Polymorphisms in the SOX9 region and testicular disorder of sex development (38,XX; SRY -negative) in pigs

XX/XY Chimerism in Internal Genitalia of a Virilized Heifer

Five DSD heifers underwent genetic analysis in the present study. We cytogenetically analyzed in vitro cultured leukocytes and searched for SRY, AMELX/AMELY and ZFX/ZFY genes in leukocytes and hair follicles, finding that four of the studied heifers were freemartins (XX/XY leukocyte chimerism). The fifth case had an underdeveloped vulva localized ventrally and cranially to the mammary gland, a normal female sex chromosome complement (60,XX) in the leukocytes, and a lack of Y-chromosome-derived genes in the leukocytes and hair follicles. Postmortem anatomical examination of this heifer revealed the presence of normal ovaries with follicles, uterus, and oviducts, but molecular detection of the SRY, ZFX, ZFY,AMELX, and AMELY genes in these organs indicated the presence of a cell line carrying the Y chromosome. Further analysis of twelve microsatellite markers revealed the presence of additional variants at six loci in DNA samples derived from the reproductive organs; XX/XY chimerism was thus suspected in these samples. On the basis of the detection of AMELY (Y-linked) versus AMELX (X-linked) and SOX9 (autosomal) versus AMELY genes by droplet digital PCR (ddPCR), the Y/X and Y/autosome ratios were evaluated; they indicated the presence of XX and XY cell lines in the reproductive tissues. Our study showed that XX/XY chimerism can be present in the internal reproductive organs of the virilized heifers with a normal female set of sex chromosomes (60,XX) and a lack of Y-chromosome-derived genes in the leukocytes. The etiology of this phenomenon remains unknown.

Whole genome sequencing identifies a missense polymorphism in PADI6 associated with testicular/ovotesticular XX disorder of sex development in dogs

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.

Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle

Background

Copy number variation (CNV) has become an essential part of genetic structural variation. Coiled‐coil domain containing 39 (CCDC39) is a gene that related to the growth and development of organs and tissues. It is identified that it has a CNV region by animal genome resequencing.

Objective

In this study, we detected the phenotypic traits and different distributions of CCDC39 gene copy numbers in five Chinese cattle breeds (Qinchuan (QC) cattle, Yunling (YL) cattle, Xianan (XN) cattle, Pinan (PN) cattle and Jiaxian (JX) cattle).

Methods

Five hundred and six cattle were randomly selected for CNV distribution detection. Blood samples were taken and genomic DNA was extracted. Different tissues were obtained from adult (n = 3) XN cattle, including heart, liver, kidney, skeletal muscle and lung. The genome qPCR experiment was performed with SYBR Green in triplicate. CDNA qPCR was used to detect the expression level of CCDC39 in different tissues and varieties. Using SPSS v20.0 software, the relationship between CCDC39 CNV and the growth traits of PN, XN, QC, NY and YL cattle breeds was analyzed by one‐way analysis of variance (ANOVA).

Results

The results showed that the expression of CCDC39 in lung was higher than that in other tissues. The expression in liver and kidney was similar, but the expression in heart and muscle was less. It can be seen that the duplication type of QC cattle CCDC39 CNV is higher than the deletion or normal in the height at hip cross. The normal type of PN cattle in body length and hip width was better than duplication and deletion (p < 0.05). In XN cattle, the deletion type of CNV had superior growth characteristics in heart girth and cannon bone circumference compared with the duplication type and the normal type (p < 0.05).

Conclusion

The study revealed a significant association between CNV of CCDC39 gene and growth traits in different Chinese cattle breeds.

Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs

XX sex reversal, also called XX disorders of sex development (XX-DSD), is a condition affecting the development of the gonads or genitalia, and is relatively common in pigs. However, its genetic etiology and transcriptional regulation mechanism in the hypothalamic-pituitary-gonadal axis (HPGA) remain mostly unknown. XX-DSD (SRY-negative) pigs and normal sows were selected by external genitalia observation. The hypothalamus, which is the integrated center of the HPGA was sampled for whole-transcriptome RNA-seq. The role of DEmiRNA was validated by its overexpression and knockdown in vitro. A total of 1,258 lncRNAs, 1,086 mRNAs, and 61 microRNAs differentially expressed in XX-DSD pigs compared with normal female pigs. Genes in the hormone biosynthesis and secretion pathway significantly up-regulated, and the up-regulation of GNRH1, KISS1 and AVP may associate with the abnormal secretion of GnRH. We also predicted the lncRNA-miRNA-mRNA co-expression triplets and constructed three competing endogenous RNA (ceRNA) potentially associated with XX-DSD. Functional enrichment studies suggested that TCONS_00340886, TCONS_00000204 and miR-181a related to GnRH secretion. Further, miR-181a inhibitor up-regulated GNRH1, PAK6, and CAMK4 in the GT1-7 cells. Conversely, transfection of miR-181a mimics obtained the opposite trends. The expression levels of FSHR, LHR, ESR1 and ESR2 were significantly higher in XX-DSD gondas than those in normal sows. Taken together, we proposed that the balance of endocrine had broken in XX-DSD pigs. The current study is the first to examine the transcriptomic profile in the hypothalamus of XX-DSD pigs. It provides new insight into coding and non-coding RNAs that may be associated with DSD in pigs.

Knockout of the HMG domain of the porcine SRY gene causes sex reversal in gene-edited pigs

The present work characterizes the porcine sex-determining region on the Y chromosome (SRY) gene and demonstrates its pivotal role in sex determination. We provide evidence that genetically male pigs with a knockout of the SRY gene undergo sex reversal of the external and internal genitalia. This discovery of SRY as the main switch for sex determination in pigs may provide an alternative for surgical castration in pig production, preventing boar taint. As the pig shares many genetic, physiological, and anatomical similarities with humans, it also provides a suitable large animal model for human sex reversal syndromes, allowing for the development of new interventions for human sex disorders.

The sex-determining region on the Y chromosome (SRY) is thought to be the central genetic element of male sex development in mammals. Pathogenic modifications within the SRY gene are associated with a male-to-female sex reversal syndrome in humans and other mammalian species, including rabbits and mice. However, the underlying mechanisms are largely unknown. To understand the biological function of the SRY gene, a site-directed mutational analysis is required to investigate associated phenotypic changes at the molecular, cellular, and morphological level. Here, we successfully generated a knockout of the porcine SRY gene by microinjection of two CRISPR-Cas ribonucleoproteins, targeting the centrally located “high mobility group” (HMG), followed by a frameshift mutation of the downstream SRY sequence. This resulted in the development of genetically male (XY) pigs with complete external and internal female genitalia, which, however, were significantly smaller than in 9-mo-old age-matched control females. Quantitative digital PCR analysis revealed a duplication of the SRY locus in Landrace pigs similar to the known palindromic duplication in Duroc breeds. Our study demonstrates the central role of the HMG domain in the SRY gene in male porcine sex determination. This proof-of-principle study could assist in solving the problem of sex preference in agriculture to improve animal welfare. Moreover, it establishes a large animal model that is more comparable to humans with regard to genetics, physiology, and anatomy, which is pivotal for longitudinal studies to unravel mammalian sex determination and relevant for the development of new interventions for human sex development disorders.

Recent genetic advances on boar taint reduction as an alternative to castration: a review

Boar taint is an unpleasant odor in male pig meat, mainly caused by androstenone, skatole, and indole, which are deposited in the fat tissue. Piglet castration is the most common practice to prevent boar taint. However, castration is likely to be banished in a few years due to animal welfare concerns. Alternatives to castration, such as genetic selection, have been assessed. Androstenone and skatole have moderate to high heritability, which makes it feasible to select against these compounds. This review presents the latest results obtained on genetic selection against boar taint, on correlation with other traits, on differences in breeds, and on candidate genes related to boar taint. QTLs for androstenone and skatole have been reported mainly on chromosomes 6, 7, and 14. These chromosomes were reported to contain genes responsible for synthesis and degradation of androstenone and skatole. A myriad of work has been done to find markers or genes that can be used to select animals with lower boar taint. The selection against boar taint could decrease performance of some reproduction traits. However, a favorable response on production traits has been observed by selecting against boar taint. Selection results have shown that it is possible to reduce boar taint in few generations. In addition, modifications in diet and environment conditions could be associated with genetic selection to reduce boar taint. Nevertheless, costs to measure and select against boar taint should be rewarded with incentives from the market; otherwise, it would be difficult to implement genetic selection.

Genetic disorders of sex development in cats: An update

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.

The combination between NCSTN gene copy number variation and growth traits in Chinese cattle

Copy number variation (CNV) has been used as an important source of phenotypic and genetic diversity in recent years. Nicastrin (NCSTN) gene is usually attached to human diseases such as Alzheimer's disease, and Acne inversa. However, there are no essays about the NCSTN gene combining with cattle breeds. In our study, we discovered different distributions of NCSTN gene copy number and associated it with phenotypic traits in four Chinese yellow cattle breeds (XN, PN, QC and YL). The result turned out that the CNV of the NCSTN gene was associated with several growth traits, such as cannon circumference, chest girth and rump length (p < 0.05). In general, we revealed the eminence over CNV of NCSTN gene and economic traits, suggesting that the CNV of the NCSTN gene can be considered to be a promising molecular breeding marker of Chinese beef cattle.

Association between polymorphisms in the SOX9 region and canine disorder of sex development (78,XX; SRY-negative) revisited in a multibreed case-control study

Testicular or ovotesticular disorders of sex development (DSD) in individuals with female karyotype (XX) lacking the SRY gene has been observed in several mammalian species, including dogs. A genetic background for this abnormality has been extensively sought, and the region harboring the SOX9 gene has often been considered key in canine DSD. Three types of polymorphism have been studied in this region to date: a) copy number variation (CNV) in a region about 400 kb upstream of SOX9, named CNVR1; b) duplication of SOX9; and c) insertion of a single G-nucleotide (rs852549625) approximately 2.2 Mb upstream of SOX9. The aim of this study was thus to comprehensively analyze these polymorphisms in a large multibreed case-control cohort containing 45 XX DSD dogs, representing 23 breeds. The control set contained 57 fertile females. Droplet digital PCR (ddPCR) was used to study CNVR1 and the duplication of SOX9. Fluorescent in situ hybridization (FISH) was used to visualize copy numbers on a cellular level. The Sanger sequencing approach was performed to analyze the region harboring the G-insertion. We confirmed that CNVR1 is highly polymorphic and that copy numbers varied between 0 and 7 in the case and control cohorts. Interestingly, the number of copies was significantly higher (P = 0.038) in XX DSD dogs (mean = 2.7) than in the control females (mean = 2.0) but not in all studied breeds. Duplication of the SOX9 gene was noted only in a single XX DSD dog (an American Bully), which had three copies of SOX9. Distribution of the G-nucleotide insertion was similar in the XX DSD (frequency 0.20) and control (frequency 0.14) cohorts. Concluding, our study showed that CNVR1, located upstream of SOX9, is associated with the XX DSD phenotype, though in a breed-specific manner. Duplication of the SOX9 gene is a rare cause of this disorder in dogs. Moreover, we did not observe any association of G-insertion with the DSD phenotype. We assume that the genetic background of XX DSD can be different in certain breeds.

Pre-determination of sex in pigs by application of CRISPR/Cas system for genome editing

In livestock industries, one sex is usually preferred because of the impact on the production (e.g. milk from cows, eggs from laying hens). Furthermore, in pig production, the male-specific boar taint is a big hurdle for consumer acceptance. Consequently, a shift in the ratio towards the desired sex would be a great benefit. The most widely applied method for pre-determination of the sex is fluorescence-activated sperm sorting, which relies on the different DNA content of the X- and Y-chromosomal sperm. However, the successful practical adaption of this method depends on its ease of use. At present, sperm sexing via fluorescence-activated cell sorting (FACS) has only reached commercial application in cattle. Nevertheless, sperm sexing technology still needs to be improved with respect to efficiency and reliability, to obtain high numbers of sexed sperm and less invasive sperm treatment to avoid damage. New genome editing technologies such as Zinc finger nucleases (ZFN), Transcription-activator like endonucleases (TALENs) and the CRISPR/Cas system have emerged and offer great potential to affect determination of the sex at the genome level. The sex-determining region on the Y chromosome (SRY) serves as a main genetic switch of male gender development. It was previously shown that a knockout of the SRY gene in mice and rabbits displayed suppressed testis development in the fetal gonadal ridges resulting in a female phenotype. These new technologies hold great opportunities to pre-determine sex in pigs. However, further investigations are needed to exploit their full potential for practical application.