Increased inbreeding is an inevitable consequence of selection in livestock populations. The analysis of high-density single nucleotide polymorphisms (SNPs) facilitates the identification of long and uninterrupted runs of homozygosity (ROH) that can be used to identify chromosomal regions that are identical by descent. In this work, the distribution of ROH of different lengths in five Italian cattle breeds is described. A total of 4095 bulls from five cattle breeds (2093 Italian Holstein, 749 Italian Brown, 364 Piedmontese, 410 Marchigiana and 479 Italian Simmental) were genotyped at 54K SNP loci. ROH were identified and used to estimate molecular inbreeding coefficients (FROH ), which were compared with inbreeding coefficients estimated from pedigree information (FPED ) and using the genomic relationship matrix (FGRM ). The average number of ROH per animal ranged from 54 ± 7.2 in Piedmontese to 94.6 ± 11.6 in Italian Brown. The highest number of short ROH (related to ancient consanguinity) was found in Piedmontese, followed by Simmental. The Italian Brown and Holstein had a higher proportion of longer ROH distributed across the whole genome, revealing recent inbreeding. The FPED were moderately correlated with FROH > 1 Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with FGRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH > 8 Mb in the inbreeding calculation improved the correlation of FROH with FPED and FGRM . ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data. In populations with high linkage disequilibrium (LD) and recent inbreeding (e.g. Italian Holstein and Italian Brown), a medium-density marker panel, such as the one used here, may provide a good estimate of inbreeding. However, in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.

It is widely documented that a pool of multipotent stem cells located in humans and mice hair follicle outer root sheath (bulge region) is involved in the restoration of the whole follicular unit during each anagen phase. To the authors' knowledge, data regarding the location and characterization of hair follicle stem compartment in dogs have not been reported in the recent relevant literature. In this study, we investigated the haematopoietic stem and progenitor cell antigen CD34 as a marker of putative stem cells located in a bulge-like region of canine hair follicles. The presence of CD34 mRNA and glycoprotein was assessed on formalin-fixed, paraffin-embedded canine skin samples by in situ hybridization technique and by standard immunohistochemistry, respectively. A strong expression of CD34 mRNA and glycoprotein was observed in a well-defined area of the hair follicle isthmic region and appeared uniformly concentrated at the level of the basal layer of the outer root sheath. These findings provide compelling support to the hypothesis that in dogs, a subpopulation of basal keratinocytes located in the hair follicle isthmic region and characterized by the selective expression of CD34 is potentially associated with the stem cell compartment of this skin appendage.

Several market research studies have shown that consumers are primarily concerned with the provenance of the food they eat. Among the available identification methods, only DNA-based techniques appear able to completely prevent frauds. In this study, a new method to discriminate among different bovine breeds and assign new individuals to groups was developed. Bulls of three cattle breeds farmed in Italy - Holstein, Brown, and Simmental - were genotyped using the 50K SNP Illumina BeadChip. Multivariate canonical discriminant analysis was used to discriminate among breeds, and discriminant analysis (DA) was used to assign new observations. This method was able to completely identify the three groups at chromosome level. Moreover, a genome-wide analysis developed using 340 linearly independent SNPs yielded a significant separation among groups. Using the reduced set of markers, the DA was able to assign 30 independent individuals to the proper breed. Finally, a set of 48 high discriminant SNPs was selected and used to develop a new run of the analysis. Again, the procedure was able to significantly identify the three breeds and to correctly assign new observations. These results suggest that an assay with the selected 48 SNP could be used to routinely track monobreed products.

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo-Bruna and Sardo-Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within-breed genetic heterogeneity. The F comparison revealing the largest number of significant SNPs was Sardo-Bruna vs. Sardo-Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo-Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo-Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi-dimensional scaling and the admixture analysis the Sardo-Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo-Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.

BackgroundDomestication and selection are processes that alter the pattern of within- and between-population genetic variability. They can be investigated at the genomic level by tracing the so-called selection signatures. Recently, sequence polymorphisms at the genome-wide level have been investigated in a wide range of animals. A common approach to detect selection signatures is to compare breeds that have been selected for different breeding goals (i.e. dairy and beef cattle). However, genetic variations in different breeds with similar production aptitudes and similar phenotypes can be related to differences in their selection history.MethodsIn this study, we investigated selection signatures between two Italian beef cattle breeds, Piemontese and Marchigiana, using genotyping data that was obtained with the Illumina BovineSNP50 BeadChip. The comparison was based on the fixation index (Fst), combined with a locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach. In addition, analyses of Fst were carried out to confirm candidate genes. In particular, data were processed using the varLD method, which compares the regional variation of linkage disequilibrium between populations.ResultsGenome scans confirmed the presence of selective sweeps in the genomic regions that harbour candidate genes that are known to affect productive traits in cattle such as DGAT1, ABCG2, CAPN3, MSTN and FTO. In addition, several new putative candidate genes (for example ALAS1, ABCB8, ACADS and SOD1) were detected.ConclusionsThis study provided evidence on the different selection histories of two cattle breeds and the usefulness of genomic scans to detect selective sweeps even in cattle breeds that are bred for similar production aptitudes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0128-2) contains supplementary material, which is available to authorized users.

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A genomewide association study was carried out on a sample of Marchigiana breed cattle to detect markers significantly associated with carcass and meat traits. Four hundred and nine young bulls from 117 commercial herds were genotyped by Illumina 50K BeadChip assay. Eight growth and carcass traits (average daily gain, carcass weight, dressing percentage, body weight, skin weight, shank circumference, head weight and carcass conformation) and two meat quality traits (pH at slaughter and pH 24 h after slaughter) were measured. Data were analysed with a linear mixed model that included fixed effects of herd, slaughter date, fixed covariables of age at slaughter and SNP genotype, and random effects of herd and animal. A permutation test was performed to correct SNP genotype significance level for multiple testing. A total of 96 SNPs were significantly associated at genomewide level with one or more of the considered traits. Gene search was performed on genomic regions identified on the basis of significant SNP position and level of linkage disequilibrium. Interesting loci affecting lipid metabolism (SOAT1), bone (BMP4) and muscle (MYOF) biology were highlighted. These results may be useful to better understand the genetic architecture of growth and body composition in cattle.