A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations

Copy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina's 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized

Copy number variation in cattle breeds

Detecting all classes of genetic variation in livestock species, such as cattle, is a pre-requisite to studying their association to traits of interest. Copy Number Variations (CNVs) are classes of polymorphic DNA regions including deletions, duplications and insertions of DNA fragments of at least 0.5 kb to several Mb, that are copy number variable when compared to a reference genome. CNVs can be identified using various approaches, among those the SNP array data are low cost, dense coverage, and high throughput. The aim of this study was to obtain a consensus genome map of Copy Number Variable Regions (CNVRs) in the Brown Swiss (dataset of 192 bulls), Red Pied Valdostana (dataset of 143 bulls) and Finnish Ayrshire (dataset of 243 bulls) cattle breeds all genotyped on the Illumina Bovine HD BeadChip, and two SNP based CNV calling algorithms. Brown Swiss cattle originated in the Swiss Alps, kept as a triple purpose breed. Once imported in the US, it was mainly selected for increased milk production. The Valdostana Red Pied cattle is the most common autochthonous dual purpose breed in the region Valle d\u2019Aosta in Italy (13,000 animals in 2013, almost all of them registered in the Herd Book). The Finnish Ayrshire is the most common cattle in Finland. CNVs were called with the PennCNV and SVS7 software and were summarized to CNVRs at the population level as overlapping CNV calls within breed. PennCNV identified 2,377, 1,723 and 1,689 for the Italian Brown Swiss, the Red Pied Valdostana and the Finnish Ayrshire, respectively. SVS7 detected 370, 235 and 2,063 for the three cattle breeds. These regions were annotated with Ensembl v78 Bos taurus gene set (UMD3.1) and genomic regions harboring QTL for production and functional traits. The comparison among CNVRs here identified provided common regions in the breeds. The results of this study are a comprehensive genomic analysis of cattle CNVs derived from SNP data, which will be a valuable genomic variation resource and will enrich the bovine CNV map in the cattle genome, providing new information for association studies with traits included in the selection programs

Genetic evaluation for cow fighting ability in the Valdostana breed

This study aimed to exploit the genetic components of cow fighting ability in Valdostana breed. Data from 41 knockout competitions in three different weight categories (WC) performed over two years were used. Two different variables to express fighting ability were considered: 1) a \u201cplacing score\u201d (PS) dependent on the position reached in each WC, and 2) a \u201crelative placing score\u201d (RPS), calculated as relative position within WC. A complete data set (COMP) accounting for all fights (n=7157) or a reduced data set (REDU) considering only the best annual PS or RPS for each cow (n=4563), were also compared through ANOVA, REML variance components\u2019 estimates and EBVs\u2019 correlation. The PS in the COMP showed the highest R2 (0.44), and h2 resulted 0.163. The PS in the REDU showed a lower R2 (0.25), similar h2 value (0.189), but higher repeatability than PS in the COMP (0.373 vs. 0.294). The RPS variable in both data sets gave similar genetic parameters, but the R2 models resulted very low (0.02-0.04). The use of the PS variable and the COMP seems the most promising system to evaluate cow fighting ability in Valdostana breed, and a substantial genetic component for this ability seems to exist

The genomic variation in the Aosta cattle breeds raised in an extensive alpine farming system

The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler\uae(GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were 120.003, 120.01 and 120.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed

Imputation of microsatellite from dense SNP in the Valdostana Red Pied cattle - A Master thesis in Animal Production

Microsatellite markers (MS) have been used efficiently for parentage verification in various livestock species and their impact on the industry to certify exact pedigree information has been massive for long time. In cattle, the International Society of Animal Genetics (ISAG) recommended a panel of 12 bovine MS markers for the individual parentage verification testing and a large MS database contains the historical data of populations. Recently, there is an increasing interest from the stakeholders in agriculture and the research community to use Single Nucleotide Polymorphism (SNP) for parental verification due to their higher genotyping accuracies, speed of genotyping, lower overall cost per genotype, and simplicity of automation. Thus, ISAG opened the parentage testing in cattle to SNP chips methodology. A tool to link the MS database to SNP markers tool have been developed in USA for main populations such as the Holstein and Brown Swiss cattle. The objective of the thesis is to develop a SNP-MS haplotype reference panel set in the Valdostana Red Pied cattle (the most common autochthonous dual purpose breed in the region Valle d\u2019Aosta in Italy). The information on MS alleles recognized from ISAG are available from the National Association of Valdostana Breeders (A.N.A.Bo.Ra.Va.) and the genotypes obtained from the llumina BovineHD BeadChip (777,962 SNPs) array for 143 bulls are already accessible at UNIMI. Specific imputation software (e.g.: Beagle) and pipelines will be used for the haplotype estimation. This strategy may be employed in any species that has dense SNP genotypes and MS alleles information on a subset of the population large enough to define phase associations among MS alleles and SNP haplotypes. Moreover, this methodology will validate the parentage among individuals when different genotyping platforms have been used through the generations and will assess the sensitivity of such a conversion system using HD SNP data

Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

Mastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip

Synthesis, biological evaluation and structure-activity relationships of novel substituted N-phenyl ureidobenzenesulfonate derivatives blocking cell cycle progression in S-phase and inducing DNA double-strand breaks

Twenty-eight new substituted N-phenylureidobenzenesulfonate (PUB-SO) and 18 Nphenylureidobenzenesulfonamide (PUB-SA) derivatives were prepared. Several PUB-SOs exhibited antiproliferative activity at the micromolar level against the HT-29, M21 and MCF-7 cell lines and blocked cell cycle progression in S-phase similarly to cisplatin. In addition, PUBSOs induced histone H2AX (γH2AX) phosphorylation, evidencing that these molecules induce DNA double-strand breaks. In contrast, PUB-SAs were less active than PUB-SOs and did not block cell cycle progression in S-phase. Finally, PUB-SOs 4 and 46 exhibited potent antitumor activity in HT-1080 fibrosarcoma cells grafted onto chick chorioallantoic membranes, which was similar to cisplatin and combretastatin A-4 and without significant toxicity towards chick embryos. These new compounds are members of a promising new class of anticancer agents

Iron supplementation for unexplained fatigue in non-anaemic women: double blind randomised placebo controlled trial

Objective To determine the subjective response to iron therapy in non-anaemic women with unexplained fatigue. Design Double blind randomised placebo controlled trial. Setting Academic primary care centre and eight general practices in western Switzerland. Participants 144 women aged 18 to 55, assigned to either oral ferrous sulphate (80 mg/day of elemental iron daily; n=75) or placebo (n=69) for four weeks. Main outcome measures Level of fatigue, measured by a 10 point visual analogue scale. Results 136 (94%) women completed the study. Most had a low serum ferritin concentration; ≤ 20 μg/l in 69 (51%) women. Mean age, haemoglobin concentration, serum ferritin concentration, level of fatigue, depression, and anxiety were similar in both groups at baseline. Both groups were also similar for compliance and dropout rates. The level of fatigue after one month decreased by -1.82/6.37 points (29%) in the iron group compared with -0.85/6.46 points (13%) in the placebo group (difference 0.95 points, 95% confidence interval 0.32 to 1.62; P=0.004). Subgroups analysis showed that only women with ferritin concentrations ≤ 50 μg/l improved with oral supplementation. Conclusion Non-anaemic women with unexplained fatigue may benefit from iron supplementation. The effect may be restricted to women with low or borderline serum ferritin concentrations