Copy number variations in high and low fertility breeding boars

Beta-defensins as marker for male fertility: a comprehensive review†

Bovine male fertility in animals has a direct impact on the productivity of dairy herds. The epididymal sperm maturations involve extensive sperm surface modifications to gain the fertilizing ability, especially by absorptions of the plethora of biomolecules, including glycoprotein beta-defensins (BDs), enzymes, organic ions, protein, and phospholipids. Defensins are broad-range nonspecific antimicrobial peptides that exhibit strong relations with innate and adaptive immunity, but their roles in male fertility are relatively recently identified. In the course of evolution, BD genes give rise to different clusters with specific functions, especially reproductive functions, by undergoing duplications and nonsynonymous mutations. BD polymorphisms have been reported with milk compositions, disease resistance, and antimicrobial activities. However, in recent decades, the link of BD polymorphisms with fertility has emerged as an appealing improvement of reproductive performance such as sperm motility, membrane integrity, cervical mucus penetration, evading of uterus immunosurveillance, oviduct cell attachment, and egg recognition. The reproductive-specific glycosylated BD class-A BDs (CA-BDs) have shown age- and sex-specific expressions in male reproductive organs, signifying their physiological pleiotropism, especially in the sperm maturation and sperm transport in the female reproductive tract. By considering adult male reproductive organ-specific BD expressions, importance in sperm functionalities, and bioinformatic analysis, we have selected two bovine BBD126 and BBD129 genes as novel potential biomarkers of bovine male fertility. Despite the importance of BDs, however, genomic characterization of most BD genes across most livestock and nonmodel organisms remains predictive/incomplete. The current review discusses our understanding of BD pleiotropic functions, polymorphism, and genomic structural attributes concerning the fertilizability of the male gamete in dairy animals.

Analysis of amplification and association polymorphisms in the bovine beta-defensin 129 (BBD129) gene revealed its function in bull fertility

β-defensins are adsorbable on the sperm surface in the male reproductive tract (MRT) and enhance sperm functional characteristics. The beta-defensin 129 (DEFB129) antimicrobial peptide is involved in sperm maturation, motility, and fertilization. However, its role in bovine fertility has not been well investigated. This study examines the relationship between the bovine BBD129 gene and Bos indicus x Bos taurus bull fertility. The complete coding sequence of BBD129 mRNA was identified by RNA Ligase Mediated-Rapid Amplification of cDNA End (RLM-RACE) and Sanger sequencing methodologies. It consisted of 582 nucleotides (nts) including 5' untranslated region (UTR) (46nts) and 3'UTR (23nts). It conserves all beta-defensin-like features. The expression level of BBD129 was checked by RT-qPCR and maximal expression was detected in the corpus-epididymis region compared to other parts of MRT. Polymorphism in BBD129 was also confirmed by Sanger sequencing of 254 clones from 5 high fertile (HF) and 6 low fertile (LF) bulls at two positions, 169 T > G and 329A > G, which change the S57A and N110S in the protein sequence respectively. These two mutations give rise to four types of BBD129 haplotypes. The non-mutated TA-BBD129 (169 T/329A) haplotype was substantially more prevalent among high-fertile bulls (P < 0.005), while the double-site mutated GG-BBD129 (169 T > G/329A > G) haplotype was significantly more prevalent among low-fertile bulls (P < 0.005). The in silico analysis confirmed that the polymorphism in BBD129 results in changes in mRNA secondary structure, protein conformations, protein stability, extracellular-surface availability, post-translational modifications (O-glycosylation and phosphorylation), and affects antibacterial and immunomodulatory capabilities. In conclusion, the mRNA expression of BBD129 in the MRT indicates its region-specific dynamics in sperm maturation. BBD129 polymorphisms were identified as the deciding elements accountable for the changed proteins with impaired functionality, contributing to cross-bred bulls' poor fertility.

Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs

Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, VST, and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs.

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Simple Summary

It is known that many different breeds of cattle are widely distributed in China. However, due to a lengthy selection of draught direction, there are obvious shortcomings in Chinese cattle, such as less meat production, slow weight gain, poor meat quality, and a lack of specialized beef cattle breeds. Animal breeding heavily benefits from molecular technologies, among which molecular genetic markers were widely used to improve the economic traits of beef cattle. Because the copy number variation (CNV) involves a longer DNA sequence or even the entire functional gene, it may have a greater impact on the phenotype. Recent studies have indicated that CNVs are widespread in the Chinese cattle genome. By investigating the effects of CNVs on gene expression and cattle traits, we aim to find those genomic variations which could significantly affect cattle traits, and which could provide a basis for genetic selection and molecular breeding of local Chinese cattle.

Abstract

Currently, studies of the SYT11 gene mainly focus on neurological diseases such as schizophrenia and Parkinson’s disease. However, some studies have shown that the C2B domain of SYT11 can interact with RISC components and affect the gene regulation of miRNA, which is important for cell differentiation, proliferation, and apoptosis, and therefore has an impact on muscle growth and development in animals. The whole-genome resequencing data detected a CNV in the SYT11 gene, and this may affect cattle growth traits. In this study, CNV distribution of 672 individuals from four cattle breeds, Yunling, Pinan, Xianan, and Qinchuan, were detected by qPCR. The relationship between CNV, gene expression and growth traits was further investigated. The results showed that the proportion of multiple copy types was the largest in all cattle breeds, but there were some differences among different breeds. The normal type had higher gene expression than the abnormal copy type. The CNVs of the SYT11 gene were significantly correlated with body length, cannon circumference, chest depth, rump length, and forehead size of Yunling cattle, and was significantly correlated with the bodyweight of Xianan cattle, respectively. These data improve our understanding of the effects of CNV on cattle growth traits. Our results suggest that the CNV of SYT11 gene is a protentional molecular marker, which may be used to improve growth traits in Chinese cattle.

Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population

Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings.

Genomic breed composition of Ningxiang pig via different SNP panels

The genomic breed composition (GBC) reflects the genetic relationship between individual animal and ancestor breeds in composite or hybrid breeds. Also, it can estimate the genomic contribution of each breed (ancestor) to the genome of each individual animal. Using genomic SNP information to estimate Ningxiang pig GBC is of great significance. First of all, GBC was widely used in cattle and had significant effects, but there is almost no using experience in Chinese endemic pig breeds. Importantly, High-density SNPs are expensive but can be economized by deploying a relatively small number of highly informative SNP scattered evenly across the genome. Moreover, the impact of low-density SNPs selection strategy on estimating the GBC of individual animals has not been fully explained. Using SNP data from different databases and organizations, we established reference (N = 2015) and verification (N = 302) data sets. Twelve successively smaller SNP panels (500, 1K, 5K, 10K) were built from those SNP in the reference data by three selection methods (uniform, maximized the Euclidean distance (MED) and random distribution method). For each panel, the GBC of Ningxiang pigs in the reference dataset was estimated. Then combining Shannon entropy and the GBC results, the optimal panel (the 10K SNP panel constructed by MED method) was picked out to estimate the GBC of verification Ningxiang pig, which detected that 230 individuals were purebred Ningxiang pigs and the remaining 72 impure individuals contained 6.44% blood related with Rongchang pigs and 4.09% with Bamaxiang pigs in the verification Ningxiang population. Finally, the genetic structure analysis of verification population was performed combining with the results of GBC, multi-dimensional scaling (MDS) analysis and hierarchical cluster analysis. These results showed: (a) GBC could accurately identify purebred Ningxiang pigs and, scientifically, calculate the genomic contribution of each breed of each hybrid animal. (b) GBC could carry out population genetic structure and understand the genetic background of Ningxiang pigs. Such findings highlight a variety of opportunities to better protect and identify other endangered local breeds in China facing the same situation as Ningxiang pig and provide more accurate, economical and efficient new technical support in GBC estimation breeding work.

Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective

The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.

Impaired Reproductive Function in Equines: From Genetics to Genomics

Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Comparative and selection sweep analysis of CNV was associated to litter size in Dazu black goats

This study aims to identify the relative Copy number variation (CNV) associated with the litter size of Dazu black goats based on the unpublished CNV analytical results of our previously published sequencing data, in which the litter-size groups were classified into extreme low- and high-yield groups. Firstly, to compare the existence of valuable CNV in Dazu black goats with different fertility levels with mixed pools. We obtained 4992 and 4888 CNVs from the HY and LY, which overlapping 1461 genes, and classified on the original CNV type. Three genes [LOC108633278, PPP1R12A, and YIPF4] were observed in the intersection between the HY deletion and the LY duplication groups. Secondly, on individuals level, we identified a novel candidate CNV (Chr1_50215501, F_ST = 0.148, V_ST = 0.347) from 214 autosomal credible CNVs to be significant with litter size in the Dazu black goat, which located in the CBLB gene. This finding indicates the CBLB gene may affect the litter size of the Dazu black goats through structural variations, and Chr1_50215501 can be an effective genetic marker for marker-assisted selection breeding, and this study was also helps understand the molecular mechanism related to the goat litter size.

A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence

Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.

Comparative proteomic analysis of Tibetan pig spermatozoa at high and low altitudes

Background

To illuminate the mechanisms underlying the high-altitude tolerance of Tibetan pig spermatozoa, proteomes of spermatozoa from Tibetan pigs raised in high and low altitudes were compared using a tandem mass tag (TMT)-labeled quantitative proteomics approach.

Results

A total of 77 differentially expressed proteins (DEPs) were identified. Gene Ontology (GO) analysis revealed DEPs that were predominantly associated with the actin cytoskeleton, the tricarboxylic acid (TCA) cycle, and adenosine triphosphate (ATP) metabolism, and were from 12 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three subnetworks were significantly enriched and 10 centric proteins were identified by protein-protein interaction (PPI) network analysis. Relative expression levels of the proteins (ATP5H, CYCS, MYH9 and FN1) were confirmed using Western blotting.

Conclusions

Our study is the first to use a tandem mass tag (TMT) approach to analyze Tibetan pig spermatozoa, and provides a foundation to understand the mechanisms underlying the reproductive adaptations of Tibetan pigs to high-altitude environments.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5873-0) contains supplementary material, which is available to authorized users.

Copy number variations of MTHFSD gene across pig breeds and its association with litter size traits in Chinese indigenous Xiang pig

Copy number variation (CNV) is a major proportion of genetic variation, which changes the gene structure and dosage and affects gene expression and function. To validate the presence and the function of CNV in pig, we used real-time quantitative polymerase chain reaction (qPCR) method to validate a 496 kb CNV region comprising MTHFSD gene on chromosome 6 of Xiang pig detected by single nucleotide polymorphism (SNP) array. Then we investigated the distribution of the MTHFSD CNV in a total of 545 pigs in four breeds. About 46.2% and 32.7% individuals in the four pig breeds were detected to be types of loss and gain of MTHFSD locus. The relative copy numbers of MTHFSD gene showed the largest variation range (0-55 copies) in the Xiang pig population. The copy numbers of MTHFSD gene presented the positive correlations with the transcript level of MTHFSD gene in adult ovaries. Statistical analysis indicated that CNVs of MTHFSD gene was significantly changed the litter size traits of Xiang pigs, and the individuals with CNV gain showed more litter size than the CNV loss pigs. We have reasons to believe that the MTHFSD as RNA-binding protein play an important role in pig reproduction as a result of regulating MTHFS mRNA metabolism.

Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs

The aim of the study was to investigate the SINE polymorphism in Xiang, Kele, Qianbei black, Jiangkouluobo, Large White, and Duroc pig breeds. The PCR based detection method was conducted to identify the short interspersed nuclear element (SINE) polymorphism in the PDIA4 gene. There were greater frequencies of the SINE-/- genotypes in Xiang pigs (55.9%) as compared with other pig breed groups. There was an association between this 275 bp SINE polymorphism and litter size (P = 0.003). The homozygous SINE+/+ genotype of the PDIA4 gene had a 1.45-piglets larger litter sizes compared to those with the homozygous SINE-/- genotype. Furthermore, there were assessments of mRNA and protein abundances as a result of PDIA4 gene expression in the ovaries of Xiang pigs for the three different SINE genotypes, and the results indicated that relative abundances of PDIA4 mRNA and protein was greater for the SINE-/- and SINE-/+ genotypes compared with the SINE+/+ genotype (P < 0.05). These findings suggested that the 275 bp SINE polymorphism might change the expression of the PDIA4 gene and could be used as a candidate DNA marker for the selection for litter size in Xiang pigs.

Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes

To gain a better knowledge of structural variations (SVs) in Xiang pig, we used next-generation sequencing to analyze the Xiang pigs with larger (XL) or smaller litter sizes (XS). Our analysis yielded 28,040 putative SVs in the Xiang pig. These SVs distributed throughout all of chromosomes. Some functional regions including exons and untranslated regions were less varied than introns and intergenic regions. We detected 4637 and 4119 specific SVs, which contained 1697 and 1582 genes in XL and XS group, respectively. These genes were mainly enriched in the well-known pathways involved in development and reproduction processes. Population validation was carried out on 50 SVs candidates using PCR method in 144 Xiang pig crowds. All of 50 SVs were confirmed by PCR method and 14 SVs were associated with the litter size of Xiang pigs. These results may be helpful for the elucidation of growth and reproduction regulation in Xiang pig.

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.

Somatic Mosaicism in Bulls Estimated from Genome-Wide CNV Array and TSPY Gene Copy Numbers

Somatic mosaicism has become a focus in human research due to the implications of individual genetic variability in disease. Here, we assessed somatic copy number variations (CNVs) in Holstein bulls in 2 respects. We estimated genome-wide CNVs and assayed CNVs of the TSPY gene, the most variable bovine gene from the Y chromosome. Somatic tissues (blood, lung, heart, muscle, testis, and brain) of 4 bulls were arrayed on the Illumina Bovine SNP50k chip and qPCR tested for TSPY copy numbers. Our results showed extensive copy number divergence in tissues within the same animal as well as significant copy number alterations of TSPY. We detected a mean of 31 CNVs per animal among which 14 were of germline origin, as they were constantly present in all investigated tissues of the animal, while 18 were specific to 1 tissue. Thus, 57% of the total number of detected CNVs was the result of de novo somatic events. Further, TSPY copy number was found to vary significantly among tissues as well as among the same tissue type from different animals in a wide range from 7 to 224% of the calibrator. Our study shows significant autosomal and Y-chromosomal de novo somatic CNV in bulls.

Genome-Wide Copy Number Variations Using SNP Genotyping in a Mixed Breed Swine Population

Copy number variations (CNVs) are increasingly understood to affect phenotypic variation. This study uses SNP genotyping of trios of mixed breed swine to add to the catalog of known genotypic variation in an important agricultural animal. PorcineSNP60 BeadChip genotypes were collected from 1802 pigs that combined to form 1621 trios. These trios were from the crosses of 50 boars with 525 sows producing 1621 piglets. The pigs were part of a population that was a mix of ¼ Duroc, ½ Landrace and ¼ Yorkshire breeds. Merging the overlapping CNVs that were observed in two or more individuals to form CNV regions (CNVRs) yielded 502 CNVRs across the autosomes. The CNVRs intersected genes, as defined by RefSeq, 84% of the time – 420 out of 502. The results of this study are compared and contrasted to other swine studies using similar and different methods of detecting CNVR. While progress is being made in this field, more work needs to be done to improve consistency and confidence in CNVR results.

The Porcine TSPY Gene Is Tricopy but Not a Copy Number Variant

The testis-specific protein Y-encoded (TSPY) gene is situated on the mammalian Y-chromosome and exhibits some remarkable biological characteristics. It has the highest known copy number (CN) of all protein coding genes in the human and bovine genomes (up to 74 and 200, respectively) and also shows high individual variability. Although the biological function of TSPY has not yet been elucidated, its specific expression in the testis and several identified binding domains within the protein suggests roles in male reproduction. Here we describe the porcine TSPY, as a multicopy gene with three copies located on the short arm of the Y-chromosome with no variation at three exon loci among 20 animals of normal reproductive health from four breeds of domestic pigs (Piétrain, Landrace, Duroc and Yorkshire). To further investigate the speculation that porcine TSPY is not a copy number variant, we have included five Low-fertility boars and five boars with exceptional High-fertility records. Interestingly, there was no difference between the High- and Low-fertile groups, but we detected slightly lower TSPY CN at all three exons (2.56-2.85) in both groups, as compared to normal animals, which could be attributed to technical variability or somatic mosaicism. The results are based on both relative quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). Chromosomal localization of the porcine TSPY was done using fluorescence in situ hybridization (FISH) with gene specific PCR probes.