Variance component estimation for SCS in different local breeds and species

A Comparative Analysis of Copy Number Variation of the Sheep and Goat Genomes

Recent studies have shown that copy number variants (CNVs) are important sources of variability of mammalian genomes. We applied a cross species array comparative genome hybridization (aCGH) experiment using as reference the cattle genome to investigate, for the first time, variability in the sheep and goat genomes derived from copy number variation and identified 431 and 358 CNVs, respectively. A comparison of these results to those obtained in other mammals for similar experiments is reported. The identified CNVs could be important in determining phenotypic and production differences between and within breeds. Further studies will be carried out to evaluate the identified CNVs from both f…

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in local cattle breeds

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…

Distribution of functional variants within Runs of Homozygosity in four Italian cattle breeds

Several methods have been used to identify genomic regions subjected to selective sweeps. An alternative method can make use of runs of homozygosity (ROH), defined as stretches of homozygous regions in a genome. The aim of the present study was to detect selective sweeps using ROH in four cattle breeds. Individuals of Cinisara (71), Modicana (72),Reggiana (168) and Italian Holstein (96) were genotyped with the Illumina Bovine50SNP v2 BeadChip. To identify genomic regions that were most commonly associated with ROH within each breed, the percentage of occurrences of a single nucleotide polymorphism (SNP) in ROH was calculated across animals. The genomic regions most commonly associated with …