Alex Clop

Centre for Research in Agricultural Genomics

The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated t...

The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm’s chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genom...

The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated t...

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in...

Understanding the cell molecular changes occurring as a results of climatic circumstances is crucial in the current days in which climate change and global warming are one of the most serious challenges that living organisms have to face. Sperm are one of the mammals' cells most sensitive to heat, therefore evaluating the impact of seasonal changes...

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very ofte...

RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain...

Background: The mammalian mature spermatozoon has a unique chromatin structure in which the vast majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The chromatin structure of sperm remains unresolved in most livestock species, including the pig...

Background Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm qua...

Piwi‐interacting RNAs (piRNAs) are a class of non‐coding RNAs that are essential in the transcriptional silencing of transposable elements and warrant genome stability in the mammalian germline. In this study, we have identified piRNAs in porcine sperm using male germline and zygote datasets from human, mice, cow and pig, and evaluated the relation...

Transmission Ratio Distortion (TRD), the uneven transmission of an allele from a parent to its offspring, can be caused by allelic differences affecting gametogenesis, fertilization or embryogenesis. However, TRD remains vaguely studied at a genomic scale. We sequenced the diploid and haploid genomes of 3 boars from leukocytes and spermatozoa at 50...

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput charac...

Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. circRNAs have been studied in different tissues and cell types across several animal species. However, a thorough characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we p...

Background: Genetic pressure in animal breeding is sparking the interest to select for elite boars with higher sperm quality to maximize ejaculate doses and fertility rates. However, the molecular basis of sperm quality remains largely unexplored. In this study, we sought to identify candidate genes, pathways and DNA variants associated to sperm qu...

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar’s reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, a high throughput characte...

Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs which main reported function consists on the silencing of transposable elements and genome stability in mammalian germline. In this study we have identified piRNAs in porcine sperm, using male germline and zygote datasets from human, mice, cow and swine, and evaluated the relation betwee...

Domestic animal species constitute an ideal model to investigate the genetic regulation of lipid metabolism phenotypes, such as fatness and intramuscular fat content and composition; because these traits are systematically recorded by the breeding industry and high throughput genotyping methods and genome sequences are readily available. At a metab...

Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. Although circRNAs have been studied in several tissues and cell types across several animal species, the characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we profiled t...

Summary statistics of the de novo transcriptome assembly. Summary statistics of the Trinity output based on the number of potential novel genes and transcripts, and size (in bp) of the contigs based on all transcripts isoforms or based only on the longest isoform for each potential gene.

Non-redundant list of genes identified by de novo analysis. 768 potentially novel genes were identified from the unmapped reads. The gene symbol IDs were retrieved with Uniprot from the Trinity output protein names. These genes were detected in at least one species (detailed in column 2 of Supplementary File S8). The majority of these genes were an...

List of long non-coding RNAs detected in porcine sperm. Ensembl IDs of the lncRNAs identified in this study, their genome coordinates, average RNA abundance across the 10 samples and length. Most of the lncRNAs presented, as an average across all samples, low RNA abundances.

RNA abundance levels and coefficient of variation of miRNAs, tRNAs, and piRNAs in the porcine sperm. RNA abundance is measured in CPM (Counts Per Million) across the 10 samples. We only considered the miRNAS with >0 CPMs in all the samples. The genomic coordinates of piRNAs refer to the Sscrofa10.2 built instead of Sscrofa11.1 as provided by the pi...

Novel piRNA clusters identified in the pig sperm RNA. We detected 17 potential clusters of piRNAs that were found in at least 3 of the 10 samples analyzed in this study. Mean and standard deviation (SD) in CPM (Counts Per Million).

RNA-seq quality and mapping statistics. Average and Standard Deviation (SD) for the 10 boar sperm samples processed, including: amount of RNA extracted and several RNA-seq bioinformatics statistics for both total and small RNA-seq.

Distribution of the top decile most abundant SREs (Sperm RNA Elements) into SRE types and gene biotypes. Number of SREs (within the top decile) for each SRE type (exonic, intronic, upstream/downstream 10 kb and orphan). Total non-redundant number of genes and their biotype for each SRE class.

List of human and bovine genes identified by syntenic alignment of the orphan SREs. Orphan SRE genome coordinates were liftover to human and bovine coordinates, and the genes mapped in these regions were extracted. A total of 45 genes shared in both species were found. From these genes, 44 were already annotated in the Sscrofa Ensembl v.91 annotati...

Gene Ontology analysis of the different SRE abundance variance groups. GO biological process terms with significant Bonferroni corrected p-values (p-val < 0.05) and their associated genes.

Concordance of miRNA identification between our dataset and other sperm RNA-seq studies. Comparison of the miRNAs identified in our study with other sperm RNA-seq experiments in pig, in human, and cattle.

Gene Ontology analysis of the genes including the top decile most abundant and the orphan SREs detected in the SRE pipeline. GO biological process terms with significant Bonferroni corrected p-values (p-val < 0.05) and their associated genes.

Correlation between transcript integrity across samples, with transcript abundance and coding sequence length. Correlation of the TIN (Transcripts Integrity Number) between samples, with the transcript abundance and with the coding sequence length of the transcripts. This table shows the correlation of the TIN (Transcripts Integrity Number) between...

List of proteins identified by de novo analysis, with the species in which they were detected and transcript abundance. De novo analysis of the unmapped reads resulted in 1,060 proteins which passed the quality control filters. For each protein, we include the cognate species, the predicted RNA mean abundance in the 10 samples (in FPKM), the Standa...

Distribution of the short RNA-seq reads mapping to different RNA types. Proportion and standard deviation (SD) across the 10 samples.

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to the characterization of the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and deca...

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to characterize the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and decays in the s...

Abbreviations: FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous RNA; Mt rRNA: mitochondrial ribosomal RNA; Mt tRNA: mitochondrial transference RNA; OAZ3: ornithine decarboxylase antizyme 3; ORT: osmotic resistance test; piRNA: Piwi-interacting RNA; PRM1: protamine 1; PTP...

Taste receptors (TASRs) and appetite and reward (AR) mechanisms influence eating behaviour, which in turn affects food intake and risk of obesity. In a previous study, we used next generation sequencing to identify potentially functional mutations in TASR and AR genes and found indications for genetic associations between identified variants and gr...

The relationship between vitamin D deficiency and the risk of suffering from a plethora of health disorders, ranging from autoimmune processes to infectious diseases has been widely described. Nonetheless, the potential role of vitamin D in visceral leishmaniasis remains uncharacterized. In the Mediterranean basin, where the dog is leishmania’s mai...

In this study, we have analysed the variation of 81 Italian pigs from the Calabrese, Casertana, Cinta Senese, Sarda and Nero Siciliano breeds as well as 54 Italian wild boars by using a dataset of mitochondrial control region sequences generated by us and others. Diversity parameters were rather low in Italian native pigs, with haplotype and nucleo...

We performed a genome-wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with the Porcine SNP60 BeadChip. Association analyses were carried out using the gemma software. The proportion of phenotypic variance explained by the SNPs ranged between negligible to moderate (= 0.01–0.30) depending on the trait...

Toll-like receptors (TLR) are crucial in innate immunity for the recognition of a broad range of microbial pathogens and are expressed in multiple cell types. There are 10 TLR genes described in the pig genome. With a twofold objective i.e. to catalogue genetic variants in porcine TLR genes and develop a genotyping array for genetic association stu...

Background Toll-like receptors (TLR) are crucial in innate immunity for the recognition of a broad range of microbial pathogens and are expressed in multiple cell types. There are 10 TLR genes described in the pig genome.ResultsWith a twofold objective i.e. to catalogue genetic variants in porcine TLR genes and develop a genotyping array for geneti...

Background Taste receptors (TASRs) are essential for the body’s recognition of chemical compounds. In the tongue, TASRs sense the sweet and umami and the toxin-related bitter taste thus promoting a particular eating behaviour. Moreover, their relevance in other organs is now becoming evident. In the intestine, they regulate nutrient absorption and...

Taste receptors (TASR) have been associated to taste preferences, infection and intoxication in mammals. On the other side, reward genes are responsible for promoting a behaviour followed by a pleasant stimulus. Therefore, both gene groups of genes are likely to have an important impact in production traits in the pig. We captured the coding sequen...

Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that...

Candidate susceptibility SNPs co-localize with Pol-II, POU2F2 and NF-κB Chip-Seq peaks. (DOCX)

Software pipeline used to analyze the sequence of the two BACs spanning the PSORS1 locus. (DOC)

Distribution of PSORS1 active chromatin marks in control T lymphocytes. (XLSX)

The PSORS1 epigenetic profile of patient T-lymphocytes is comparable to that observed in controls. (DOCX)

Sequence coverage statistics for the ChIP-Seq analysis of H3K4me1 and H3K27ac marks. (XLSX)

PCR primers and restriction enzymes used in the CoBRA analysis. (XLSX)

Genomic location of the two BAC clones spanning the PSORS1 locus. (DOCX)

Details of the 144 candidate PSORS1 variants. (XLSX)

Sequence coverage statistics for the two BAC clones spanning the refined PSORS1 locus. (XLSX)

Psoriasis is a common, chronic, inflammatory skin disorder. A number of genetic loci have been shown to confer risk for psoriasis. Collectively, these offer an integrated model for the inherited basis for susceptibility to psoriasis that combines altered skin barrier function together with the dysregulation of innate immune pathogen sensing and ada...

Female sexual dysfunction (FSD) is an important but controversial problem with serious negative impact on women's quality of life. Data from twin studies have shown a genetic contribution to the development and maintenance of FSD. We performed a genome-wide association study (GWAS) on 2.5 million single-nucleotide polymorphisms (SNPs) in 1,104 fema...

Copy number variation (CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characteriz...

The history of African pig breeds is still controversial due to the relative scarcity of archaeological and genetic data clarifying their origins. While these breeds might descend from Near Eastern pigs entering the continent via Egypt during the Neolithic, Africa may be a primary domestication locus for pigs, as indicated for other species such as...

Milk caseins are the major protein source for the newborn, providing amino acids that are essential to sustain growth as well as peptides with immunomodulatory activities. Caseins have also a remarkable impact on the dairy industry, being the main determinant of the efficiency with which milk is transformed into cheese. Casein genes have been thoro...

Psoriasis is an inflammatory skin disorder that is inherited as a complex trait. Genetic studies have repeatedly highlighted HLA-C as the major determinant for psoriasis susceptibility, with the Cw*0602 allele conferring significant disease risk in a wide range of populations. Despite the potential importance of HLA-C variation in psoriasis, either...

MicroRNA (miRNA) are expected to regulate 30% of coding genes. Moreover, dbSNP database reports more than 23 million SNP in the human genome (April 2010), many of which might alter miRNA-related genes. Thus, polymorphisms affecting miRNA gene regulation may have a widespread effect on phenotypes. Polymorphisms directly altering miRNA gene regulatio...

General principles of cytokine-dependent immune cell population interactions. (1.09 MB PDF)

Author Summary A functional immune system requires complex interactions among diverse cell types, mediated by a variety of cytokines. These interactions include phenomena such as positive and negative feedback loops that can be experimentally characterized by dose-dependent cytokine production measurements. However, any experimental approach is not...

Genetic and archaeological findings suggest that pig domestication began about 9000–10000 YBP at multiple sites across Eurasia, followed by their subsequent spread at a worldwide scale. Development of local types throughout the centuries led to the foundation, mostly during the nineteenth century, of current modern breeds with defined phenotypes an...

This study aimed at verifying previously identified QTL affecting growth and carcass traits on ovine chromosome 18 (OAR18) in Texel sheep (n = 1844), and on OAR1 in Charollais (n = 851) and Suffolk (n = 998) sheep. The QTL were investigated using regression and variance component mapping (VCA) of body weight, muscle and fat depth measurements. In a...

The main goal of the current work was to identify single nucleotide polymorphisms (SNP) that might create or disrupt microRNA (miRNA) target sites in the caprine casein genes. The 3' untranslated regions of the goat alpha(S1)-, alpha(S2)-, beta-, and kappa-casein genes (CSN1S1, CSN1S2, CSN2, and CSN3, respectively) were resequenced in 25 individual...

We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populatio...

To assess whether the same mutation(s) were responsible for similar phenotypes attributed to ovine chromosome 2 (OAR2) quantitative trait loci (QTL) in different sheep breeds, Suffolk, Texel and Charollais rams from British commercial flocks were genotyped for two single nucleotide polymorphisms (SNPs) located in the myostatin (GDF8) region of OAR2...