0000000000894570

AUTHOR

Luca Fontanesi

showing 49 related works from this author

Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochth…

2018

Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and …

0301 basic medicineGenetic MarkersLinkage disequilibriumGenotypePopulationAnimal Identification SystemsSNPSingle-nucleotide polymorphismBiologyBreedingPolymorphism Single NucleotideSF1-1100Linkage Disequilibrium03 medical and health sciencesSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoSNPAnimalsBos tauruSelection GeneticeducationSelection (genetic algorithm)Geneticseducation.field_of_studyPrincipal Component AnalysisRandom ForestBos taurus; breed assignment; Random Forest; SNP; Animal Science and Zoology0402 animal and dairy science04 agricultural and veterinary sciencesPhenotypic trait040201 dairy & animal scienceBos taurusSNP genotypingAnimal culture030104 developmental biologyPhenotypeItalyGenetic markerSNP breed assignment Random Forest Bos taurusCattleAnimal Science and Zoologybreed assignmentAnimal
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A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products

2011

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set …

AUTHENTICATION OF FOOD PRODUCTSCoatVeterinary medicineSNPFood ContaminationSingle-nucleotide polymorphismBiologyPolymerase Chain ReactionPolymorphism Single NucleotideSensitivity and SpecificityMASSESECow milkSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoGene FrequencySpecies SpecificityCheesePolymorphism (computer science)MC1RAnimalsAlleleGeneticsSheepfood and beveragesDNAGeneral MedicineBreedMilkFemaleAnimal Science and ZoologyDairy Productsauthentication Massese MC1R mono-breed products sheep breeds SNPReceptor Melanocortin Type 1DAIRY SHEEPPolymorphism Restriction Fragment LengthMc1r geneFood ScienceMelanocortin 1 receptor
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Sequence characterization of the melanocortin 1 receptor (MC1R) gene in sheep with different coat colour and identification of the putative e allele …

2010

Abstract Sequence of the melanocortin 1 receptor (MC1R) gene (the Extension locus) was obtained from a panel of 73 animals belonging to 9 Italian sheep breeds or populations (Appenninica, Bergamasca, Comisana, Cornigliese-like, Delle Langhe, Massese, Merinizzata Italiana, Sarda and Valle del Belice) with different coat colours. Evaluation of the identified polymorphisms on this phenotype was reported with in silico predictions and comparative approaches within and across breeds and across species. Five novel single nucleotide polymorphisms (SNPs), organized in three haplotypes, were detected. Another haplotype, including the two missense mutations already described for the ED allele, was id…

GeneticsHaplotypeCoat colour; MC1R; Missense mutation; Ovine breedsSingle-nucleotide polymorphismLocus (genetics)BiologyOvine breedsSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoCOAT COLOURFood AnimalsSHEEPBREEDSMC1REpistasisAnimal Science and ZoologyMissense mutationAlleleGeneAllele frequencyPOLYMORPHISMSMelanocortin 1 receptor
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Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: association with red and black coat colour phenotype…

2009

Abstract Background Agouti and Extension loci control the relative amount of eumelanin and pheomelanin production in melanocytes that, in turn, affects pigmentation of skin and hair. The Extension locus encodes the melanocortin 1 receptor (MC1R) whose permanent activation, caused by functional mutations, results in black coat colour, whereas other inactivating mutations cause red coat colour in different mammals. Results The whole coding region of the MC1R gene was sequenced in goats of six different breeds showing different coat colours (Girgentana, white cream with usually small red spots in the face; Maltese, white with black cheeks and ears; Derivata di Siria, solid red; Murciano-Granad…

Silent mutationCoatlcsh:QH426-470GenotypeMolecular Sequence DataNonsense mutationPopulationMutation MissenseMELANISMBiologyPolymorphism Single NucleotideAGOUTI PROTEINSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoMSH RECEPTORBREEDSMC1RGeneticsAnimalsMissense mutationGenetics(clinical)Amino Acid Sequencecoat colour; MC1R; goatAlleleHair ColoreducationAllele frequencyPOPULATIONPOLYMORPHISMSAllelesGenetics (clinical)Geneticseducation.field_of_studySTIMULATING-HORMONE-RECEPTORGoatsgoatCATTLE BREEDSSequence Analysis DNAMolecular biologyCOAT COLORlcsh:GeneticsPhenotypeCodon NonsensePIGMENTATIONWHITEReceptor Melanocortin Type 1EXTENSIONcoat colourResearch ArticleMelanocortin 1 receptorBMC Genetics
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Analysis of the melanocortin receptor 1 (MC1R) gene in Sicilian goat breeds

2010

AbstractMammalian coat colour is mainly determined by the distribution of two different types of melanins: pheomelanin (red/yellow pigments) and eumelanin (black pigments). Their synthesis is regulated by the melanocortin 1 receptor (MC1R/Extension locus) that binds the α-melanocyte-stimulating hormone (α-MSH) and the agouti signalling protein (ASIP, coded by the Agouti locus). In mammals, several studies have reported that loss-of-function mutations in MC1R lead to red/yellow pigmentation, while gain-of-function mutations lead to black/dark colours. Mutations at the Agouti locus exert, in general, epistatic interactions on the Extension locus. In goats, classical genetic studies have indic…

GeneticsCoatintegumentary systemMUTATIONSdigestive oral and skin physiologygoatLocus (genetics)Phenotypic traitCOAT COLOUR GENESBiologySettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoBREEDSMC1RMelanocortin Receptor 1EpistasisAnimal Science and Zoologylcsh:Animal cultureMc1r genelcsh:SF1-1100Melanocortin 1 receptor
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A new system for animal products traceability and authentication: Use of DNA analysis of natural tracers and example of application to dry cured hams

2010

A few DNA based approaches have been developed to trace animal products from the farm to the consumer “fork”. These approaches make use of the animal DNA that can be recovered during all steps of t...

AuthenticationTraceabilitybusiness.industryDRY CURED HAMSfungiMICROSATELLITESfood and beveragesBiologyBiotechnologychemistry.chemical_compoundchemistryDNA ANALYSISTRACEABILITYAnimal Science and ZoologyBiochemical engineeringlcsh:Animal culturebusinessDry curedDNAlcsh:SF1-1100AUTHENTICATION
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The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

2014

Genomic technologies, such as high- throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to inves- tigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 eco- nomically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic rela- tionship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that…

GeneticsGenetic diversityContext (language use)General MedicineBiologyBreedEffective population sizeEvolutionary biologyGeneticsInbreeding depressionAnimal Science and ZoologyGenetic variabilityAssociation mappingInbreedingFood ScienceJournal of Animal Science
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Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

2016

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH (F-ROH) in three local dairy cattle breeds. F-ROH values were compared with F estimated from the genomic relati…

0301 basic medicineSingle-nucleotide polymorphismRuns of HomozygosityBiologyPolymorphism Single NucleotideSF1-1100local cattle breedSettore AGR/17 - Zootecnica Generale E Miglioramento Genetico03 medical and health sciencesAnimal sciencegenomic inbreeding; local cattle breeds; runs of homozygosity; Animal Science and ZoologyGenetic variationInbreeding depressionAnimalsInbreedinglocal cattle breedsDairy cattleGeneticsGenetic diversityruns of homozygositygenomic inbreedingHomozygote0402 animal and dairy scienceGenetic Variation04 agricultural and veterinary sciences040201 dairy & animal scienceBreedAnimal culture030104 developmental biologyItalyCattleFemaleAnimal Science and ZoologyInbreedingAnimal
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Conservation status and historical relatedness of Italian cattle breeds

2018

Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Ou…

0301 basic medicineIn situ conservation[SDV]Life Sciences [q-bio]Animals; Animals Domestic; Breeding; Cattle; Conservation of Natural Resources; Evolution Molecular; Genetics Population; Genome-Wide Association Study; Linkage Disequilibrium; Phylogeny; Population Density; Genetic Variation; Polymorphism Single Nucleotide;Italian Bovine Genetic VariabilityRuns of HomozygosityBreedingLinkage DisequilibriumSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoItalian cattle breeds Bovine Genetic Variability Bovine SNP Bovine Genomocs Markers Italian Bovine Genetic VariabilityConservation of Natural ResourceDomesticPhylogenylcsh:SF1-11002. Zero hungereducation.field_of_studyEcologySettore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICOBiodiversity04 agricultural and veterinary sciencesGeneral MedicineSingle NucleotideItalyAnimals DomesticBovine SNPLivestockItalian cattle breeds Bovine Genetic VariabilityEcology Evolution Behavior and Systematics; Animal Science and Zoology; GeneticsInbreedingGenetic isolateResearch ArticleConservation of Natural Resourceslcsh:QH426-470EvolutionAnimals; Animals Domestic; Breeding; Cattle; Conservation of Natural Resources; Evolution Molecular; Genetics Population; Genome-Wide Association Study; Linkage Disequilibrium; Phylogeny; Population Density; Genetic Variation; Polymorphism Single NucleotidePopulationPopulationBiologyPolymorphism Single NucleotideBovine Genomocs MarkersEvolution Molecular03 medical and health sciencesBehavior and SystematicsSNP local cattle structureGenetic variationGeneticsAnimalsPolymorphismeducationEcology Evolution Behavior and SystematicsPopulation DensityGenetic diversityAnimalbusiness.industry0402 animal and dairy scienceAnimals; Animals Domestic; Breeding; Cattle; Conservation of Natural Resources; Evolution Molecular; Genetics Population; Genome-Wide Association Study; Linkage Disequilibrium; Phylogeny; Population Density; Genetic Variation; Polymorphism Single Nucleotide; Ecology Evolution Behavior and Systematics; Animal Science and Zoology; GeneticsMolecularGenetic VariationEcology Evolution Behavior and Systematic040201 dairy & animal sciencelcsh:GeneticsBiodiversity cattle ItalyGenetics Population030104 developmental biologyEvolutionary biologyCattleAnimal Science and Zoologylcsh:Animal culturebusinessGenome-Wide Association Study
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Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds

2018

Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly…

Male0301 basic medicineCandidate generuns of homozygosity islandGenotypeRuns of homozygosity islands genomic regions candidate genes local dairy cattle bovine beadchip 50KLocus (genetics)Single-nucleotide polymorphismBiologyRuns of HomozygosityPolymorphism Single NucleotideGenomeSF1-1100bovine beadchip 50K; candidate genes; genomic regions; local dairy cattle; runs of homozygosity islands; Animal Science and ZoologySettore AGR/17 - Zootecnica Generale E Miglioramento Genetico03 medical and health sciencesAnimalsInbreedinggenomic regionsGeneDairy cattleGeneticslocal dairy cattleGenomeReproductionHomozygote0402 animal and dairy sciencecandidate gene04 agricultural and veterinary sciences040201 dairy & animal sciencegenomic regionAnimal cultureruns of homozygosity islandsDairyingPhenotype030104 developmental biologybovine beadchip 50KCattleFemaleAnimal Science and Zoologycandidate genesInbreeding
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An initial comparative map of copy number variations in the goat (Capra hircus) genome

2010

Abstract Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi,…

BreedingGenomePolymerase Chain ReactionSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoMOUSE STRAINSChromosome regionsCapra hircusGOATCopy-number variationANGORA-GOATSGENE-EXPRESSIONGenetics0303 health sciencesComparative Genomic HybridizationGenomeGoatsChromosome Mapping04 agricultural and veterinary sciencesBovine genomeDatabases Nucleic AcidBiotechnologyResearch Articlelcsh:QH426-470DNA Copy Number VariationsSEGMENTAL DUPLICATIONSlcsh:BiotechnologyMolecular Sequence DataBiologyFluorescenceStructural variationPRODUCTION TRAITSBirds03 medical and health sciencesFAMILY BOVIDAEGene mappinglcsh:TP248.13-248.65Sequence Homology Nucleic AcidGeneticsFINE-SCALEAnimalsHumansFalse Positive Reactions030304 developmental biologyCOPY NUMBER VARIATION0402 animal and dairy scienceReproducibility of Results040201 dairy & animal scienceChromosomes MammalianDNA-SEQUENCESSTRUCTURAL VARIATIONlcsh:GeneticsCANDIDATE LOCIcopy number variation goatsCattleComparative genomic hybridizationBMC Genomics
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Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes

2012

Massese is an Italian dairy sheep breed characterized by animals with black skin and horns and black or apparent grey hairs. Owing to the presence of these two coat colour types, this breed can be considered an interesting model to evaluate the effects of coat colour gene polymorphisms on this phenotypic trait. Two main loci have been already shown to affect coat colour in sheep: Agouti and Extension coding for the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes, respectively. The Agouti locus is affected by a large duplication including the ASIP gene that may determine the Agouti white and tan allele (A(Wt)). Other disrupting or partially inactivating mutations ha…

GeneticsCoatsheepHaplotypeLocus (genetics)coat colour sheep ASIP MC1R mutationsBiologymutationsSF1-1100Animal cultureMASSESEExonSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoCOAT COLOURASIPGene duplicationMC1RAnimal Science and ZoologyAlleleSHEEP BREEDGeneMelanocortin 1 receptor
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Copy Number Variation and Missense Mutations of the Agouti Signaling Protein (<i>ASIP)</i> Gene in Goat Breeds with Different Coat Colors

2009

In goats, classical genetic studies reported a large number of alleles at the <i>Agouti</i> locus with effects on coat color and pattern distribution. From these early studies, the dominant <i>A</i><sup>Wt</sup> (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat <i>ASIP</i> gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-ri…

GeneticsCoatdigestive oral and skin physiologySingle-nucleotide polymorphismLocus (genetics)BiologyGenotypeGeneticsMissense mutationCopy-number variationAlleleMolecular BiologyGeneGenetics (clinical)Cytogenetic and Genome Research
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Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling appro…

2016

European sea bass (Dicentrarchus labrax) is an important marine species for commercial and sport fisheries and aquaculture production. Recently, the European sea bass genome has been sequenced and assembled. This resource can open new opportunities to evaluate and monitor variability and identify variants that could contribute to the adaptation to farming conditions. In this work, two DNA pools constructed from cultivated European sea bass were sequenced using a next generation semiconductor sequencing approach based on Ion Proton sequencer. Using the first draft version of the D. labrax genome as reference, sequenced reads obtained a total of about 1.6 million of single nucleotide polymorp…

0301 basic medicinefood.ingredientIon ProtonSNPBiologyAquatic ScienceGenomePolymorphism Single NucleotideCultivated sea baDNA sequencing03 medical and health sciencesBass (fish)Settore AGR/17 - Zootecnica Generale E Miglioramento Genetico0302 clinical medicinefoodChromosome regionsNext generation sequencingCultivated sea bass Next generation sequencing Ion Proton SNPGeneticsAnimalsSea bassGeneGeneticsGenomeCultivated sea bass; Ion Proton; Next generation sequencing; SNP; Aquatic Science; GeneticsHigh-Throughput Nucleotide SequencingIon semiconductor sequencingSequence Analysis DNA030104 developmental biologyItalyBassSelective sweepCultivated sea bass030217 neurology & neurosurgery
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Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese prod…

2020

Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that c…

MaleCoat040301 veterinary sciencesPopulationselection signatureBreedingQuantitative trait locusBiologyPolymorphism Single NucleotideSF1-1100Fixation index0403 veterinary scienceCheeseAnimalsBos taurueducationAllele frequencygenomeeducation.field_of_studyGenomeAutochthonous breedHaplotypeautochthonous breed Bos taurus genome selection signature selection sweep0402 animal and dairy scienceGenomics04 agricultural and veterinary sciencesSelection signature040201 dairy & animal scienceBreedBos taurusAnimal cultureselection sweepautochthonous breedItalyEvolutionary biologyHerdCattleFemaleAnimal Science and ZoologySelection sweepAnimal
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A first comparative map of copy number variations in the sheep genome.

2011

article i nfo We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle a…

Ovis ariesDNA Copy Number VariationsRuminantSheep breedsaCGH; Comparative map; Copy number variation; Ovis aries; Ruminants; Sheep breedsGenomicsOvis arieBiologyGenomeChromosomesSettore AGR/17 - Zootecnica Generale E Miglioramento Genetico03 medical and health sciencesaCGHChromosome regionsGeneticsAnimalsCopy-number variationGene030304 developmental biologyOligonucleotide Array Sequence AnalysisGeneticsCOMPARATIVE MAPPING0303 health sciencesComparative Genomic HybridizationGenomeSheepCopy number variation0402 animal and dairy scienceComparative Genome HybridizationChromosome Mapping04 agricultural and veterinary sciencesRuminantsbiology.organism_classification040201 dairy & animal scienceBovine genomeSardaCattleComparative mapGenomics
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MOESM13 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 13: Figure S7. Genetic relationship defined with multidimensional scaling analysis between Italian and 62 European cattle breeds. The breeds were grouped according to their geographical origins and distributions. Northern_Europe (Belgian Blue, Dexter, Kerry, Lithuanian Light Grey, Lithuanian White Backed, Groningen Whitehead, Lakenvelder, Meuse-Rhine-Ijjsel, Norwegian Red, Finnish Ayrshire, Belted Galloway, Galloway, Angus, Scottish Highland, South Devon), England (Devon, Guernsey, Hereford, Longhorn, Lincoln Red, Milking Shorthorn, Red Poll, Beef Shorthorn, Sussex, Welsh Blach, White Park), Spain (Berrenda en Negro, Berrenda en Colorado, Cardena Andaluza, Menorquina, Pirena…

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MOESM6 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 6: Figure S3. Distribution of all ROH within breeds according to their size (kb).

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MOESM2 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 2: Table S1. Name of the breeds, geographic coordinates (longitude and latitude) of the center of origin, sample size before (n-PreQC) and after (n-PostQC) genotyping quality control, and origin of genotyping data.

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Additional file 11 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 11:PANTHER categories significantly overrepresented in goat CNVRs. PANTHER annotation has been obtained for the whole cattle genome. (DOC 101 KB)

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MOESM3 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 3: Figure S1. Trends in historic effective population size (Ne) (from 13 to 98 generations).

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MOESM1 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 1. Description of each Italian local cattle breed involved in this study [68].

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Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.

2009

In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…

Comparative Genomic HybridizationBase SequenceDNA Copy Number VariationsGoatsCapra hircuCNVMolecular Sequence DataMutation MissenseSNPColorBreedingPolymorphism Single NucleotideCOAT COLORSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoBREEDSaCGHAgouti locuASIP GENEGOATAgouti Signaling ProteinAnimalsHumansAmino Acid SequenceSequence AlignmentCytogenetic and genome research
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MOESM10 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 10: Figure S6. Scatter plot of correlations between genetic differentiation (FST) and geographical distances for all breeds.

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Additional file 10 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 10:Gene ontology (GO) categories significantly overrepresented in goat CNVRs at different False Discovery Rate (FDR) levels. GO categories were Molecular function, Biological process, and Cellular component. (DOC 118 KB)

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MOESM4 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 4: Table S2. Pearson correlation coefficients between genetic diversity indices. Observed (Ho) and expected (He) heterozygosity, average minor allele frequency (MAF), inbreeding coefficient (FHOM), contemporary effective population size (cNe), mean ROH-based inbreeding coefficient (FROH>4Mb) and recent and historical Ne estimated 13 (Ne13), 20 (Ne_20 and 80 (Ne_80) generations ago. (* p- valueâ

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MOESM7 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 7: Figure S4. Model-based clustering of the estimated membership fractions of individuals from the 32 breeds analyzed in each of the K inferred clusters revealed by the ADMIXTURE software (Kâ =â 12, 16, 20, 28, 32). For a full definition of breeds see Table S1 (see Additional file 2: Table S1).

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Additional file 5 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 5:Tables reporting the P values for the overlapping between goat and cattle CNVRs and among the four CNVR datasets available in cattle. Table S1 reports the results obtained comparing the goat CNVRs with the cattle CNVRs. Table S2 reports the results obtained comparing the different cattle datasets. (DOC 110 KB)

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Additional file 15 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Authors’ original file for figure 3

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Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

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Additional file 6 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 6:Primers and PCR conditions used to validate goat CNVRs. The table includes the goat CNVRs number, the corresponding bovine chromosome, gene symbol, amplified gene fragment data (including Ensembl number), sequence of the PCR primers, length of the amnplified fragment and PCR conditions. (DOC 38 KB)

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MOESM8 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 8: Figure S5. Cross-validation errors of admixture analysis at different K values.

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Additional file 8 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 8:Gene Ontology (GO) annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using GO for Biological process, Cellular component, and Molecular function. (XLS 108 KB)

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MOESM12 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 12: Table S5. Results of the f4 test.

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Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

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MOESM11 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 11: Table S4. Results of the f3 test.

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Additional file 12 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 12:List of goat CNVRs with human orthologous genes. EntrezGene ID and gene name are reported for human orthologous genes. The file includes genes already mapped in goat and genes for which mutations in human cause or are associated with human genetic diseases (data have been retrieved from OMIM database, May 2010). (XLS 60 KB)

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Additional file 16 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Authors’ original file for figure 4

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Additional file 3 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 3:Extension of CNVRs in the different chromosomes. Proportion of the CNVRs identified in goat compared to the dimension of the bovine chromosomes. (XLS 14 KB)

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Additional file 14 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Authors’ original file for figure 2

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Additional file 7 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 7:Semiquantitative fluorescent multiplex-PCR (SQF-PCR) results obtained for different goats. The averaged SQF-PCR ratio normalized against the reference Camosciata delle Alpi goat is reported for the goats of the aCGH panel and for additional goats (additional panel) for the validated CNVs. (XLS 20 KB)

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Additional file 9 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 9:PANTHER annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using PANTHER. (XLS 102 KB)

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Additional file 4 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 4:List of cattle CNVRs reported in four other experiments[49–52]and overlapping with goat CNVRs. CNVRs identified in cattle have been merged from the four reported experiments [49–52]. Progressive CNVR number has been assigned using the complete list. CNVRs are indicated with nucleotide positions (begin and end) on the Btau_4.0 version. Information reported for the four different experiments includes the progressive number and in parenthesis the chromosome number and the nucleotide positions (start and end). The goat CNVRs are reported. (XLS 128 KB)

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Additional file 1 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 1:List of CNVs identified in the analysed goats. The Excel file reports the chromosome, the nucleotides position of the CNV start and end (referred to the Btau_4.0 genome assembly), the size of the CNV in bp, the number of valid probes in the CNV (additional probes are included in CNV considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNV), log2 mean of the probes in the CNV (see Methods), the type of CNV (gain/loss), the goat sample (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen; numbers after the breed symbols indicate the different animals used in the aCGH experiment), and t…

genetic structuressense organseye diseases
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Additional file 17 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Authors’ original file for figure 5

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Additional file 13 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Authors’ original file for figure 1

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MOESM5 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 5: Figure S2. Relationship between the number of ROH and the length of the genome (Mb) covered by ROH per individual.

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MOESM9 of Conservation status and historical relatedness of Italian cattle breeds

2018

Additional file 9: Table S3. Pairwise FST values between cattle populations.

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Additional file 2 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

2021

Additional file 2:List of CNVRs obtained by merging overlapping CNVs across animals. The Excel file reports the progressive CNVR number, the chromosome, the nucleotides position of the CNVR start and end (referred to the Btau_4.0 genome assembly), the size of the CNVR in bp, the number of valid probes in the CNVR (additional probes are included in CNVR considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNVR), the type of CNVR (gain/loss), the frequency of CNVR in the analysed goat panel, the goat breed (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen), and the goat subject (numbers after the bre…

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