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Copy-number variation (CNV) is an important source of genetic variation, and one that played a role in the process of domestication. The adaptation to a new diet is a characteristic feature of dog domestication. We therefore sought genomic signatures of this process. The pancreatic alpha-amylase gene (AMY2B), expressed in the pancreas, exhibits a variable number of copies. It has been shown that the multiplication of this gene is associated with the adaptation of dogs to a starch-rich diet. To date, there has been no information made available on the copy-number variation of AMY2B in canid farm animals. The aim of the present study was to examine the AMY2B copy number in the red fox, the arctic fox, and in the Chinese raccoon dog. Droplet digital PCR (ddPCR) was used to count the gene copies in 152 animals (60 red foxes, 53 arctic foxes, and 39 Chinese raccoon dogs). We found that the majority (91%) of the animals had two copies of this gene. Of the red foxes and Chinese raccoon dogs, only 8% had three copies, while 32% of the arctic foxes had three copies. Our study showed that the multiplication of the AMY2B gene did not occur over several decades of breeding selection, which may reflect the low-starch feeding regime.

Background X monosomy is the most common disorder of sex development in horses. Although cytogenetic analysis is still the gold standard in the diagnosis of equine X monosomy, novel molecular techniques are being sought to quickly and reliably detect this chromosome abnormality. Objectives The goal of this study was to evaluate the usefulness of a novel variant of the PCR technique-namely, droplet digital PCR (ddPCR)-in the detection of X monosomy in mares. Study design A proof of concept of the usefulness of ddPCR in diagnosing an abnormal number of X chromosomes in mares. Methods We examined an infertile mare using cytogenetic (fluorescent in situ hybridisation-FISH) and molecular (droplet digital PCR-ddPCR) techniques. The X chromosome copy number in ddPCR was estimated via detection of the AMELX gene copy number. In addition, 70 mares homozygous for X-linked microsatellite marker (LEX3) were examined by ddPCR. For all mares, a PCR search for the Y-linked SRY gene was also performed. Results Cytogenetic analysis and ddPCR gave concordant results, indicating pure X monosomy in the studied mare. Of the 70 additional mares examined by ddPCR, a single copy of the X chromosome was found in two cases. All mares were SRY-negative and thus both freemartinism, manifested by leucocyte XX/XY chimerism, and sex reversal syndrome (XX, SRY-positive) could be excluded. Main limitations The ddPCR approach does not allow for unequivocal identification of mosaicism (63,X/64,XX or 65,XXX/64,XX), but may give an indication that further cytogenetic analysis is necessary. Conclusion The ddPCR approach appeared to be useful for diagnosing nonmosaic X monosomy in mares. If the number of X chromosome copies in a mare, as determined by ddPCR, differs from two (in our study, 2.2), additional cytogenetic investigation is recommended with the aim of detecting the mosaicism.

The normal course of DNA methylation depends on the correct functioning of the DNA methylation machinery, which include DNA methyltransferase enzymes (DNMTs) and methyl-CpG-binding domain proteins (MBDs). So far, little is known about the activity of these components during adipogenesis in the pig. The aim of this study was to analyze the expression of ten genes (DNMT1, DNMT3a, DNMT3b, MBD1, MBD2, MBD3, MBD4, MeCP2, UHRF1, and CBX5) during in vitro differentiation into adipocytes of porcine mesenchymal stem cells derived from adipose (AD-MSC) and from bone marrow tissue (BM-MSC). We found that, in undifferentiated cells, the global methylation level was higher in BM-MSC than in AD-MSC, but had similar levels in adipocytes. The transcript level of the DNMT1 gene increased at the beginning of adipogenesis and then decreased, while DNMT3a and DNMT3b transcripts increased during differentiation. All the examined MBD genes show similar expression patterns within the studied system (AD-MSC and BM-MSC). The transcript abundance of UHRF1 and CBX5 decreased in both systems. The changes in the expression patterns of these genes points to the dynamic nature of DNA methylation during porcine adipogenesis.

Simple Summary Inflammation of the mammary gland (mastitis) is an important disease of dairy sheep. Mastitis management depends mainly on the diagnosis. Conventional diagnostic methods including somatic cell count, California Mastitis Test, and microbial culture have limitations. Therefore researchers are looking for new diagnostic biomarkers of mastitis including specific proteins produced by the liver in case of disease (acute phase proteins), unique genetic sequences (miRNAs), or antimicrobial peptides produced by immune cells during inflammation (cathelicidines). Abstract This review aims to characterize promising novel markers of ovine mastitis. Mastitis is considered as one of the primary factors for premature culling in dairy sheep and has noticeable financial, productional, and animal welfare-related implications. Furthermore, clinical, and subclinical mammary infections negatively affect milk yield and alter the milk composition, thereby leading to lowered quality of dairy products. It is, therefore, crucial to control and prevent mastitis through proper diagnosis, treatment or culling, and appropriate udder health management particularly at the end of the lactation period. The clinical form of mastitis is characterized by abnormalities in milk and mammary gland tissue alteration or systemic symptoms consequently causing minor diagnostic difficulties. However, to identify ewes with subclinical mastitis, laboratory diagnostics is crucial. Mastitis control is primarily dependent on determining somatic cell count (SCC) and the California Mastitis Test (CMT), which aim to detect the quantity of cells in the milk sample. The other useful diagnostic tool is microbial culture, which complements SCC and CMT. However, all mentioned diagnostic methods have their limitations and therefore novel biomarkers of ovine subclinical mastitis are highly desired. These sensitive indicators include acute-phase proteins, miRNA, and cathelicidins measurements, which could be determined in ovine serum and/or milk and in the future may become useful in early mastitis diagnostics as well as a preventive tool. This may contribute to increased detection of ovine mammary gland inflammation in sheep, especially in subclinical form, and consequently improves milk quality and quantity.

Disorders of sex development (DSDs) are congenital malformations defined as discrepancies between sex chromosomes and phenotypical sex. Testicular or ovotesticular XX DSDs are frequently observed in female dogs, while monogenic XY DSDs are less frequent. Here, we applied whole genome sequencing (WGS) to search for causative mutations in XX DSD females in French Bulldogs (FB) and American Staffordshire Terries (AST) and in XY DSD Yorkshire Terries (YT). The WGS results were validated by Sanger sequencing and ddPCR. It was shown that a missense SNP of the PADI6 gene, is significantly associated with the XX DSD (SRY-negative) phenotype in AST (P = 0.0051) and FB (P = 0.0306). On the contrary, we did not find any associated variant with XY DSD in YTs. Our study suggests that the genetic background of the XX DSD may be more complex and breed-specific.

Introduction A comprehensive description is presented of four novel cases ofamorphus globosus (ag) foetuses originating from multiple pregnancies of Polish Holstein cows. Material and Methods Four amorphic foetuses were delivered by three cows. Tissue samples were collected during autopsy, embedded in paraffin, sectioned, and stained with haematoxylin and eosin. Genomic DNA was isolated from tissue samples of abnormal foetuses and from blood leukocytes of their healthy siblings. PCR reactions were used to reveal the presence of Y-linked genes (SRY and AMELY) and an X-linked gene (AMELX). Results All foetuses were classified to the groupholoacardius amorphous (anideus). Molecular analysis clearly showed that at 17 microsatellite loci, the studied amorphous foetuses had identical genotypes to the viable co-twins. Conclusion Foetuses had monozygotic origin. Histological analysis showed a low level of development of tissues of meso- and ectodermal origin, as well as features of degrading patterns.

Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene’s nuclear positioning for its activity during in vitro adipogenesis in the pig. We used an established system of differentiation of mesenchymal stem cells derived from bone marrow and adipose tissue into adipocytes. The differentiation process was carried out for 7 days, and the cells were examined using the 3D DNA/immuno-FISH and RNA/DNA-FISH approaches. PPARG transcript level was measured using real-time PCR, and PPARγ activity was detected with colorimetric assay. Changes in the nuclear location of the PPARG gene were observed when we compared undifferentiated mesenchymal stem cells with mature adipocytes. The gene moved from the nuclear periphery to the nuclear center as its transcriptional activity increased. The RNA/DNA-FISH approach shows that differences in primary transcript production correlated with the allele’s nuclear positioning. Transcriptionally active alleles preferentially occupy the central part of the nucleus, while inactive alleles are found on the nuclear periphery. We also show that transcription of PPARG begins with one allele, but that both alleles are active in later stages of differentiation. Our results provide evidence that functionally distinct alleles of the PPARG gene are positioned in different parts of the cell nucleus. This confirms the importance of nuclear architecture to the regulation of PPARG gene transcription, and thus to the fate of the adipose cell. Electronic supplementary material The online version of this article (10.1007/s10577-019-09604-2) contains supplementary material, which is available to authorized users.

Disorders of sex development (DSD) are a well-known cause of sterility and reduced fertility in dogs. Here, we report on 6 new cases of DSD in French bulldogs diagnosed by us within the last year. The animals were phenotypical females who underwent detailed diagnosis due to the presence of an enlarged clitoris or a penis-like structure with atypically located urethral orifice (hypospadias). A female karyotype (78,XX) and lack of Y-linked genes (SRY and ZFY) were observed in 5 cases, which were classified as XX (SRY-negative) DSD. Gonads histology could be performed in 4 XX DSD cases: testicular tissue was observed in 3 cases and ovotesticular tissue in 1 case. In the last case, leukocyte chimerism (XX/XY) was detected alongside an ovotestis with epididymis and fallopian tubes. This case was classified as freemartinism. Our study and a literature review showed that heritable XX (SRY-negative) DSD is quite common in French bulldogs, but spontaneously developed freemartinism can be also diagnosed. In conclusion, we postulate that the description of the sexual phenotype of DSD females (enlarged clitoris and presence of testicular tissue) does not distinguish between hereditary XX DSD and nonhereditary freemartinism. Cytogenetic and molecular analyses are thus necessary to correctly diagnose such cases. This is especially important for the French bulldog breed, as a rapid increase in its population could spread hereditary DSD.

Freemartinism is a disorder of sex development (DSD) caused by the formation of placental anastomoses between fetuses of different sex. It leads to development of an abnormal reproductive tract in the female fetus, including the presence of testes or ovotestes. In pig production, such conditions can affect both reproductive performance and meat quality, through undesired boar taint. A common approach to diagnosing freemartinism is to detect leukocyte chimerism (XX/XY). In the study described here, we performed a complex evaluation of 28 DSD pigs with ambiguous external genitalia (enlarged clitoris, presence of scrotum, etc.). Sex chromosomes were cytogenetically identified by Giemsa staining, as well as with fluorescence in situ hybridization (FISH), while Y-linked (ZFY) and X-linked (ZFX) genes were detected by PCR-RFLP. Histological analysis of the gonads was performed on eosin–hematoxylin-stained microscope slides. Chromosome studies revealed that, of 28 DSD animals, 20 were freemartins (38,XX/38,XY), 2 had a female karyotype (38,XX), and 6 had a male karyotype (38,XY). Analysis of breeding data showed that the mean litter size in which DSD animals occurred was about 17. Histology of the gonads could be performed for 8 DSD pigs, including 6 freemartins and 2 XX DSD. In all these cases, testicular tissue without signs of spermatogenesis was seen. In XX DSD pigs, a copy number variation (CNV) polymorphism downstream from SOX9, tentatively associated with this type of DSD, was detected by FISH. On the other hand, the background of the XY DSD remains unknown. Since cytogenetic analysis is labor-intensive and time-consuming, we evaluated the usefulness of the droplet digital PCR (ddPCR) approach to diagnosing XX/XY leukocyte chimerism. Estimation of X and Y chromosome copy numbers was based on the quantitative detection of AMELX and AMELY genes. Different sex chromosome sets (XX, XY and XX/XY) were unequivocally identified by ddPCR. In conclusion, we suggest that freemartinism, beside testicular or ovotesticular XX DSD, is an emerging problem in highly prolific pigs and that detection of XX/XY leukocyte chimerism can be performed using a fast and reliable ddPCR approach.

Simple Summary Congenital malformations, defined as defects of morphogenesis present at birth, are an important problem in livestock production, if they are caused by hereditary mutations. They can lead to animal death, reduce their productive ability and influence animal welfare. Thus, the identification of the causes of congenital abnormalities are greatly needed. In the present report, we described a Holstein-Fresian calf with multiple congenital malformations including head asymmetry, the relocation of the frontal sinus and eye orbits, hypoplastic thymus, ductus Botalli, unfinished obliteration in umbilical arteries, and a bilateral series of tooth germs in the temporal region. Cytogenetic examination revealed a unique mosaic karyotype with a small marker chromosome, which could not be identified by standard banding techniques. It can be assumed that the presence the marker chromosome may be associated with observed congenital malformations in the studied calf. Abstract A Holstein-Fresian calf with multiple congenital malformations was subjected postmortem to anatomical and genetic investigation. The calf was small (20 kg), had shortened limbs and was unable to stand up. It lived only 44 days. Detailed anatomical investigation revealed the following features: head asymmetry, the relocation of the frontal sinus and eye orbits, hypoplastic thymus without neck part, ductus Botalli, unfinished obliteration in umbilical arteries, and a bilateral series of tooth germs in the temporal region. Cytogenetic examination, performed on in vitro cultured fibroblasts, showed a unique mosaic karyotype with a marker chromosome—60,XX[9 2%]/60,XX,+mar[8%], which was for the first time described in cattle. No other chromosome abnormalities indicating chromosome instabilities, like chromatid breaks or gaps were identified, thus teratogenic agent exposure during pregnancy was excluded. The marker chromosome (mar) was small and it was not possible to identify its origin, however, sequential DAPI/C (4’,6-diamidino-2-phenylindole) band staining revealed a large block of constitutive heterochromatin, which is characteristic for centromeric regions of bovine autosomes. We suppose that the identified marker chromosome was a result of somatic deletion in an autosome and its presence could be responsible for the observed developmental malformations. In spite of the topographic distance among the affected organs, we expected a relationship between anatomical abnormalities. To the of our best knowledge, this is the first case of a mosaic karyotype with a cell line carrying a small marker chromosome described in a malformed calf.

Disorders of sex development (DSD) are important causes of infertility and sterility, and are risk factors for gonadal carcinogenesis. Many DSDs are caused by genetic factors, mainly sex chromosome abnormalities or mutations of genes involved in sexual development, as well as structural variants (SVs) - large deletions, duplications, and insertions, if these overlap genes involved in sex development. The aim of this study was to determine if there were SVs in four candidate genes - NR0B1 (DAX1), NR5A1, RSPO1, and SOX3 - using droplet digital PCR (ddPCR). There was study of two cohorts of dogs with DSD, including 55 animals with XX DSD and 15 with XY DSD. In addition, 40 control females and 10 control males were included in the study. Among cases, for which there were evaluations, a large deletion consisting of four exons of the NR5A1 gene was identified in a Yorkshire Terrier with a rudimentary penis, hypospadias, bilateral cryptorchidism, and spermatogenesis inactive testes. This is the first mutation in the NR5A1 gene leading to XY DSD phenotype to be reported in domestic animals. There were no SVs in the genes evaluated in the present study in the cohort of dogs with XX DSD. The results from this study provide evidence that the large structural variants of these genes are rarely associated with the DSD phenotype in dogs.

The tortoiseshell coat colour is characteristic to female cats, and its occurrence in tomcats is very rare and associated with chromosome abnormalities (additional copy of X chromosome). The aim of this study was identification of the genetic basis of a case of tortoiseshell colour in a fertile Maine coon tomcat. Cytogenetic and molecular genetic studies were carried out with painting molecular probes (WCPP) specific to the X and Y sex chromosomes as well as a DNA microsatellite panel for the parentage verification of cats. Cytogenetic analysis revealed only a single set of sex chromosomes typical for male - 38,XY. The results of the microsatellite polymorphism obtained from DNA showed three alleles in locus FCA201 and four alleles in loci FCA149 and FCA441 in different tissues (blood, hair roots and testicles). Based on these results, the case was diagnosed as a true chimerism 38,XY/38,XY. To the best of our knowledge, this is the first case of a 38,XY/38,XY chimera diagnosed in cats, confirmed by genetic analysis.

The possibility of using stem cell-derived cardiomyocytes opens a new platform for modeling cardiac cell differentiation and disease or the development of new drugs. Progress in this field can be accelerated by high-throughput screening (HTS) technology combined with promoter reporter system. The goal of the study was to create and evaluate a responsive promoter reporter system that allows monitoring of iPSC differentiation towards cardiomyocytes. The lentiviral promoter reporter system was based on troponin 2 (TNNT2) and alpha cardiac actin (ACTC) with firefly luciferase and mCherry, respectively. The system was evaluated in two in vitro models. First, system followed the differentiation of TNNT2-luc-T2A-Puro-mCMV-GFP and hACTC-mcherry-WPRE-EF1-Neo from transduced iPSC line towards cardiomyocytes and revealed the significant decrease in both inserts copy number during the prolonged in vitro cell culture (confirmed by I-FISH, ddPCR, qPCR). Second, differentiated and contracting control cardiomyocytes (obtained from control non-reporter transduced iPSCs) were subsequently transduced with TNNT2-luc-T2A-Puro-CMV-GFP and hACTC-mcherry-WPRE-EF1-Neo lentiviruses to observe the functionality of obtained cardiomyocytes. Our results indicated that the reporter modified cell lines can be used for HTS applications, but it is essential to monitor the stability of the reporter sequence during extended cell in vitro culture.

The pig oocyte maturation protocol differs from other mammalian species due to dependence on follicular fluid (FF) supplementation. One of the most abundant components of the porcine follicular fluid are fatty acids (FAs). Although evidence from other mammalian models revealed a negative impact of saturated fatty acids (SFA) on developmental competence of oocytes, pig has not yet been widely analyzed. Therefore, we aimed to investigate whether supplementation of IVM medium with 150 μM of stearic acid (SA) and oleic acid (OA) affects lipid content and expression of genes related to fatty acid metabolism in porcine cumulus–oocyte complexes and parthenogenetic embryo development. We found significant influence of fatty acids on lipid metabolism in cumulus cells without affecting the oocyte proper. The expression of ACACA, SCD, PLIN2, FADS1, and FADS2 genes was upregulated (P, Cumulus cells are the main target of exogenous fatty acids during in vitro maturation of porcine oocytes.

Hypospadias, the abnormal position of the urethral orifice, is considered a rare congenital malformation of the reproductive organs in male dogs. We present 5 new cases of hypospadias - 2 of the penile type in German Shepherd Dogs and 3 perineal types in a Bavarian Mountain Hound, a French Bulldog, and an American Staffordshire Terrier. Other abnormalities (rudimentary or underdeveloped penis, incompletely formed preputial sheath, and bilateral cryptorchidism) were also observed. Molecular analysis of all cases revealed the presence of Y-linked genes (SRY and ZFY). Cytogenetic and histological analysis could be performed for only 2 cases: a normal male sex chromosome complement (78,XY) and spermatogenetically inactive testicles were observed. A retrospective search for hypospadias in 19,950 medical records of male dogs from a single veterinary clinic in Poland (2006-2017) was also performed. Altogether, 10 reports of penile hypospadias were found (0.05%). The majority of the reports concerned German Shepherd Dogs (8 cases among 1,511 male dogs of this breed), and thus, the estimated incidence of hypospadias in this breed was 0.5%. Moreover, we performed a review of 26 cases of canine hypospadias reported in the years 2004-2017. Our study and the review of the literature suggest that hypospadias is not rare in dogs and that some breeds (such as German Shepherd Dog and Boston Terrier) may be prone to this disorder.

Simple Summary The period of heat is a time of naturally increased interest of the male in the female. Males recognizing specific chemical signals are able to find the female in estrus and try to mate with her. According to current knowledge, there is a specific hormonal play accompanying this process, with the rise of estrogens and progesterone in the female thought to be responsible for stimulating sexual arousal in males. In this paper we describe the cases of atypically increased attractiveness in a male, that clearly influenced the behavior of adult, intact males, which made mating attempts during contact with him, even though he had no detectable signs of clinical estrogenization. The “case” animal had a basal level of the hormones considered to be involved in the stimulation of sexual arousal. The case animal was a castrated male with confirmed genetic sex and confirmed lack of gonads, and a urinary chemical profile similar to that of a female in estrus. Even though similar cases are noted in breeding and veterinary practice, to our knowledge this is the first report of cases that include clinical and laboratory examination. As a hypothesis, we propose the involvement of other hormones in the creation of incidental attractiveness, or an increased production of compounds responsible for attractiveness (sex pheromones) resulting from metabolic events unrelated to reproductive processes. Further studies are needed to determine the cause of this phenomenon, which would expand our knowledge about the mechanisms involved in the creation of semiochemical communication and the production of the compounds responsible for the modification of behavior in the signal recipients. Abstract During the ovarian cycle in domestic dogs, females do not accept males during the first days of estrus but become attractive to males from the beginning of proestrus, with this attractiveness persisting until the end of the estrus phase. It is believed that increased estradiol is responsible for the female attractiveness to the males. In this paper we describe the case of strong, but atypical attractiveness of a castrated male to various, adult, intact males, influenced by the emitted semiochemical signals. Any significant changes in the level of hormones typically involved in the process connected with estrus and responsible for sexual arousal in the males were assessed. The case animal was a 4 year old castrated male Border Collie that was extremely attractive to various males, which presented high levels of sexual arousal, with intensive sniffing and licking of the preputial area, specific vocalization, increased salivation and, finally, mating attempts. Clinical examination of the castrated male revealed a lack of testes in the scrotum and abdominal cavity confirmed by USG. Laboratory tests indicated basal levels of estradiol, testosterone, and progesterone (15.23 pg/mL

Histone modification is a well-known epigenetic mechanism involved in regulation of gene expression; however, it has been poorly studied in adipose tissues of the pig. Understanding the molecular background of adipose tissue development and function is essential for improving production efficiency and meat quality. The objective of this study was to identify the association between histone modification and the transcript level of genes important for lipid droplet formation and metabolism. Histone modifications at the promoter regions of 6 genes (, , , , , and ) were analyzed using a chromatin immunoprecipitation assay. Two modifications involved in activation of gene expression (acetylation of H3 histone at lysine 9 and methylation of H3 histone at lysine 4) as well as methylation of H3 histone at lysine 27, which is known to be related to gene repression, were examined. The level of histone modification was compared with transcript abundance determined using real-time PCR in tissue samples (subcutaneous fat, visceral fat, and longissimus dorsi muscle) derived from 3 pig breeds significantly differing in fatness traits (Polish Large White, Duroc, and Pietrain). Transcript levels were found to be correlated with histone modifications characteristic to active loci in 4 of 6 genes. A positive correlation between histone H3 lysine 9 acetylation modification and the transcript level of ( = 0.53, < 4.8 × 10), ( = 0.34, < 0.02), and ( = 0.43, < 1.0 × 10) genes was observed. The histone H3 lysine 4 trimethylation modification correlated with transcripts of ( = 0.64, < 4.6 × 10) and ( = 0.37, < 0.01) genes. No correlation was found between transcript level of all studied genes and histone H3 lysine 27 trimethylation level. This is the first study on histone modifications in porcine adipose tissues. We confirmed the relationship between histone modifications and expression of key genes for adipose tissue accumulation in the pig. Epigenetic modulation of the transcriptional profile of these genes (e.g., through nutritional factors) may improve porcine fatness traits in future.

Testicular XX disorder of sex development (XX DSD, SRY -negative), causing sterility, is quite frequently diagnosed in pig populations, however, its molecular background is still unknown. This disorder may affect carcass quality (boar taint) due to the presence of testicular tissue in animals with ambiguous female external genitalia. A chromosome fragment encompassing the SOX9 gene was previously considered as a candidate region in functional and association studies. We analyzed distribution of polymorphic variants in 5’UTR and in 3’-flanking regions of the SOX9 gene in a cohort of 12 XX DSD pigs and a panel of 116 normal females. Altogether, 8 previously known polymorphic sites were analyzed and no significant association under Bonferroni correction (P>0.0063) between DSD phenotype and identified SNPs was found. The region harboring the SOX9 gene was also searched for the presence of copy number variation (CNV) by fluorescence in situ hybridization technique (FISH), using a set of 7 BAC probes. A potential CNV region, manifested by size variation (large and small) of fluorescence signals, produced by a single BAC probe hybridizing downstream (approx. 500 kb) of the SOX9 gene, was observed in 4 DSD cases. We conclude, that a new CNV polymorphism in the region harboring SOX9 gene can be considered as a promising marker for the DSD phenotype.

Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor best known for mediating xenobiotic-induced toxicity. AhR requires aryl hydrocarbon receptor nuclear translocator (ARNT) to form an active transcription complex and promote the activation of genes which have dioxin responsive element in their regulatory regions. The present study was performed to determine the complete cDNA sequences of porcine AhR and ARNT genes and their chromosomal localization. Total RNA from porcine livers were used to obtain the sequence of the entire porcine transcriptome by next-generation sequencing (NGS; lllumina HiSeq2500). In addition, both, in silico analysis and fluorescence in situ hybridization (FISH) were used to determine chromosomal localization of porcine AhR and ARNT genes. In silico analysis of nucleotide sequences showed that there were two transcript variants of AhR and ARNT genes in the pig. In addition, computer analysis revealed that AhR gene in the pig is located on chromosome 9 and ARNT on chromosome 4. The results of FISH experiment confirmed the localization of porcine AhR and ARNT genes. In the present study, for the first time, the full cDNAs of AhR and ARNT were demonstrated in the pig. In future, it would be interesting to determine the tissue distribution of AhR and ARNT transcript variants in the pig and to test whether these variants are associated with different biological functions and /or different activation pathways.

Summary A disorder of sex development (DSD) in dogs with female sex chromosomes (78, XX), a lack of the SRY gene and the presence of testes or ovotestes is commonly diagnosed in numerous breeds. The molecular background of DSD is not fully recognized but has been linked to the copy number variation in the region harboring the SOX9 gene. We applied a genome-wide association study and targeted next-generation sequencing techniques to compare DSD and normal female dogs. The genome-wide association study did not indicate a significant chromosome region. Targeted next-generation sequencing of a 1.5-Mb region on canine chromosome 9 harboring the SOX9 gene revealed two putatively DSD-associated copy number variations 355 kb upstream and 691 kb downstream of SOX9, four blocks of low polymorphism and two blocks of an elevated heterozygosity. An initial next-generation sequencing analysis showed an association with two SNPs, but validation in larger cohorts did not confirm this result. We identified a large homologous fragment (over 243.8 kb), named hfMAGI2, located upstream of SOX9, that overlaps a known copy number variation region. It shows a high sequence similarity with the 5′ flanking region of the MAGI2 gene located on canine chromosome 18 that encodes a protein involved in ovary formation during early embryonic development. Our study showed that the identified copy number variation region located upstream of the SOX9 gene contains potential regulatory sequences (long non-coding RNA and hfMAGI2) and led to the assumption that a multiplication of this element may alter expression of the SOX9 gene, triggering the DSD phenotype.

Freemartinism is the most common type of disorder of sex development in cattle. It leads to sterility in the female co-twin in heterosexual twin pregnancy, and is thus a serious problem in cattle production. The incidence of freemartin syndrome is directly dependent on the prevalence of twinning, which has increased in dairy cattle populations in recent years. Thus, early and rapid identification of freemartins is needed to reduce economic loss. Of the various methods used to diagnose this condition, identifying the XX and XY cell lines in blood samples using cytogenetic techniques is the gold standard; however, this technique is time consuming. Faster and more reliable techniques are thus being sought. Droplet digital PCR (ddPCR) is a third-generation PCR method and it has not previously been used to detect XX/XY leukocyte chimerism in cattle. The aim of the present study was to verify the usefulness of ddPCR to detect and quantify leukocyte chimerism in this species. The X and Y copy numbers were estimated by identifying the copy numbers of 2 genes located on the sex chromosomes: amelogenin X-linked (AMELX) on the X chromosome and amelogenin Y-linked (AMELY) on the Y chromosome. In the first step, we performed ddPCR on samples prepared from female DNA mixed with male DNA in serially diluted proportions. We determined that the sensitivity of this method was sufficient to detect a low-frequency (

Testicular or ovotesticular disorder of sex development (DSD) in genetic females (78,XX; SRY-negative) has been reported quite frequently in numerous dog breeds and is usually diagnosed due to the presence of female external genitalia with an enlarged clitoris. The molecular background of this disorder, diagnosed also in human and other mammals, is not fully understood. However, it has recently been proposed that a copy number variation (CNV) in the region upstream of the SOX9 gene is associated with it. We described a rare case of this disorder in a French Bulldog with abdominal testes and male external genitalia (a slightly malformed penis). FISH studies showed a female karyotype, lack of a translocation involving the Y chromosome, and a distinct size variation in the CNV region (CNVR) upstream of the SOX9 gene, located on chromosome 9 (CFA9). A large FISH variant on a single CFA9 and a lack of the variant on its homologue was observed. Surprisingly, in the mother of this DSD dog, 2 normal-sized variants were identified which means that the CNV in the DSD dog was de novo. Our observations are in agreement with earlier suggestions that a high number of copies at the CNVR upstream of SOX9 may be associated with this type of DSD.

The miR-30 gene family includes potential regulators of adipogenesis. We searched for polymorphism in this gene family in 4 pig breeds: Duroc, Pietrain, Polish Landrace (PL), Polish Large White (PLW) and a synthetic line (L990). Altogether 5 single nucleotide polymorphisms (SNPs) in 3 genes were found, including one already known SNP rs340704946 within the pre-miR-30d genomic sequence. An association of the rs340704946 with intramuscular fat (IMF) content, abdominal fat accumulation and daily body mass gain in L990 was found. Moreover, the AG genotype was associated with an increased content of monounsaturated fatty acids (MUFA) in subcutaneous (P=0.027) and visceral fat (P=0.007) tissues when compared to the GG genotype. Analysis of PLW pigs revealed an association of the rs340704946 with transcript level of the ME1 gene in longissimus dorsi (LD) muscle (P=0.002), as well as the ME1 protein product in the LD muscle (P

Disorders of sex development (DSD) are rarely reported in cats, but this does not mean these occurrences are an insignificant reproductive and health problem in this species. The DSD condition affects reproduction and can be associated with an increased risk of gonadal tumorigenesis. In this review, an overview of findings since 2012 are presented that focus on cytogenetic and molecular genetic studies of cats with abnormal external genitalia. Results from advanced cytogenetic analysis of sex chromosomes indicate there is a range of abnormalities, including aneuploidies, structural rearrangements and freemartinism, which manifests as leukocyte XX/XY chimerism. The molecular abnormalities that result in feline monogenic and multifactorial DSD (such as hypospadias and cryptorchidism) are very few. There are only two mutations of genes (CYP11B1 and TAC3) which are known to be responsible for syndromes associated with abnormal sexual development. Several candidate genes (SRY, AR, SRD5A2, MAMLD1, DHH, HSD3B2, and HSD17B3) have also been examined, but no associations were identified between these polymorphisms and DSD phenotypes. The findings in developing the present review indicate sex chromosome abnormalities are quite common causes of feline DSD. The study of the molecular disorders that lead to the development of DSD in cats with normal XX or XY sex chromosome complements is still in its infancy, and further research is needed into this topic. It can be anticipated that the use of next generation sequencing technologies to study the genetic disorders that result in the DSD condition in cats will lead to an increase the detection of several causative mutations.

Background The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle. Results Quantification of allelic proportions by pyrosequencing revealed that both alleles of PPARG and SREBF1 are expressed at similar levels. PPARGC1A showed the greatest ASE imbalance in fat deposits in Polish Large White (PLW), Polish Landrace and Pietrain pigs; and PPARA in PLW pigs. Significant deviations of mean PPARGC1A allelic transcript ratio between cDNA and genomic DNA were detected in all tissues, with the most pronounced difference (p

The genetic background of disorders of sex development (DSDs) in cats is poorly understood, due to a relatively low number of such studies in this species. Here we present three new DSD cases with different complements of sex chromosomes. The first, an Oriental Shorthair cat with a rudimentary penis, abdominal atrophic testicles and lack of uterus appeared to be a freemartin, since leucocyte chimerism XX/XY and a lack of Y-linked genes (SRY and ZFY) were observed in DNA isolated from hair follicles. XXY trisomy was identified in the second case, a tortoiseshell Devon Rex male cat with atrophic scrotal testicles and a normal penis. Finally, a European Shorthair cat with atrophic testicles in a bifid scrotum, rudimentary penis and a lack of uterus had XY complement, including Y chromosome of normal size and morphology. Also presence of eight Y-linked genes, detected by PCR, was confirmed. Due to the low testosterone level in this last patient, we searched for a causative mutation in two candidate genes (HSD3B2 and HSD17B3) involved in the metabolism of this steroid hormone. Altogether, five polymorphic sites in HSD3B2 and two in HSD17B3 were found, but none of them showed associations with DSD phenotype. We thus excluded a possibility that the causative mutation is present in these genes. In conclusion, we confirmed that analysis of the sex chromosome complement is a crucial step in diagnosis of DSDs. However, extensive molecular studies of the genes involved in sex development are needed to elucidate the causes of DSDs in cats with normal complements of sex chromosomes.

Disorders of sex development (DSD) are a serious health problem in dogs. Different types of DSD have been described, including persistent Mullerian duct syndrome (PMDS), for which the molecular background has been identified in miniature schnauzers. Human patients with PMDS are at increased risk for cancers of the gonads (predominantly) or the Mullerian duct structures (rarely). This report describes two miniature schnauzer dogs with PMDS caused by a known nonsense mutation in the AMHR2 gene, with concurrent development of genital neoplasia. The first case (78,XY and SRY-positive) had unilateral cryptorchidism and a Sertoli cell tumour in the abdominal testicle. The second case (mosaic karyotype 77,XY,rob/78,XY and SRY-positive) had both gonads descended in the scrotum and developed an abdominal mass derived from the uterine wall, which showed histological features typical of leiomyoma.

A variety of self-interacting domains, defined at different levels of resolution, have been described in mammalian genomes. These include Chromatin Compartments (A and B)1, Topologically Associated Domains (TADs)2,3, contact domains4,5, sub-TADs6, insulated neighbourhoods7 and frequently interacting regions (FIREs)8. Whereas many studies have found the organisation of self-interacting domains to be conserved across cell types389, some do form in a lineage-specific manner6710. However, it is not clear to what degree such tissue-specific structures result from processes related to gene activity such as enhancer-promoter interactions or whether they form earlier during lineage commitment and are therefore likely to be prerequisite for promoting gene expression. To examine these models of genome organisation in detail, we used a combination of high-resolution chromosome conformation capture, a newly-developed form of quantitative fluorescence in-situ hybridisation and super-resolution imaging to study a 70 kb self-interacting domain containing the mouse α-globin locus. To understand how this self-interacting domain is established, we studied the region when the genes are inactive and during erythroid differentiation when the genes are progressively switched on. In contrast to many current models of long-range gene regulation, we show that an erythroid-specific, decompacted self-interacting domain, delimited by convergent CTCF/cohesin binding sites, forms prior to the onset of robust gene expression. Using previously established mouse models we show that formation of the self-interacting domain does not rely on interactions between the α-globin genes and their enhancers. As there are also no tissue-specific changes in CTCF binding, then formation of the domain may simply depend on the presence of activated lineage-specific cis-elements driving a transcription-independent mechanism for opening chromatin throughout the 70 kb region to create a permissive environment for gene expression. These findings are consistent with a model of loop-extrusion in which all segments of chromatin, within a region delimited by CTCF boundary elements, can contact each other. Our findings suggest that activation of tissue-specific element(s)within such a self-interacting region is sufficient to influence all chromatin within the domain.

Differentiation of progenitor cells into adipocytes is accompanied by remarkable changes in cell morphology, cytoskeletal organization, and gene expression profile. Mature adipocytes are filled with a large lipid droplet and the nucleus tends to move to the cell periphery. It was hypothesized that the differentiation process is also associated with changes of nuclear organization. The aim of this study was to determine the number and distribution of selected components of nuclear architecture during porcine in vitro adipogenesis. The pig is an important animal model sharing many similarities to humans at the anatomical, physiological, and genetic levels and has been recognized as a good model for human obesity. Thus, understanding how cellular structures important for fundamental nuclear processes may be altered during adipocyte differentiation is of great importance. Mesenchymal stem cells (MSCs) were derived from bone marrow (BM-MSCs) and adipose tissue (AD-MSCs) and were cultured for 7 days in the adipogenic medium. A variable differentiation potential of these cell populations towards adipogenic lineage was observed, and for further study, a comparative characteristic of the nuclear organization in BM-MSCs and AD-MSCs was performed. Nuclear substructures were visualized by indirect immunofluorescence (nucleoli, nuclear speckles, PML bodies, lamins, and HP1α) or fluorescence in situ hybridization (telomeres) on fixed cells at 0, 3, 5, and 7 days of differentiation. Comprehensive characterization of these structures, in terms of their number, size, dynamics, and arrangement in three-dimensional space of the nucleus, was performed. It was found that during differentiation of porcine MSCs into adipocytes, changes of nuclear organization occurred and concerned: (1) the nuclear size and shape; (2) reduced lamin A/C expression; and (3) reorganization of chromocenters. Other elements of nuclear architecture such as nucleoli, SC-35 nuclear speckles, and telomeres showed no significant changes when compared to undifferentiated and mature fat cells. In addition, the presence of a low number of PML bodies was characteristic of the studied porcine mesenchymal stem cell adipogenesis system. It has been shown that the arrangement of selected components of nuclear architecture was very similar in MSCs derived from different sources, whereas adipocyte differentiation involves nuclear reorganization. This study adds new data on nuclear organization during adipogenesis using the pig as a model organism.

There is relatively little information about the karyotype structure of the chinchilla (Chinchilla lanigera Mol.), an endemic South American rodent with 2n = 64 chromosomes and “duplicate-type X ch...

Freemartinism, a primary disorder of sex development (DSD) in cattle, is associated with leu - kocyte chimerism (60,XX/60,XY). The diagnosis of DSD is easy if it is known that a heifer with abnormally developed reproductive tracts originates from a heterosexual twin birth, but it is not so obvious in the case of single born calves. In the present study twelve DSD heifers which were single born (singletons) and culled due to the abnormal development of internal genitalia were studied using cytogenetic and molecular tech - niques. Among the heifers 7 appeared to be chimeric (60,XX/60,XY and the presence of the genes residing in the Y chromosome: SRY and AMELY) and 5 had a normal female karyotype (60,XX and a lack of the Y-linked genes). In addition, milk productivity was analyzed in relation to the incidence of twinning at a local Dairy Cattle Breeding Centre, from which 8 studied singletons (6 chimeric and 2 with a normal female karyotype) originated. It was found that in the years 2005-2013 an upward trend for average milk yield (from 9700 kg in 2005 to 11 500 kg in 2013) was associated with the increase of twin births (from 1.5% in 2005 to 5.9% in 2013). Our study showed that approximately 60% of single born heifers with abnormally developed internal genitalia were freemartins (a male co-twin died during pregnancy), while DSD etiology of the other cases (60,XX and a lack of the Y-linked genes) remains unknown. It cannot be excluded that some of these heifers represent a testicular/ovotesticular DSD (60,XX and SRY-negative). In conclusion, our study suggests that the occurrence of freemartins and other DSD in single born heifers seems to be an underestimated problem in cattle breeding.

An 18-month-old European shorthair cat was subjected to genetic studies due to ambiguous external genitalia (underdeveloped both penis and scrotum). Further anatomic and histopathological studies revealed the presence of abdominal, atrophic testes and uterus. Cytogenetic analysis showed two cell lines, one with X monosomy-37,X [90% of the analysed metaphase spreads], and other line had 38 chromosomes with normal X chromosome and abnormally small Y-derived chromosome-38,X,der(Y) [10%]. Further fluorescence in situ hybridization study with telomeric probe revealed a ring structure of the der(Y). Eight Y chromosome-specific genes, SRY, TETY1, TETY2, CUL4BY, CYORF15, HSFY, FLJ36031Y and ZFY, were detected. We conclude that the described abnormality of the reproductive system, leading to sterility, was caused by a very rare type of chromosomal mosaicism-37,X/38,X,r(Y).