1 (MyoD1) gene is a crucial regulator of muscle formation and differentiation. However, there are few studies on the mRNA expression pattern of the goat MyoD1 gene and its effect on goat growth and development. To address this, we investigated the mRNA expression of the MyoD1 gene in several tissues of fetal and adult goats, containing heart, liver, spleen, lung, kidney and skeletal muscle. The results focused on the expression of the MyoD1 gene in skeletal muscle of fetal goats was much higher than adult goats, suggesting its important role in skeletal muscle formation and development. Following, a total of 619 Shaanbei White Cashmere goats (SBWCs) were used to monitor the InDel (Insertion/Deletion) and CNV (Copy Number Variation) variations of the MyoD1 gene. Three InDel loci were identified, and there was no significant correlation with goat growth traits. Furthermore, a CNV locus containing the MyoD1 gene exon with three types (Loss type, Normal type, Gain type) were identified. The association analysis results showed that the CNV locus was significantly associated with body weight, height at hip cross, heart girth and hip width in SBWCs (P < 0.05). Meanwhile, the Gain type of CNV exhibited the best growth traits and good consistency among three types in goats, suggesting its potential as a DNA marker for marker-assisted breeding of goats. Overall, our study provided a scientific basis for breeding goats with better growth and development traits.

The copy number variation of DMBT1 gene effects body traits in two Chinese cattle breeds

Copy number variations (CNVs) belong to mutations in the genome level with loci in the region of genic or intergenic. It is through different effects (such as position effect and dose effect) that influence complex traits and diseases. Deleted in Malignant Brain Tumors 1 (DMBT1) gene is a member of the scavenger receptor cysteine-rich super family. In cattle, this gene has been associated with the susceptibility to bovine tuberculosis. In this study, a new CNV was found in DMBT1 gene of Chinese cattle breeds and tested in two different Chinese cattle breeds (Jiaxian red and Pinan) for frequency distribution analysis. Besides, the body size data such as body length, body height, chest girth, chest width, rump length, and rump girth for Jiaxian (JX) and Pinan (PN) cattle were collected and associated with the newly identified CNV. The CNV was significantly associated with the body length and chest girth of JX cattle, and the rump length of PN cattle (P < 0.05). Furthermore, the expression profile of the DMBT1 gene was tested in calves' tissues and the myoblasts differentiation. It was found that the DMBT1 gene expression was high in tuberculosis susceptible tissues (liver and lungs) at the calf stage and high in myoblast early differentiation. These tests were done using the qPCR method. As the result, the CNV of DMBT1 gene could be used as a candidate marker for bovine growth and health in marker-assisted selection (MAS) breeding.

GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers

The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.

Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex

The Nubian ibex (Capra nubiana) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species with a specific focus on the environment of Capra nubiana. CNVs are structural genomic variations that have been implicated in phenotypic differences between species and could play a role in species adaptation. CNVs were inferred from Capra nubiana sequence data relative to the domestic goat reference genome using read-depth approach. We identified 191 CNVs overlapping with protein-coding genes mainly involved in biological processes such as innate immune response, xenobiotic metabolisms, and energy metabolisms. We found copy number variable genes involved in defense response to viral infections (Cluster of Differentiation 48, UL16 binding protein 3, Natural Killer Group 2D ligand 1-like, and Interferon-induced transmembrane protein 3), possibly suggesting their roles in Nubian ibex adaptations to viral infections. Additionally, we found copy number variable xenobiotic metabolism genes (carboxylesterase 1, Cytochrome P450 2D6, Glutathione S-transferase Mu 4, and UDP Glucuronosyltransferase-2B7), which are probably an adaptation of Nubian ibex to desert diets that are rich in plant secondary metabolites. Collectively, this study's results advance our understanding of CNVs and their possible roles in the adaptation of Nubian ibex to its environment. The copy number variable genes identified in Nubian ibex could be considered as subjects for further functional characterizations.

SeeCiTe: a method to assess CNV calls from SNP arrays using trio data

Motivation

Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling.

Results

We developed SeeCiTe (Seeing CNVs in Trios), a novel CNV-quality control tool that postprocesses output from current CNV-calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge, it is the first tool that utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artifacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies.

Availability and implementation

The software is implemented in R with the source code freely available at https://github.com/aksenia/SeeCiTe

Supplementary information

Supplementary data are available at Bioinformatics online.

Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins

Heifer conception rate (HCR) is defined as the percentage of inseminated heifers that become pregnant at each service. The genome-wide association analyses in this study focused on identifying the loci associated with Holstein heifer (n = 2013) conception rate at first service (HCR1) and the number of times bred (TBRD) to achieve a pregnancy. There were 348 unique loci associated (p < 5 × 10⁻⁸) with HCR1 and 615 unique loci associated (p < 5 × 10⁻⁸) with TBRD. The two phenotypes shared 302 loci, and 56 loci were validated in independent cattle populations. There were 52 transcription factor binding sites (TFBS) and 552 positional candidate genes identified in the HCR1- and TBRD-associated loci. The positional candidate genes and the TFBS associated with HCR1 and TBRD were used in the ingenuity pathway analysis (IPA). In the IPA, 11 pathways, 207 master regulators and 11 upstream regulators were associated (p < 1.23 × 10⁻⁵) with HCR1 and TBRD. The validated loci associated with both HCR1 and TBRD make good candidates for genomic selection and further investigations to elucidate the mechanisms associated with subfertility and infertility.

Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations

Simple Summary

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.

Abstract

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

Background

The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number.

Results

For 97.0% of CNVs called from the high-density genotypes, the corresponding genomic position on the medium-density of the animal did not contain a called CNV. The average accuracy of imputation for CNV deletions was 0.281, with a standard deviation of 0.286. The average accuracy of imputation of the CNV normal state, i.e. the absence of a CNV, was 0.982 with a standard deviation of 0.022. Two CNV duplications were imputed in the Charolais, a single CNV duplication in the Limousins, and a single CNV duplication in the Holstein-Friesians; in all cases the CNV duplications were incorrectly imputed.

Conclusion

The vast majority of CNVs called from the high-density genotypes were not detected using the medium-density genotypes. Furthermore, CNVs cannot be accurately predicted from flanking SNP haplotypes, at least based on the imputation algorithms routinely used in cattle, and using the SNPs currently available on the high-density genotype panel.

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.

Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome

Simple Summary

Chickens have been bred for meat and egg production as a source of animal protein. With the increase of productivity as the main purpose of domestication, factors such as metabolism and immunity were boosted, which are detectable signs of selection on the genome. This study focused on copy number variation (CNV) to find evidence of domestication on the genome. CNV was detected from whole-genome sequencing of 65 chickens including Red Jungle Fowl, broilers, and layers. After that, CNV region, the overlapping region of CNV between individuals, was made to identify which genomic regions showed copy number differentiation. The 663 domesticated-specific CNV regions were associated with various functions such as metabolism and organ development. Also, by performing population differentiation analyses such as clustering analysis and ANOVA test, we found that there are a lot of genomic regions with different copy number patterns between broilers and layers. This result indicates that different genetic variations can be found, depending on the purpose of artificial selection and provides considerations for future animal breeding.

Abstract

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.