How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds
International audience; Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribe…
Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color
Simple Summary In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait. Abstract Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is a…
Genomic characterization of the Braque Français type Pyrénées dog and relationship with other breeds
The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain uncharacterized. Braque Français type Pyrénées (BRA) is a dog breed originating from a very old type of gun-dog used for pointing the location of game birds to hunters. Despite the ancient background, the knowledge about levels of genetic diversity, degree of inbreeding and population structure is scarce. This may raise concerns on the possibility …
Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens
Abstract Background Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homoz…
Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed
Objective Braque Français, type Pyrénées is a French hunting-dog breed whose origin is traced back to old pointing gun-dogs used to assist hunters in finding and retrieving game. This breed is popular in France, but seldom seen elsewhere. Despite the ancient background, the literature on its genetic characterization is surprisingly scarce. A recent study looked into the demography and inbreeding using pedigree records, but there is yet no report on the use of molecular markers in this breed. The aim of this work was to genotype a population of Braque Français, type Pyrénées dogs with the high-density SNP array to study the genomic diversity of the breed. Results The average observed (\docum…
MOESM1 of Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed
Additional file 1. Plink command lines. File with the Plink command lines used to: (i) edite the SNP data; (ii) select unlinked SNP loci for the estimation of $$N_e$$ N e ; (iii) detect runs of homozygosity (ROH).
Le varianti A1 e A2 della ?-caseina non hanno un effetto significativo sul microbiota del latteThe A1 and A2 ?-casein variants have not impact on milk microbiota
Objective: Milk is composed by a complex microbiota which can be influenced by numerous factors such as the season, the diet, the type of litter, the facility. As well, the animal's genotype can affect the composition of the milk microbiota. In milk, ?-casein is characterized by a high-level of polymorphism. The aim of this study was to verify if A1 and A2 ?-casein variants could in- fluence the milk microbioma. Materials and methods: Thirty Holstein cows were genotyped for ?-casein locus and divided into three groups. In two different sea- sons, milk samples (individual and bulk tank for each experi- mental group) and mozzarella cheese were collected separately from each group. Bacterial D…
Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomi…