Armand Sanchez - Academia.edu (original) (raw)
Papers by Armand Sanchez
Genetics Selection Evolution, May 15, 2001
This study was undertaken to determine the genetic structure, evolutionary relationships, and the... more This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F st = 0.07; P < 0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples. local beef cattle breeds / microsatellite / genetic diversity
Journal of Animal Science, Aug 10, 2023
PID2020-112677RB-C22. We also acknowledge the support of the Spanish Ministerio de Economía y Com... more PID2020-112677RB-C22. We also acknowledge the support of the Spanish Ministerio de Economía y Competitividad for the "Severo Ochoa" Programme for Centres of Excellence in R&D (Project No. CEX2019-000902-S) to the Centre for Research in Agricultural Genomics (CRAG) and to the programmes of Centres de Recerca de Catalunya (CERCA). Funding organizations were not involved in the execution of the project or the interpretation of results. All experimental protocols were approved by the ethical committee of the University of Milan (OPBA 22/2020). We also thank for help of Dr. Eleonora Munari and the University of Milan farm personnel with the in-vivo trials, and Dr. Sara Panseri and Giacomo Mosconi for fatty acid analysis.
Genetics Selection Evolution, 1992
The phylogenetic relationships between 10 Spanish dog breeds were studied using the gene frequenc... more The phylogenetic relationships between 10 Spanish dog breeds were studied using the gene frequency values obtained from the electrophoretic analysis of 21 structural genic loci that code for blood-soluble proteins and enzymes. In addition, we studied the genetic differentiation within breeds. In some cases the genetic distances between subpopulations of the same breed were greater than the genetic distances between different breeds. The average between-breed distance has a value of 0.0197 (t 0.0128), with extreme values of D = 0.000 between Gos d'Atura and Podenco lb6rico, and of D = 0.051 for the Mastin Espanol-Ca de Bestian pair. The groupings of Spanish dog breeds obtained in our study from morphological and biochemical data were apparently quite similar. The correlation between enzymatic and morphological distances was, however, low (r = 0.07) and non-significant. The estimates of the divergence times among the 4 ancestral trunks suggest that the ancestral trunks separated independently in a relatively short interval of time, between 30 000 and 55 000 years ago. Spanish dog breeds / biochemical polymorphisms / electrophoresis / genetic distance / genetic relationships Résumé-Relations génétiques entre des races canines espagnoles. II. Analyse du polymorphisme biochimique. À partir des valeurs des fréquences géniques, obtenues par l'analyse électrophorétique de 21 locus qui codent pour des enzymes et des protéines solubles du sang, on a étudié les relations phylogénétiques existant entre dix races canines espagnoles. On a déterminé aussi le niveau de di,!j'érenciation intraracial, et constaté que, dans certains cas, les distances génétiques entre sous-populations d'une même race sont supérieures à celles existant entre races di,!"érentes. La distance moyenne entre races prend une valeur de 0,0197 (f 0,0128), avec des valeurs extrêmes de D = 0, 000 entre « Gos d'Atura» et «Podenco Ibérico», et de D = 0,051 pour le couple « Mastin Espanol»-« Ca de Bestiar». Les groupements obtenus dans notre étude, à partir de données morphologiques et biochimiques, sont apparemment assez similaires. La corrélation entre distances enzymatiques et morphologiques est cependant très faible (r = 0,07) et non significative. L'estimation des origines de la divergence entre les quatre troncs ancestraux, suggère que ces troncs se sont séparés dans un intervalle de temps relativement court, il y a 30 000 à 5 000 ans. races canines espagnoles / polymorphisme biochimique / électrophorèse / distance génétique an anticoagulant. The samples were separated into the 3 main blood components; plasma, red blood cells and white blood cells, and stored at-20°C.
Animal Genetics, Nov 23, 2020
Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that are essential in the transcrip... more 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 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 between their abundances and sperm quality traits. In our analysis, we identified 283,382 piRNAs, 1,355 of which correlated with P 0.01 to at least one semen quality trait. Fifty-seven percent of the correlated piRNAs mapped less than 50kb apart from any other piRNA in the pig genome. Furthermore, piRNA location was significantly enriched near Long Interspersed Nuclear Elements (LINEs). Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.
Scientific Reports, Jun 7, 2016
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds... more The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. Since their domestication in the Fertile Crescent, sheep have been bred for producing milk, meat and wool 1. Artificial selection for these and other phenotypic traits probably began thousands of years ago by keeping as breeders individuals with certain external features (e.g. color, size, morphology etc) and productive abilities (rapid growth and high fertility). The speed of this process of genetic change accelerated enormously in the last decades as a consequence of the implantation of intensive breeding schemes based on artificial insemination, extensive trait and genealogical recording, and the introduction of best linear unbiased predictor approaches to estimate genetic values 2. Certain cosmopolitan breeds became strongly specialized in either meat, wool or dairy production, while others, with a more local distribution, kept a more balanced production profile. Currently, in Spain there are 43 officially recognized ovine breeds that encompass 16 million individuals (the 2 nd largest census of
Scientific Reports, Jul 11, 2018
The goal of the current study is to analyse the gene expression profile of the ovine skeletal mus... more The goal of the current study is to analyse the gene expression profile of the ovine skeletal muscle as well as to characterize the genetic variation of transcripts expressed in such tissue. This aim has been achieved by sequencing the longissimus dorsi transcriptomes of 50 sheep distributed in five pools representing the Canaria de Pelo, Roja Mallorquina, Gallega, Xisqueta and Ripollesa Spanish autochthonous breeds. Approximately, 363 million reads per pool have been produced and 71.9-82.9% have been successfully mapped to the ovine genome in a paired-end mode (2 × 75 bp). The 200 most expressed muscle transcripts (≈1% of the total transcript count) account for 51% (Canaria de Pelo) to 67% (Gallega) of the total ovine skeletal muscle mRNA expression. These highly expressed genes play key roles in pathways related with striated muscle contraction, gluconeogenesis, glycolysis, citric acid cycle and respiratory electron transport. RNA-Sequencing of muscle transcripts has also revealed that ~72% of the SNPs detected with this approach are shared by at least two pools, and 10% of them segregate in the five pools under analysis. Most of the substitutions detected by RNA-Seq are synonymous or missense and only a minority are predicted to have consequences on protein function.
Journal of Veterinary Internal Medicine, Sep 19, 2022
Background: Reliable biomarkers to differentiate gastrointestinal cancer (GIC) from chronic infla... more Background: Reliable biomarkers to differentiate gastrointestinal cancer (GIC) from chronic inflammatory enteropathy (CIE) in dogs are needed. Fecal and serum micro-RNAs (miRNAs) have been proposed as diagnostic and prognostic markers of GI disease in humans and dogs. Hypothesis/Objectives: Dogs with GIC have fecal and serum miRNA profiles that differ from those of dogs with CIE. Aims: (a) identify miRNAs that differentiate GIC from CIE, (b) use high-throughput reverse transcription quantitative real-time PCR (RT-qPCR) to establish fecal and serum miRNA panels to distinguish GIC from CIE in dogs.
Resumen del trabajo presentado a la 37 International Society for Animal Genetics Conference (ISAG... more Resumen del trabajo presentado a la 37 International Society for Animal Genetics Conference (ISAG), celebrada en Lleida (Espana) del 7 al 12 de julio de 2019.
Background: the effect of the production environment and different management practices in rabbit... more Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at...
Background: the effect of the production environment and different management practices in rabbit... more Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes ( ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rDNA-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals ...
Hereditas, 2002
Repetitive DNA sequences represent a substantial component of eukaryotic genomes. These sequences... more Repetitive DNA sequences represent a substantial component of eukaryotic genomes. These sequences have been described and characterized in many mammalian species. However, little information about repetitive DNA sequences is available in bat species. Here we describe an EcoRI family of repetitive DNA sequences present in the species Miniopterus schreibersi. These repetitive sequences are 57.85 % AT rich, organized in tandem, and with a monomer unit length of 904 bp. Methylation analysis using the isoesquizomer pair MspI and HpaII indicates that the cytosines present in the sequences CCGG are partially methylated. Furthermore, Southern blot analysis demonstrated that these DNA sequences are absent in the genomes of four related microbat species and suggest that it could be specific to the M. schreibersi genome.
PLOS ONE, May 4, 2023
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids wit... more Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine diets tend to over-supplement with n-6 PUFAs, which may increase the likelihood of developing inflammatory diseases and affect the overall well-being of the animals. However, it is still poorly understood how n-6/n-3 PUFA ratios affect the porcine transcriptome expression and how messenger RNAs (mRNAs) and microRNAs (miRNAs) might regulate biological processes related to PUFA metabolism. On account of this, we selected a total of 20 Iberian × Duroc crossbred pigs with extreme values for n-6/n-3 FA ratio (10 high vs 10 low), and longissimus dorsi muscle samples were used to identify differentially expressed mRNAs and miRNAs. The observed differentially expressed mRNAs were associated to biological pathways related to muscle growth and immunomodulation, while the differentially expressed microRNAs (ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-15b and ssc-miR-7142-3p) were correlated to adipogenesis and immunity. Relevant miRNA-to-mRNA regulatory networks were also predicted (i.e., mir15b to ARRDC3; mir-7142-3p to METTL21C), and linked to lipolysis, obesity, myogenesis, and protein degradation. The n-6/n-3 PUFA ratio differences in pig skeletal muscle revealed genes, miRNAs and enriched pathways involved in lipid metabolism, cell proliferation and inflammation.
Molecules
Elevated omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) ratios in swine diet... more Elevated omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) ratios in swine diets can potentially impose a higher risk of inflammatory and metabolic diseases in swine. A low ratio between the two omega PUFAs has beneficial effects on sows’ and piglets’ production performance and immunity status. At present, there are few studies on how sow nutrition directly affects the protein and fat deposition in suckling piglets. Two groups of sows were fed diets with high or low n-6/n-3 polyunsaturated ratios of 13:1 (SOY) and 4:1 (LIN), respectively, during gestation and lactation. Longissimus dorsi muscle and adipose tissue from newborn piglets, nourished only with sow’s milk, were subjected to fatty acid profiling by gas chromatography–mass spectrometry (GC-MS) and to proteomics assays based on nano-liquid chromatography coupled to high-resolution tandem mass spectrometry (nLC-HRMS). Fatty acid profiles on both muscle and adipose tissues resembled the magnitude of the differ...
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population hist... more By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expan...
Recent work using 16s rRNA sequencing has led to the understanding that milk microbiota is comple... more Recent work using 16s rRNA sequencing has led to the understanding that milk microbiota is complex, harboring great multifunctional diversity. An important question is if milk in the mammary gland is sterile and bacteria come from the external environment or if there are endogenous bacteria present in milk. In the present study, we performed a preliminary metagenome analysis of bovine milk by sequencing the V1-V2 hypervariable regions of 16S rRNA gene. Milk samples were collected from the same cow at 3 different stages of lactation (15, 90, 120 dim), with and without using a cannula. Microbial DNA was extracted from two tissues, somatic cells and fat. Our findings showed: 1) The microbiota structure of the two tissues was completely different (adonis R 2 = 0.68, p-value=0.001). Fat samples present a uniform profile composed of three highly abundant bacterial genera: Janthinobacterium, Acinetobacter and Pseudomonas. Microbiota from somatic cells presents significantly higher diversity and more variability in the taxonomic profile. 2) Most of the taxonomic divergences among lactation days were found in fat samples obtained with no cannula. 3) Comparing milk fat samples from mastitic and healthy quarters, taxonomic profiles of healthy quarters were more homogeneous then affected quarters. This observation could be linked to the so called, Anna Karenina Principle, that states that dysbiotic samples vary more in microbial community composition than healthy samples (Zaneveld et al. Nat. Micro 2017). The focus of this study was to develop the sampling and analytical methodology to assess milk microbiota in somatic cells and fat tissues. Although a larger number of samples are needed to support some of our observations, we feel examining milk microbiota in these two tissues will prove to be scientifically insightful.
Journal of Dairy Science, 2020
The identification of milk microbial communities in ruminants is relevant for understanding the a... more The identification of milk microbial communities in ruminants is relevant for understanding the association between milk microbiota and health status. The most common approach for studying the microbiota is amplifying and sequencing specific hypervariable regions of the 16S rRNA gene using massive sequencing techniques. However, the taxonomic resolution is limited to family and, in some cases, genus level. We aimed to improve taxonomic classification of the water buffalo milk microbiota by amplifying and sequencing the full-length 16S rRNA gene (1,500 bp) using Nanopore sequencing (single-molecule sequencing). When comparing with short-read results, we improved the taxonomic classification, reaching species level. We identified the main microbial agents of subclinical mastitis at the species level that were in accordance with the microbiological culture results. These results confirm the potential of single-molecule sequencing for in-depth analysis of microbial populations in dairy animals.
Nano Research, 2015
A novel triple lines lateral-flow assay (LFA) with enhanced sensitivity for the detection of Leis... more A novel triple lines lateral-flow assay (LFA) with enhanced sensitivity for the detection of Leishmania infantum DNA in dog blood samples was designed and successfully applied. The enhanced LFA methodology takes advantage of the gold nanoparticle tags (AuNPs) conjugated to polyclonal secondary antibodies, which recognize anti-FITC antibodies. The polyclonal nature of the secondary antibodies allows for multiple binding to primary antibodies, leading to enhanced AuNP plasmonics signal. Furthermore, endogenous control consisting of the amplified dog 18S rRNA gene was introduced to avoid false negatives. Using this strategy, 0.038 spiked Leishmania parasites per DNA amplification reaction (1 parasite/100 μL of DNA sample) were detected. Detection limit of LFA was found to be lower than that of the conventional techniques. In summary, our novel LFA design is a universal and simple sensing alternative that can be extended to several other biosensing scenarios.
Veterinary Immunology and Immunopathology, 2008
Promastigotes of Leishmania infantum undergo a series of extracellular developmental stages insid... more Promastigotes of Leishmania infantum undergo a series of extracellular developmental stages inside the natural sand fly vector Lutzomyia longipalpis to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis mapped the sequences corresponding to the procyclic, nectomonad, leptomonad or metacyclic promastigote stage into distinct positions, with the procyclic stage being the most divergent population. Transcriptional levels across genes varied on average between 10-to 100-fold. Comparison between procyclic and nectomonad promastigotes resulted in 836 differentially expressed (DE) genes; between nectomonad and leptomonad promastigotes in 113 DE genes; and between leptomonad and metacyclic promastigotes in 302 DE genes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple stage-specific markers for L. Infantum. Leading stage-specific marker candidates include genes encoding a zinc transporter in procyclics, a beta-fructofuranidase in nectomonads, a surface antigen-like protein in leptomonads, and an amastin-like surface protein in metacyclics. Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of stage-specific markers for further development as molecular tools for epidemiological studies. made available for use under a CC0 license.
Genetics Selection Evolution, 1992
The relationships between 10 Spanish dog breeds have been studied using qualitative and quantitat... more The relationships between 10 Spanish dog breeds have been studied using qualitative and quantitative analyses of data from 32 morphological characters. The average distance between breeds, measured as a morphological index, has a value of 4.228 (! 0.681), with extreme values of 1.732 between Mastin del Pirineo and Mastin Espanol, and of 5.099 for the Gos d'Atura-Sabueso Espanol pair. The morphological phylogeny obtained in this study confirms the classifications made previously by means of dental, cranial, historical and behavioral comparative criteria. The results suggest the formation of 2 large clusters; one formed by the breeds belonging to the ancestral trunks Canis fa7rciliaris intermedius and Canis familiaris inostranzewi, and the other which includes the members of the Canis familiaris leineri and Canis familiaris metris-optirrtae trunks. Spanish dog breeds / genetic distance / morphological character / dendrogram / morphological analysis Résumé-Relations génétiques entre des races canines espagnoles. I. Analyse des caractères morphologiques. À partir de l'analyse qualitative et quantitative des données provenant de 3! caractères morphologiques, on a étudié les relations existant entre 10 races canines espagnoles. La distance moyenne entre ' races, mesurée par un indice de distance morphologique, prend une valeur de 4,228 (::1:: 0,681), avec des valeurs extrêmes de 1,7.i2 entre Mastin del Pirineo et Mastin Espanol, et 5,099 pour le couple Gos d'Atura-Sabueso Espanol. La phylogénie morphologique obtenue dans ce travail, confirme les classifications précédentes, réalisées à partir de critères comparatifs dentaires, crâniens, historiques et comportementaux. Les résultats suggèrent la formation de deux grands groupes. L'un comprend les races qui appartiennent aux troncs ancestraux du Canis familiaris intermedius et du Canis familiaris inostranzewi, et l'autre serait formé par les composants des troncs du Canis familiaris leineri et du Canis familiaris metris-optimae. ' races canines espagnoles / distance génétique / caractère morphologique / dendrogramme / analyse morphologique
Biotechnol. Agron. Soc …, 2004
Genetics Selection Evolution, May 15, 2001
This study was undertaken to determine the genetic structure, evolutionary relationships, and the... more This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F st = 0.07; P < 0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples. local beef cattle breeds / microsatellite / genetic diversity
Journal of Animal Science, Aug 10, 2023
PID2020-112677RB-C22. We also acknowledge the support of the Spanish Ministerio de Economía y Com... more PID2020-112677RB-C22. We also acknowledge the support of the Spanish Ministerio de Economía y Competitividad for the "Severo Ochoa" Programme for Centres of Excellence in R&D (Project No. CEX2019-000902-S) to the Centre for Research in Agricultural Genomics (CRAG) and to the programmes of Centres de Recerca de Catalunya (CERCA). Funding organizations were not involved in the execution of the project or the interpretation of results. All experimental protocols were approved by the ethical committee of the University of Milan (OPBA 22/2020). We also thank for help of Dr. Eleonora Munari and the University of Milan farm personnel with the in-vivo trials, and Dr. Sara Panseri and Giacomo Mosconi for fatty acid analysis.
Genetics Selection Evolution, 1992
The phylogenetic relationships between 10 Spanish dog breeds were studied using the gene frequenc... more The phylogenetic relationships between 10 Spanish dog breeds were studied using the gene frequency values obtained from the electrophoretic analysis of 21 structural genic loci that code for blood-soluble proteins and enzymes. In addition, we studied the genetic differentiation within breeds. In some cases the genetic distances between subpopulations of the same breed were greater than the genetic distances between different breeds. The average between-breed distance has a value of 0.0197 (t 0.0128), with extreme values of D = 0.000 between Gos d'Atura and Podenco lb6rico, and of D = 0.051 for the Mastin Espanol-Ca de Bestian pair. The groupings of Spanish dog breeds obtained in our study from morphological and biochemical data were apparently quite similar. The correlation between enzymatic and morphological distances was, however, low (r = 0.07) and non-significant. The estimates of the divergence times among the 4 ancestral trunks suggest that the ancestral trunks separated independently in a relatively short interval of time, between 30 000 and 55 000 years ago. Spanish dog breeds / biochemical polymorphisms / electrophoresis / genetic distance / genetic relationships Résumé-Relations génétiques entre des races canines espagnoles. II. Analyse du polymorphisme biochimique. À partir des valeurs des fréquences géniques, obtenues par l'analyse électrophorétique de 21 locus qui codent pour des enzymes et des protéines solubles du sang, on a étudié les relations phylogénétiques existant entre dix races canines espagnoles. On a déterminé aussi le niveau de di,!j'érenciation intraracial, et constaté que, dans certains cas, les distances génétiques entre sous-populations d'une même race sont supérieures à celles existant entre races di,!"érentes. La distance moyenne entre races prend une valeur de 0,0197 (f 0,0128), avec des valeurs extrêmes de D = 0, 000 entre « Gos d'Atura» et «Podenco Ibérico», et de D = 0,051 pour le couple « Mastin Espanol»-« Ca de Bestiar». Les groupements obtenus dans notre étude, à partir de données morphologiques et biochimiques, sont apparemment assez similaires. La corrélation entre distances enzymatiques et morphologiques est cependant très faible (r = 0,07) et non significative. L'estimation des origines de la divergence entre les quatre troncs ancestraux, suggère que ces troncs se sont séparés dans un intervalle de temps relativement court, il y a 30 000 à 5 000 ans. races canines espagnoles / polymorphisme biochimique / électrophorèse / distance génétique an anticoagulant. The samples were separated into the 3 main blood components; plasma, red blood cells and white blood cells, and stored at-20°C.
Animal Genetics, Nov 23, 2020
Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that are essential in the transcrip... more 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 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 between their abundances and sperm quality traits. In our analysis, we identified 283,382 piRNAs, 1,355 of which correlated with P 0.01 to at least one semen quality trait. Fifty-seven percent of the correlated piRNAs mapped less than 50kb apart from any other piRNA in the pig genome. Furthermore, piRNA location was significantly enriched near Long Interspersed Nuclear Elements (LINEs). Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.
Scientific Reports, Jun 7, 2016
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds... more The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. Since their domestication in the Fertile Crescent, sheep have been bred for producing milk, meat and wool 1. Artificial selection for these and other phenotypic traits probably began thousands of years ago by keeping as breeders individuals with certain external features (e.g. color, size, morphology etc) and productive abilities (rapid growth and high fertility). The speed of this process of genetic change accelerated enormously in the last decades as a consequence of the implantation of intensive breeding schemes based on artificial insemination, extensive trait and genealogical recording, and the introduction of best linear unbiased predictor approaches to estimate genetic values 2. Certain cosmopolitan breeds became strongly specialized in either meat, wool or dairy production, while others, with a more local distribution, kept a more balanced production profile. Currently, in Spain there are 43 officially recognized ovine breeds that encompass 16 million individuals (the 2 nd largest census of
Scientific Reports, Jul 11, 2018
The goal of the current study is to analyse the gene expression profile of the ovine skeletal mus... more The goal of the current study is to analyse the gene expression profile of the ovine skeletal muscle as well as to characterize the genetic variation of transcripts expressed in such tissue. This aim has been achieved by sequencing the longissimus dorsi transcriptomes of 50 sheep distributed in five pools representing the Canaria de Pelo, Roja Mallorquina, Gallega, Xisqueta and Ripollesa Spanish autochthonous breeds. Approximately, 363 million reads per pool have been produced and 71.9-82.9% have been successfully mapped to the ovine genome in a paired-end mode (2 × 75 bp). The 200 most expressed muscle transcripts (≈1% of the total transcript count) account for 51% (Canaria de Pelo) to 67% (Gallega) of the total ovine skeletal muscle mRNA expression. These highly expressed genes play key roles in pathways related with striated muscle contraction, gluconeogenesis, glycolysis, citric acid cycle and respiratory electron transport. RNA-Sequencing of muscle transcripts has also revealed that ~72% of the SNPs detected with this approach are shared by at least two pools, and 10% of them segregate in the five pools under analysis. Most of the substitutions detected by RNA-Seq are synonymous or missense and only a minority are predicted to have consequences on protein function.
Journal of Veterinary Internal Medicine, Sep 19, 2022
Background: Reliable biomarkers to differentiate gastrointestinal cancer (GIC) from chronic infla... more Background: Reliable biomarkers to differentiate gastrointestinal cancer (GIC) from chronic inflammatory enteropathy (CIE) in dogs are needed. Fecal and serum micro-RNAs (miRNAs) have been proposed as diagnostic and prognostic markers of GI disease in humans and dogs. Hypothesis/Objectives: Dogs with GIC have fecal and serum miRNA profiles that differ from those of dogs with CIE. Aims: (a) identify miRNAs that differentiate GIC from CIE, (b) use high-throughput reverse transcription quantitative real-time PCR (RT-qPCR) to establish fecal and serum miRNA panels to distinguish GIC from CIE in dogs.
Resumen del trabajo presentado a la 37 International Society for Animal Genetics Conference (ISAG... more Resumen del trabajo presentado a la 37 International Society for Animal Genetics Conference (ISAG), celebrada en Lleida (Espana) del 7 al 12 de julio de 2019.
Background: the effect of the production environment and different management practices in rabbit... more Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at...
Background: the effect of the production environment and different management practices in rabbit... more Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes ( ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rDNA-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals ...
Hereditas, 2002
Repetitive DNA sequences represent a substantial component of eukaryotic genomes. These sequences... more Repetitive DNA sequences represent a substantial component of eukaryotic genomes. These sequences have been described and characterized in many mammalian species. However, little information about repetitive DNA sequences is available in bat species. Here we describe an EcoRI family of repetitive DNA sequences present in the species Miniopterus schreibersi. These repetitive sequences are 57.85 % AT rich, organized in tandem, and with a monomer unit length of 904 bp. Methylation analysis using the isoesquizomer pair MspI and HpaII indicates that the cytosines present in the sequences CCGG are partially methylated. Furthermore, Southern blot analysis demonstrated that these DNA sequences are absent in the genomes of four related microbat species and suggest that it could be specific to the M. schreibersi genome.
PLOS ONE, May 4, 2023
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids wit... more Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine diets tend to over-supplement with n-6 PUFAs, which may increase the likelihood of developing inflammatory diseases and affect the overall well-being of the animals. However, it is still poorly understood how n-6/n-3 PUFA ratios affect the porcine transcriptome expression and how messenger RNAs (mRNAs) and microRNAs (miRNAs) might regulate biological processes related to PUFA metabolism. On account of this, we selected a total of 20 Iberian × Duroc crossbred pigs with extreme values for n-6/n-3 FA ratio (10 high vs 10 low), and longissimus dorsi muscle samples were used to identify differentially expressed mRNAs and miRNAs. The observed differentially expressed mRNAs were associated to biological pathways related to muscle growth and immunomodulation, while the differentially expressed microRNAs (ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-15b and ssc-miR-7142-3p) were correlated to adipogenesis and immunity. Relevant miRNA-to-mRNA regulatory networks were also predicted (i.e., mir15b to ARRDC3; mir-7142-3p to METTL21C), and linked to lipolysis, obesity, myogenesis, and protein degradation. The n-6/n-3 PUFA ratio differences in pig skeletal muscle revealed genes, miRNAs and enriched pathways involved in lipid metabolism, cell proliferation and inflammation.
Molecules
Elevated omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) ratios in swine diet... more Elevated omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) ratios in swine diets can potentially impose a higher risk of inflammatory and metabolic diseases in swine. A low ratio between the two omega PUFAs has beneficial effects on sows’ and piglets’ production performance and immunity status. At present, there are few studies on how sow nutrition directly affects the protein and fat deposition in suckling piglets. Two groups of sows were fed diets with high or low n-6/n-3 polyunsaturated ratios of 13:1 (SOY) and 4:1 (LIN), respectively, during gestation and lactation. Longissimus dorsi muscle and adipose tissue from newborn piglets, nourished only with sow’s milk, were subjected to fatty acid profiling by gas chromatography–mass spectrometry (GC-MS) and to proteomics assays based on nano-liquid chromatography coupled to high-resolution tandem mass spectrometry (nLC-HRMS). Fatty acid profiles on both muscle and adipose tissues resembled the magnitude of the differ...
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population hist... more By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expan...
Recent work using 16s rRNA sequencing has led to the understanding that milk microbiota is comple... more Recent work using 16s rRNA sequencing has led to the understanding that milk microbiota is complex, harboring great multifunctional diversity. An important question is if milk in the mammary gland is sterile and bacteria come from the external environment or if there are endogenous bacteria present in milk. In the present study, we performed a preliminary metagenome analysis of bovine milk by sequencing the V1-V2 hypervariable regions of 16S rRNA gene. Milk samples were collected from the same cow at 3 different stages of lactation (15, 90, 120 dim), with and without using a cannula. Microbial DNA was extracted from two tissues, somatic cells and fat. Our findings showed: 1) The microbiota structure of the two tissues was completely different (adonis R 2 = 0.68, p-value=0.001). Fat samples present a uniform profile composed of three highly abundant bacterial genera: Janthinobacterium, Acinetobacter and Pseudomonas. Microbiota from somatic cells presents significantly higher diversity and more variability in the taxonomic profile. 2) Most of the taxonomic divergences among lactation days were found in fat samples obtained with no cannula. 3) Comparing milk fat samples from mastitic and healthy quarters, taxonomic profiles of healthy quarters were more homogeneous then affected quarters. This observation could be linked to the so called, Anna Karenina Principle, that states that dysbiotic samples vary more in microbial community composition than healthy samples (Zaneveld et al. Nat. Micro 2017). The focus of this study was to develop the sampling and analytical methodology to assess milk microbiota in somatic cells and fat tissues. Although a larger number of samples are needed to support some of our observations, we feel examining milk microbiota in these two tissues will prove to be scientifically insightful.
Journal of Dairy Science, 2020
The identification of milk microbial communities in ruminants is relevant for understanding the a... more The identification of milk microbial communities in ruminants is relevant for understanding the association between milk microbiota and health status. The most common approach for studying the microbiota is amplifying and sequencing specific hypervariable regions of the 16S rRNA gene using massive sequencing techniques. However, the taxonomic resolution is limited to family and, in some cases, genus level. We aimed to improve taxonomic classification of the water buffalo milk microbiota by amplifying and sequencing the full-length 16S rRNA gene (1,500 bp) using Nanopore sequencing (single-molecule sequencing). When comparing with short-read results, we improved the taxonomic classification, reaching species level. We identified the main microbial agents of subclinical mastitis at the species level that were in accordance with the microbiological culture results. These results confirm the potential of single-molecule sequencing for in-depth analysis of microbial populations in dairy animals.
Nano Research, 2015
A novel triple lines lateral-flow assay (LFA) with enhanced sensitivity for the detection of Leis... more A novel triple lines lateral-flow assay (LFA) with enhanced sensitivity for the detection of Leishmania infantum DNA in dog blood samples was designed and successfully applied. The enhanced LFA methodology takes advantage of the gold nanoparticle tags (AuNPs) conjugated to polyclonal secondary antibodies, which recognize anti-FITC antibodies. The polyclonal nature of the secondary antibodies allows for multiple binding to primary antibodies, leading to enhanced AuNP plasmonics signal. Furthermore, endogenous control consisting of the amplified dog 18S rRNA gene was introduced to avoid false negatives. Using this strategy, 0.038 spiked Leishmania parasites per DNA amplification reaction (1 parasite/100 μL of DNA sample) were detected. Detection limit of LFA was found to be lower than that of the conventional techniques. In summary, our novel LFA design is a universal and simple sensing alternative that can be extended to several other biosensing scenarios.
Veterinary Immunology and Immunopathology, 2008
Promastigotes of Leishmania infantum undergo a series of extracellular developmental stages insid... more Promastigotes of Leishmania infantum undergo a series of extracellular developmental stages inside the natural sand fly vector Lutzomyia longipalpis to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis mapped the sequences corresponding to the procyclic, nectomonad, leptomonad or metacyclic promastigote stage into distinct positions, with the procyclic stage being the most divergent population. Transcriptional levels across genes varied on average between 10-to 100-fold. Comparison between procyclic and nectomonad promastigotes resulted in 836 differentially expressed (DE) genes; between nectomonad and leptomonad promastigotes in 113 DE genes; and between leptomonad and metacyclic promastigotes in 302 DE genes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple stage-specific markers for L. Infantum. Leading stage-specific marker candidates include genes encoding a zinc transporter in procyclics, a beta-fructofuranidase in nectomonads, a surface antigen-like protein in leptomonads, and an amastin-like surface protein in metacyclics. Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of stage-specific markers for further development as molecular tools for epidemiological studies. made available for use under a CC0 license.
Genetics Selection Evolution, 1992
The relationships between 10 Spanish dog breeds have been studied using qualitative and quantitat... more The relationships between 10 Spanish dog breeds have been studied using qualitative and quantitative analyses of data from 32 morphological characters. The average distance between breeds, measured as a morphological index, has a value of 4.228 (! 0.681), with extreme values of 1.732 between Mastin del Pirineo and Mastin Espanol, and of 5.099 for the Gos d'Atura-Sabueso Espanol pair. The morphological phylogeny obtained in this study confirms the classifications made previously by means of dental, cranial, historical and behavioral comparative criteria. The results suggest the formation of 2 large clusters; one formed by the breeds belonging to the ancestral trunks Canis fa7rciliaris intermedius and Canis familiaris inostranzewi, and the other which includes the members of the Canis familiaris leineri and Canis familiaris metris-optirrtae trunks. Spanish dog breeds / genetic distance / morphological character / dendrogram / morphological analysis Résumé-Relations génétiques entre des races canines espagnoles. I. Analyse des caractères morphologiques. À partir de l'analyse qualitative et quantitative des données provenant de 3! caractères morphologiques, on a étudié les relations existant entre 10 races canines espagnoles. La distance moyenne entre ' races, mesurée par un indice de distance morphologique, prend une valeur de 4,228 (::1:: 0,681), avec des valeurs extrêmes de 1,7.i2 entre Mastin del Pirineo et Mastin Espanol, et 5,099 pour le couple Gos d'Atura-Sabueso Espanol. La phylogénie morphologique obtenue dans ce travail, confirme les classifications précédentes, réalisées à partir de critères comparatifs dentaires, crâniens, historiques et comportementaux. Les résultats suggèrent la formation de deux grands groupes. L'un comprend les races qui appartiennent aux troncs ancestraux du Canis familiaris intermedius et du Canis familiaris inostranzewi, et l'autre serait formé par les composants des troncs du Canis familiaris leineri et du Canis familiaris metris-optimae. ' races canines espagnoles / distance génétique / caractère morphologique / dendrogramme / analyse morphologique
Biotechnol. Agron. Soc …, 2004