Search results for "Runs of homozygosity"

showing 8 items of 28 documents

Genome‐wide survey on three local horse populations with a focus on runs of homozygosity pattern

2022

Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the…

Population Densityruns of homozygosityGenomeGenotypeHomozygotegenetic diversityGeneral MedicinePolymorphism Single Nucleotideautochthonous horseautochthonous horsesFood AnimalsAnimalsInbreedingAnimal Science and ZoologyHorsesautochthonous horses genetic diversity runs of homozygosity SNPsSNPsJournal of Animal Breeding and Genetics
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Genome-wide scan for Runs of Homozygosity in Valle del Belice sheep

2017

The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of genomic regions where a reduction in heterozygosity occurred and offers new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and the distribution of ROH in medium-density SNP genotypes (~ 50 000) in order to characterize autozygosity in 512 individuals of Valle del Belice sheep and identify the regions of the genom…

Settore AGR/17 - Zootecnica Generale E Miglioramento GeneticoOvineSNP50K sheep runs of homozygosity candidate genes
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Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area.

2021

Abstract Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (I…

TailCandidate geneGenotype040301 veterinary sciencesIntrogressionRuns of HomozygosityBiologyFat tailRuns of homozygositySF1-1100Polymorphism Single Nucleotide0403 veterinary scienceSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoAnimalsInbreedingAlleleLocal sheepGenomeSheepFat tail Genetic structure Local sheep Runs of homozygosity Selection signaturesHomozygote0402 animal and dairy science04 agricultural and veterinary sciencesSelection signature040201 dairy & animal scienceBreedAnimal cultureEvolutionary biologyGenetic structureAnimal Science and ZoologyGene poolGenetic structureInbreedingGenome-Wide Association StudyAnimal : an international journal of animal bioscience
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Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

2021

Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italia…

adaptation; body size; climate change; ecological impact; farming system; goat; inbreeding; management practiceClimateecological impactadaptationQH426-470Runs of homozygosityPolymorphism Single NucleotideSF1-1100GeneticsAnimalsfarming systemsInbreedingPolymorphismEcology Evolution Behavior and SystematicsbiodiversityGenomeSettore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICOlocal breedsAnimalGoatsROHHomozygoteGeneral MedicineSingle NucleotideAnimal cultureclimate changeAnimals; Genome; Homozygote; Inbreeding; Goats; Polymorphism Single Nucleotidelocal breeds biodiversity SNPs inbreedingGoatfarming systemRuns of homozygosity ROH Goat signatures of selection low-input system Climate farming systemsAnimal Science and Zoologybody sizeGoat signatures of selectionlow-input systemmanagement practiceResearch ArticleSNPs
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A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds.

2019

Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical F-ST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, …

lcsh:QH426-470Runs of HomozygosityBiologyRuns of homozygosityGenomeFst-outlierMerino sheep breedsSettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoGeneticsGenetics (clinical)Selection (genetic algorithm)Original ResearchGeographic areaWoollocal ancestry in admixed populationsLocal ancestry in admixed populationPhenotypeSignal onBreedGenome-wide selection signaturelcsh:GeneticsWoolEvolutionary biologyMerino sheep breedMolecular Medicinegenome-wide selection signaturesFrontiers in genetics
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Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in local cattle breeds

2015

The availability of high throughput genotyping has facilitated the quantification of inbreeding by genomic markers in farm animals. Run 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 inbreeding derived from ROH (FROH) in three Italian local cattle breeds. Individuals of Cinisara (71), Modicana (72), Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of the Italian Holstein cattle breed were included in the analysis. The following criteria were used to define a ROH: two missing SNPs; one heterozygous SNP; mi…

local cattle breedruns of homozygositySettore AGR/17 - Zootecnica Generale E Miglioramento GeneticoGenomic inbreeding
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Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds.

2022

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED), or runs of homozygosity (ROH; FROH) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each …

runs of homozygosityFood Animalsmixed modelgenomic informationAnimal Science and ZoologyGeneral Medicinegenomic information; inbreeding depression; mixed model; runs of homozygosityinbreeding depressionJournal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und ZuchtungsbiologieREFERENCES
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Analysis of runs of homozygosity of cattle living in different climate zones

2023

Abstract Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds’ country of…

runs of homozygositySettore AGR/17 - Zootecnica Generale E Miglioramento Geneticocattle breedindicutaurusGeneticsAnimal Science and ZoologyGeneral Medicineenvironmental adaptationFood Science
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