0000000000725736

AUTHOR

Alessandro Bagnato

showing 16 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
researchProduct

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep.

2019

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 C…

0301 basic medicineFalse discovery rateCandidate geneDNA Copy Number VariationsGenotypeSciencePopulationGenomic Structural VariationQuantitative Trait LociGenome-wide association studyQuantitative trait locusBiology03 medical and health sciencesSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoAnimalsLactationCopy-number variationeducationGeneGeneticseducation.field_of_studyMultidisciplinarySheepBiochemistry Genetics and Molecular Biology (all)QAnimals chromosome mapping dairying female genome-Wide association study genotype lactation sheep DNA copy number variations quantitative trait loci0402 animal and dairy scienceRChromosome Mapping04 agricultural and veterinary sciences040201 dairy & animal scienceDairying030104 developmental biologyAgricultural and Biological Sciences (all)MedicineFemaleGenome-Wide Association StudyResearch ArticlePLoS ONE
researchProduct

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
researchProduct

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…

researchProduct

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).

researchProduct

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.

researchProduct

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).

researchProduct

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].

researchProduct

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.

researchProduct

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

researchProduct

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).

researchProduct

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.

researchProduct

MOESM12 of Conservation status and historical relatedness of Italian cattle breeds

2018

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

researchProduct

MOESM11 of Conservation status and historical relatedness of Italian cattle breeds

2018

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

researchProduct

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.

researchProduct

MOESM9 of Conservation status and historical relatedness of Italian cattle breeds

2018

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

researchProduct